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RIBOSOMAL

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Current Database

  • EMDB [3717]
  • EMPIAR [47]

Current status

  • REL [3764]

Sample type

  • Complex [3612]
  • Protein [2781]
  • RNA [2275]
  • Ligand [2197]
  • Sample [222]
  • DNA [130]
  • Cellular component [70]
  • Cell [57]
  • Other [5]
  • Virus [1]

Organism

  • Homo sapiens [881]
  • Escherichia coli [829]
  • Escherichia coli [396]
  • Saccharomyces cerevisiae [308]
  • Oryctolagus cuniculus [217]
  • Saccharomyces cerevisiae [162]
  • Synthetic construct [142]
  • Sus scrofa [99]
  • Mus musculus [89]
  • Escherichia coli [76]
  • Bos taurus [75]
  • Bacillus subtilis [54]
  • Bacillus subtilis [46]
  • Mycolicibacterium smegmatis [44]
  • Chaetomium thermophilum [41]
  • Staphylococcus aureus [36]
  • Thermus thermophilus [34]
  • Meiothermus taiwanensis [32]
  • Chaetomium thermophilum [29]
  • Mycoplasma pneumoniae [29]
  • Staphylococcus aureus [26]
  • Saccharomyces cerevisiae [25]
  • Enterobacteria phage t4 [24]
  • Severe acute respiratory syndrome coronavirus [22]
  • Acinetobacter baumannii [20]
  • Apis mellifera [20]
  • Mycobacterium tuberculosis [19]
  • Pyrococcus furiosus [18]
  • Arabidopsis thaliana [18]
  • Kluyveromyces lactis [17]
  • Rattus norvegicus [16]
  • Cricket paralysis virus [15]
  • Taura syndrome virus [15]
  • Mycolicibacterium smegmatis [15]
  • Kluyveromyces lactis [15]
  • Plasmodium falciparum [15]
  • Canis lupus [15]
  • Trypanosoma brucei [14]
  • Unidentified adenovirus [13]
  • Hepacivirus c [13]
  • Sulfolobus acidocaldarius [13]
  • Spinacia oleracea [13]
  • Enterococcus faecalis [12]
  • Pyrococcus abyssi [12]
  • Schizosaccharomyces pombe [12]
  • Dictyostelium discoideum [12]
  • Escherichia coli [12]
  • Drosophila melanogaster [12]
  • Entamoeba histolytica [11]
  • Tetrahymena thermophila [11]
  • Escherichia coli [11]
  • Saccharolobus solfataricus [10]
  • Babesia divergens [10]
  • Triticum aestivum [10]
  • Escherichia coli [10]
  • Mycobacterium tuberculosis [10]
  • Cardiovirus a [9]
  • Listeria monocytogenes [9]
  • Rauchvirus bpp1 [9]
  • Chlamydomonas reinhardtii [9]
  • Leishmania major [9]
  • Hepacivirus c [8]
  • Cutibacterium acnes [8]
  • Giardia intestinalis [8]
  • Candida albicans [8]
  • Dna molecule [8]
  • Pseudomonas aeruginosa [8]
  • Schizosaccharomyces pombe [8]
  • Escherichia coli [8]
  • Xenopus laevis [8]
  • Flavobacterium johnsoniae [8]
  • African swine fever virus [7]
  • Listeria innocua [7]
  • Pseudomonas aeruginosa [7]
  • Methanosarcina acetivorans [7]
  • Escherichia phage mu [7]
  • Methylorubrum extorquens [7]
  • Thermus thermophilus [7]
  • Haloferax mediterranei [7]
  • Saccharomyces cerevisiae [7]
  • Toxoplasma gondii [7]
  • Trichoplusia ni [7]
  • Giardia intestinalis [7]
  • Tequatrovirus t6 [6]
  • Nedicistrovirus tfn-2012 [6]
  • Israeli acute paralysis virus [6]
  • Hepacivirus hominis [6]
  • Bacteriophage sp. [6]
  • Triticum sp. [6]
  • Acinetobacter baumannii [6]
  • Vibrio alginolyticus [6]
  • Gallus gallus [6]
  • Pseudomonas putida [5]
  • Middle east respiratory syndrome-related coronavirus [5]
  • Severe acute respiratory syndrome coronavirus [5]
  • (no species) [5]
  • Methanosarcina mazei [5]
  • Scytonema hofmannii [5]
  • Staphylococcus aureus [5]
  • Acinetobacter baumannii [5]

EM Method

  • Single-particle [3653]
  • Subtomogram averaging [60]
  • Tomography [2]
  • Electron Crystallography [1]
  • Helical reconstruction [1]

Resolution

  • < 2Å [38]
  • ≥ 2Å and < 3Å [1185]
  • ≥ 3Å and < 4Å [1530]
  • ≥ 4Å and < 5Å [337]
  • ≥ 5Å and < 6Å [174]
  • ≥ 6Å and < 8Å [176]
  • ≥ 8Å and < 12Å [147]
  • ≥ 12Å and < 16Å [55]
  • ≥ 16Å and < 20Å [22]
  • ≥ 20Å and < 30Å [25]
  • ≥ 30Å [25]

Model molecular weight

  • 0-50 kDa [8]
  • 50-100 kDa [18]
  • 100-250 kDa [96]
  • 250-500 kDa [157]
  • 500-1000 kDa [324]
  • 1-2 MDa [714]
  • 2-5 MDa [1412]
  • 5-10 MDa [27]
  • > 10 MDa [9]

Release Date

  • 2026 [342]
  • 2025 [534]
  • 2024 [615]
  • 2023 [587]
  • 2022 [400]
  • 2021 [289]
  • 2020 [315]
  • 2019 [146]
  • 2018 [127]
  • 2017 [94]
  • 2016 [103]
  • 2015 [49]
  • 2014 [57]
  • 2013 [26]
  • 2012 [8]
  • 2011 [16]
  • 2010 [11]
  • 2009 [2]
  • 2008 [6]
  • 2007 [24]
  • 2006 [8]
  • 2005 [2]
  • 2004 [1]
  • 2003 [2]

Author by name

  • Beckmann R [289]
  • Williamson JR [274]
  • Lyumkis D [233]
  • Berninghausen O [205]
  • Sheng K [180]
  • Cheng J [175]
  • Klinge S [162]
  • Dong X [149]
  • Wilson DN [144]
  • Vanden Broeck A [136]
  • Frank J [128]
  • Rabuck-gibbons JN [119]
  • Ban N [108]
  • Spahn CMT [105]
  • Wang C [98]
  • Zhang Y [98]
  • Hurt E [95]
  • Korostelev AA [95]
  • Li N [94]
  • Becker T [88]
  • Zhang K [86]
  • Mielke T [84]
  • Lee J [83]
  • Pestova TV [82]
  • Demo G [79]
  • Loveland AB [79]
  • Lau B [78]
  • Li Y [78]
  • Amunts A [77]
  • Li X [77]
  • Ortega J [75]
  • Gao N [74]
  • Thoms M [73]
  • Brown ZP [72]
  • Aiyer S [71]
  • Wang J [71]
  • Zhang L [71]
  • Hellen CUT [70]
  • Rappsilber J [70]
  • Zhang J [68]
  • Ramakrishnan V [67]
  • Zheng W [66]
  • Leibundgut M [65]
  • Abaeva IS [63]
  • Boehringer D [63]
  • Buschauer R [63]
  • Myasnikov AG [63]
  • Burger J [62]
  • Hirst J [62]
  • Davis JH [61]
  • De S [61]
  • Rodnina MV [61]
  • Lin J [60]
  • Ameismeier M [59]
  • Ebright RH [58]
  • Aibara S [57]
  • Chen Y [57]
  • Guo R [57]
  • Nikolay R [57]
  • Larsson DSD [55]
  • Selmer M [55]
  • Xiong Y [54]
  • Xu C [54]
  • Yonath A [54]
  • Denk T [53]
  • Bashan A [52]
  • Hashem Y [52]
  • Blaha G [51]
  • Chai P [51]
  • Scaiola A [51]
  • Yusupov M [51]
  • Devarkar SC [50]
  • Lomakin IB [50]
  • Beckert B [49]
  • Wang S [49]
  • Fucini P [48]
  • Connell SR [47]
  • Lei J [47]
  • Marquardt S [47]
  • Takacs M [47]
  • Webster MW [47]
  • Weixlbaumer A [47]
  • Wiliamson JR [47]
  • Crowe-mcauliffe C [46]
  • Gu J [46]
  • Hillen HS [46]
  • Lauer S [46]
  • Lauer SM [46]
  • Liu T [46]
  • Richter-dennerlein R [46]
  • Yang M [46]
  • Fraser JS [45]
  • Gil-carton D [45]
  • Wu S [45]
  • Hou YM [44]
  • Loerke J [44]
  • Rahil H [44]
  • Shi Y [44]
  • Urlaub H [44]
  • Kaelber JT [43]

Author by ORCID

  • Lyumkis D [189]
  • Williamson JR [183]
  • Klinge S [158]
  • Beckmann R [158]
  • Vanden Broeck A [134]
  • Wilson DN [132]
  • Cheng J [113]
  • Korostelev AA [93]
  • Demo G [79]
  • Lau B [78]
  • Berninghausen O [77]
  • Thoms M [73]
  • Amunts A [73]
  • Pestova TV [71]
  • Frank J [70]
  • Gao N [70]
  • Rappsilber J [69]
  • Li N [65]
  • Hurt E [63]
  • Hellen CUT [61]
  • Ramakrishnan V [61]
  • Hirst J [60]
  • Spahn CMT [59]
  • Nikolay R [57]
  • Brown ZP [56]
  • Ortega J [53]
  • Denk T [52]
  • Larsson DSD [51]
  • Zhang K [51]
  • Chai P [51]
  • Burger J [51]
  • Selmer M [50]
  • Xiong Y [50]
  • Davis JH [50]
  • Becker T [49]
  • Wang S [48]
  • Zhang Y [48]
  • Aiyer S [47]
  • Webster MW [47]
  • Takacs M [47]
  • Loveland AB [47]
  • Sheng K [47]
  • Weixlbaumer A [47]
  • Dong X [47]
  • Wiliamson JR [47]
  • Lee J [47]
  • Gu J [46]
  • Lomakin IB [46]
  • Richter-dennerlein R [46]
  • Hillen HS [46]
  • Yang M [46]
  • Lauer SM [46]
  • Liu T [45]
  • Fraser JS [44]
  • Boehringer D [44]
  • Rodnina MV [44]
  • Hou YM [43]
  • Kaelber JT [43]
  • Loerke J [43]
  • Fucini P [43]
  • Ebright RH [42]
  • Molodtsov V [42]
  • Connell SR [41]
  • Ban N [41]
  • Bock LV [41]
  • Graziadei A [40]
  • Rabuck-gibbons JN [40]
  • Charles K [40]
  • Walter NG [40]
  • Saint-andre C [40]
  • Rahil H [40]
  • Chauvier A [40]
  • Rehling P [39]
  • Finke AF [39]
  • Itoh Y [39]
  • Paternoga H [39]
  • Wang J [39]
  • Boshnakovska A [39]
  • Jomaa A [38]
  • Taoka M [37]
  • Yin Z [37]
  • Yusupov M [36]
  • Scaiola A [35]
  • Scheerer P [34]
  • Sharma V [34]
  • Hauryliuk V [34]
  • Liu J [34]
  • Gil-carton D [34]
  • Hussain T [34]
  • Guo W [33]
  • Lin J [33]
  • Bailey EJ [33]
  • Remme J [33]
  • Atkinson GC [33]
  • Schedlbauer A [32]
  • Blaha G [32]
  • Bashan A [32]
  • Myasnikov AG [32]
  • Bridges HR [31]
  • Zdorevskyi O [31]

Journal

  • NAT COMMUN [720]
  • SCIENCE [395]
  • NATURE [340]
  • NUCLEIC ACIDS RES [307]
  • TO BE PUBLISHED [283]
  • NAT STRUCT MOL BIOL [222]
  • BIORXIV [187]
  • CELL [149]
  • MOL CELL [144]
  • PNAS [131]
  • ELIFE [130]
  • STRUCTURE [111]
  • EMBO J [106]
  • SCI ADV [78]
  • CELL REP [51]
  • ACTA CRYSTALLOGR D STRUCT BIOL [41]
  • CELL RES [33]
  • SCI REP [32]
  • RNA [31]
  • MBIO [25]
  • PLOS ONE [25]
  • J BIOL CHEM [24]
  • NAT CHEM BIOL [21]
  • EMBO REP [20]
  • INT J MOL SCI [19]
  • J MOL BIOL [19]
  • PLOS BIOL [18]
  • NAT METHODS [16]
  • PROTEIN CELL [14]
  • FUNDAM RES [13]
  • NAT MICROBIOL [13]
  • NAT PLANTS [10]
  • COMMUN BIOL [9]
  • PROTEIN SCI [9]
  • BIOMOLECULES [8]
  • LIFE SCI ALLIANCE [8]
  • J AM CHEM SOC [7]
  • ACS CHEM BIOL [6]
  • ANTIOXID REDOX SIGNAL [6]
  • BIOCHEMISTRY [6]
  • FEBS LETT [6]
  • HEMASPHERE [6]
  • ISCIENCE [6]
  • MOLECULES [6]
  • FRONT MOL BIOSCI [5]
  • MSPHERE [5]
  • NAT CHEM [5]
  • RES SQ [5]
  • ACS PHARMACOL TRANSL SCI [4]
  • CELL DISCOV [4]
  • J.BIOCHEM. [4]
  • NAT CATAL [4]
  • PLANT CELL [4]
  • PLANT COMMUN. [4]
  • PNAS NEXUS [4]
  • ACS CENT SCI [3]
  • ACTA CRYSTALLOGR F STRUCT BIOL COMMUN [3]
  • BIOCHEM J [3]
  • PROTEINS [3]
  • CANCER DISCOV [2]
  • CHEM MED CHEM [2]
  • FEBS J [2]
  • FRONT MICROBIOL [2]
  • INT J BIOL MACROMOL [2]
  • J VIS EXP [2]
  • JOURNAL OF THE AMERICAN CHEMICAL SOCIETY [2]
  • MICROBIOL SPECTR [2]
  • NAT BIOTECHNOL [2]
  • PHILOS.TRANS.R.SOC.LOND.B BIOL.SCI. [2]
  • PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES (PNAS) [2]
  • ACS CENTRAL SCIENCE [1]
  • BIOCHEM BIOPHYS RES COMMUN [1]
  • CELL METAB. [1]
  • DRUG RESIST UPDAT. [1]
  • EMERG MICROBES INFECT [1]
  • EUR.J.MED.CHEM. [1]
  • FEBS OPEN BIO [1]
  • IUCRJ [1]
  • J CELL BIOL [1]
  • J INVEST DERMATOL. [1]
  • J MED CHEM [1]
  • J STRUCT BIOL [1]
  • METHODS [1]
  • NAT CELL BIOL [1]
  • PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES USA [1]

Software

  • RELION [1337]
  • CRYOSPARC [958]
  • CTFFIND [216]
  • GCTF [174]
  • FREALIGN [148]
  • SPIDER [82]
  • WARP [81]
  • CISTEM [50]
  • COOT [36]
  • UCSF CHIMERAX [28]
  • XMIPP [27]
  • CRYODRGN [23]
  • UCSF CHIMERA [22]
  • CHIMERA [20]
  • APPION [18]
  • CTFTILT [18]
  • SPIDER, APPION [17]
  • EMAN [16]
  • M [15]
  • PHENIX [13]
  • PYTOM [11]
  • RELION, CTFFIND3 [11]
  • SIGNATURE, CTFFIND3, SPIDER, SPARX [11]
  • MDFF [10]
  • SPIDER, RELION [10]
  • CTFFIND3, RELION [8]
  • O [8]
  • SITUS [7]
  • GAP [6]
  • SPIDER, SPARX [6]
  • EMREADY [5]
  • IMAGIC [5]
  • IMAGIC, EMAN, FREALIGN, SPIDER, GAP [5]
  • SPIDER, PACKAGE [5]
  • CHIMERA, COOT [4]
  • CHIMERA, EMFIT, COOT [4]
  • EMAN2 [4]
  • NAMD [4]
  • XMIPP, FREALIGN [4]
  • CTFFIND3 [3]
  • CTFFIND3, RELION1.3 [3]
  • IMAGIC-5, SPIDER [3]
  • ISOLDE [3]
  • SPIDER AND GAP [3]
  • SPIDER PACKAGE [3]
  • URO [3]
  • CHIMERA, O, COOT [2]
  • CTFFIND3, EMAN2.1, RELION1.3 [2]
  • CTFFIND3, RELION, 1.2, 1.3 [2]
  • CTFFIND4 [2]
  • EMAN2, IMAGIC, FREALIGN, RSAMPLE, CTFFIND3 [2]
  • GROMACS [2]
  • IMOD [2]
  • PROGRAM O [2]
  • S2S, MODERNA, MODELLER, MDFF [2]
  • SITUS, LOCALFIT [2]
  • AMIRA 3.1, TGS SOFTWARE [1]
  • AV3 [1]
  • BKPR [1]
  • CCP4 PACKAGE [1]
  • CHIMERA, CNS [1]
  • CHIMERA, MDFF [1]
  • CHIMERA, ROSETTA [1]
  • CRYOLO [1]
  • CTFFIND3, RELION, 1.2 [1]
  • DIREX [1]
  • EM [1]
  • EMAN2, IMAGIC [1]
  • ESSENS [1]
  • EYE [1]
  • FLEX-EM [1]
  • FREALIGNX [1]
  • IMAGIC, FREALIGN, SPIDER, GAP [1]
  • IMAGIC-5 [1]
  • IMAGIC-5,SPIDER [1]
  • RELION1.3 [1]
  • RSREF, TNT [1]
  • SCIPION [1]
  • SIGNATURE, SPIDER, CHIMERA [1]
  • SPARX [1]
  • SPDER [1]
  • SPHIRE [1]
  • SPIDER, IMAGIC [1]
  • SPIDER, IMAGIC-5, CTFFIND3, RELION [1]
  • STOPGAP [1]
  • TOM TOOLBOX [1]

Microscope

  • FEI TITAN KRIOS [2325]
  • TFS KRIOS [712]
  • FEI TALOS ARCTICA [217]
  • FEI POLARA 300 [121]
  • FEI TECNAI F30 [116]
  • FEI TECNAI F20 [63]
  • TFS GLACIOS [42]
  • JEOL CRYO ARM 300 [27]
  • FEI TECNAI SPIRIT [17]
  • JEOL CRYO ARM 200 [16]
  • FEI TECNAI 20 [13]
  • FEI TECNAI ARCTICA [12]
  • FEI/PHILIPS CM200FEG [11]
  • JEOL 2010F [9]
  • JEOL 3200FSC [6]
  • FEI TECNAI 12 [5]
  • FEI TITAN [5]
  • TFS TALOS [5]
  • JEOL 2200FSC [2]
  • JEOL 3200FS [2]
  • JEOL KYOTO-3000SFF [2]
  • FEI/PHILIPS CM200FEG/ST [1]
  • FEI/PHILIPS CM200FEG/UT [1]
  • FEI/PHILIPS CM300FEG/T [1]
  • JEOL 1400/HR YPS FEG [1]

Electron Source

  • FIELD EMISSION GUN [3686]
  • LAB6 [23]
  • OTHER [6]
  • TUNGSTEN HAIRPIN [2]

Film or detector model

  • GATAN K2 SUMMIT 4K X 4K [1037]
  • GATAN K3 6K X 4K [866]
  • GATAN K3 BIOQUANTUM 6K X 4K [616]
  • FEI FALCON III 4K X 4K [318]
  • FEI FALCON II 4K X 4K [278]
  • FEI FALCON IV 4K X 4K [187]
  • GATAN K2 QUANTUM 4K X 4K [117]
  • KODAK SO-163 FILM [64]
  • TFS FALCON 4I 4K X 4K [36]
  • TVIPS TEMCAM-F416 4K X 4K [33]
  • FEI EAGLE 4K X 4K [30]
  • GATAN ULTRASCAN 4000 4K X 4K [28]
  • GATAN K3 BIOCONTINUUM 6K X 4K [24]
  • GATAN K2 4K X 4K [22]
  • GATAN K2 BASE 4K X 4K [20]
  • OTHER [13]
  • DIRECT ELECTRON DE-20 5K X 3K [10]
  • DIRECT ELECTRON DE-64 8K X 8K [7]
  • FEI FALCON I 4K X 4K [5]
  • GENERIC GATAN 4K X 4K [4]
  • FEI EAGLE 2K X 2K [2]
  • GENERIC CCD [2]
  • GENERIC TVIPS 4K X 4K [2]
  • TVIPS TEMCAM-F415 4K X 4K [2]
  • DECTRIS SINGLA 1K X 1K [1]
  • DIRECT ELECTRON DE-16 4K X 4K [1]
  • GATAN K2 IS 4K X 4K [1]
  • GATAN MULTISCAN [1]

EMPIAR Experiment type

  • EMDB [44]
  • EXCEPTION [1]
  • FIB-SEM [1]
  • SBF-SEM [1]

EMPIAR Image category

  • MICROGRAPHS - MULTIFRAME [38]
  • MICROGRAPHS - SINGLE FRAME [7]
  • PICKED PARTICLES - MULTIFRAME - PROCESSED [5]
  • RECONSTRUCTED VOLUMES [3]
  • PICKED PARTICLES - SINGLE FRAME - PROCESSED [2]
  • PICKED PARTICLES - MULTIFRAME - UNPROCESSED [1]
  • PICKED PARTICLES - SINGLE FRAME - UNPROCESSED [1]
  • TILT SERIES [1]

External links

  • PDB [3690]
  • UniProt [2713]
  • AlphaFold DB [2704]
  • PDBe-Kb [2688]
  • Gene Ontology [2457]
  • InterPro [2394]
  • Pfam [2338]
  • ChEBI [2118]
  • DrugBank [2104]
  • ChEMBL [1973]
  • Complex Portal [877]
  • EMPIAR [674]
  • SCOP2 [218]
  • CATH [71]
  • EMDB [44]
Sort by: Download
Showing 1 - 10 of 3764. Page 1 of 377
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EMD-51874
Download Map
3D View
Assembly intermediate of human mitochondrial ribosome small subunit in complex with NOA1, ERAL1, METTL17, MCAT and TFB1M state N1
CryoEM
Release date: July 8, 2026
Resolution: 3.9 Å
EM Method: Single-particle
Fitted PDBs: 9h52
Q-score: 0.216

Singh V, Shiriaev D, Bilalli L, Khawaja A, Rorbach J

Nat Commun (2026) 17 [ Pubmed: 42342677 DOI: doi:10.1038/s41467-026-74700-x ]

EMD-62893
Download Map
3D View
State G of archaeal pre-50S ribosome
CryoEM
Release date: July 8, 2026
Resolution: 2.07 Å
EM Method: Single-particle
Fitted PDBs: 9l94
Q-score: 0.7

Li ZQ, Yang XY

To Be Published

EMD-62894
Download Map
3D View
State F of archaeal pre-50S ribosome
CryoEM
Release date: July 8, 2026
Resolution: 2.43 Å
EM Method: Single-particle
Fitted PDBs: 9l95
Q-score: 0.593

Li ZQ, Yang XY

To Be Published

EMD-62895
Download Map
3D View
State D of archaeal pre-50S ribosome
CryoEM
Release date: July 8, 2026
Resolution: 2.97 Å
EM Method: Single-particle
Fitted PDBs: 9l96
Q-score: 0.543

Li ZQ, Yang XY

To Be Published

EMD-62897
Download Map
3D View
State C of archaeal pre-50S ribosome
CryoEM
Release date: July 8, 2026
Resolution: 2.76 Å
EM Method: Single-particle
Fitted PDBs: 9l98
Q-score: 0.555

Li ZQ, Yang XY

To Be Published

EMD-62907
Download Map
3D View
State H of archaeal pre-50S ribosome
CryoEM
Release date: July 8, 2026
Resolution: 3.26 Å
EM Method: Single-particle
Fitted PDBs: 9l9j

Li ZQ, Yang XY

To Be Published

EMD-62908
Download Map
3D View
State E of archaeal pre-50S ribosome
CryoEM
Release date: July 8, 2026
Resolution: 2.36 Å
EM Method: Single-particle
Fitted PDBs: 9l9k
Q-score: 0.646

Li ZQ, Yang XY

To Be Published

EMD-62914
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State A of archaeal pre-50S ribosome
CryoEM
Release date: July 8, 2026
Resolution: 2.77 Å
EM Method: Single-particle
Fitted PDBs: 9l9v
Q-score: 0.59

Li ZQ, Yang XY

To Be Published

EMD-54129
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Assembly intermediate of human mitochondrial ribosome small subunit bound to METTL15 and RBFA Outward conformation State M3
CryoEM
Release date: July 1, 2026
Resolution: 3.64 Å
EM Method: Single-particle
Fitted PDBs: 9ror
Q-score: 0.251

Singh V, Shiriaev D, Bilalli L, Khawaja A, Rorbach J

Nat Commun (2026) 17 [ Pubmed: 42342677 DOI: doi:10.1038/s41467-026-74700-x ]

EMD-54130
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3D View
Assembly intermediate of human mitochondrial ribosome small subunit bound to METTL15, RBFA, and mtIF2 State M2.1
CryoEM
Release date: July 1, 2026
Resolution: 4.3 Å
EM Method: Single-particle
Fitted PDBs: 9rot
Q-score: 0.241

Singh V, Shiriaev D, Bilalli L, Khawaja A, Rorbach J

Nat Commun (2026) 17 [ Pubmed: 42342677 DOI: doi:10.1038/s41467-026-74700-x ]

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Current Database

  • EMDB [3717]
  • EMPIAR [47]

Current status

  • REL [3764]

Sample type

  • Complex [3612]
  • Protein [2781]
  • RNA [2275]
  • Ligand [2197]
  • Sample [222]
  • DNA [130]
  • Cellular component [70]
  • Cell [57]
  • Other [5]
  • Virus [1]

Organism

  • Homo sapiens [881]
  • Escherichia coli [829]
  • Escherichia coli [396]
  • Saccharomyces cerevisiae [308]
  • Oryctolagus cuniculus [217]
  • Saccharomyces cerevisiae [162]
  • Synthetic construct [142]
  • Sus scrofa [99]
  • Mus musculus [89]
  • Escherichia coli [76]
  • Bos taurus [75]
  • Bacillus subtilis [54]
  • Bacillus subtilis [46]
  • Mycolicibacterium smegmatis [44]
  • Chaetomium thermophilum [41]
  • Staphylococcus aureus [36]
  • Thermus thermophilus [34]
  • Meiothermus taiwanensis [32]
  • Chaetomium thermophilum [29]
  • Mycoplasma pneumoniae [29]
  • Staphylococcus aureus [26]
  • Saccharomyces cerevisiae [25]
  • Enterobacteria phage t4 [24]
  • Severe acute respiratory syndrome coronavirus [22]
  • Acinetobacter baumannii [20]
  • Apis mellifera [20]
  • Mycobacterium tuberculosis [19]
  • Pyrococcus furiosus [18]
  • Arabidopsis thaliana [18]
  • Kluyveromyces lactis [17]
  • Rattus norvegicus [16]
  • Cricket paralysis virus [15]
  • Taura syndrome virus [15]
  • Mycolicibacterium smegmatis [15]
  • Kluyveromyces lactis [15]
  • Plasmodium falciparum [15]
  • Canis lupus [15]
  • Trypanosoma brucei [14]
  • Unidentified adenovirus [13]
  • Hepacivirus c [13]
  • Sulfolobus acidocaldarius [13]
  • Spinacia oleracea [13]
  • Enterococcus faecalis [12]
  • Pyrococcus abyssi [12]
  • Schizosaccharomyces pombe [12]
  • Dictyostelium discoideum [12]
  • Escherichia coli [12]
  • Drosophila melanogaster [12]
  • Entamoeba histolytica [11]
  • Tetrahymena thermophila [11]
  • Escherichia coli [11]
  • Saccharolobus solfataricus [10]
  • Babesia divergens [10]
  • Triticum aestivum [10]
  • Escherichia coli [10]
  • Mycobacterium tuberculosis [10]
  • Cardiovirus a [9]
  • Listeria monocytogenes [9]
  • Rauchvirus bpp1 [9]
  • Chlamydomonas reinhardtii [9]
  • Leishmania major [9]
  • Hepacivirus c [8]
  • Cutibacterium acnes [8]
  • Giardia intestinalis [8]
  • Candida albicans [8]
  • Dna molecule [8]
  • Pseudomonas aeruginosa [8]
  • Schizosaccharomyces pombe [8]
  • Escherichia coli [8]
  • Xenopus laevis [8]
  • Flavobacterium johnsoniae [8]
  • African swine fever virus [7]
  • Listeria innocua [7]
  • Pseudomonas aeruginosa [7]
  • Methanosarcina acetivorans [7]
  • Escherichia phage mu [7]
  • Methylorubrum extorquens [7]
  • Thermus thermophilus [7]
  • Haloferax mediterranei [7]
  • Saccharomyces cerevisiae [7]
  • Toxoplasma gondii [7]
  • Trichoplusia ni [7]
  • Giardia intestinalis [7]
  • Tequatrovirus t6 [6]
  • Nedicistrovirus tfn-2012 [6]
  • Israeli acute paralysis virus [6]
  • Hepacivirus hominis [6]
  • Bacteriophage sp. [6]
  • Triticum sp. [6]
  • Acinetobacter baumannii [6]
  • Vibrio alginolyticus [6]
  • Gallus gallus [6]
  • Pseudomonas putida [5]
  • Middle east respiratory syndrome-related coronavirus [5]
  • Severe acute respiratory syndrome coronavirus [5]
  • (no species) [5]
  • Methanosarcina mazei [5]
  • Scytonema hofmannii [5]
  • Staphylococcus aureus [5]
  • Acinetobacter baumannii [5]

EM Method

  • Single-particle [3653]
  • Subtomogram averaging [60]
  • Tomography [2]
  • Electron Crystallography [1]
  • Helical reconstruction [1]

Resolution

  • < 2Å [38]
  • ≥ 2Å and < 3Å [1185]
  • ≥ 3Å and < 4Å [1530]
  • ≥ 4Å and < 5Å [337]
  • ≥ 5Å and < 6Å [174]
  • ≥ 6Å and < 8Å [176]
  • ≥ 8Å and < 12Å [147]
  • ≥ 12Å and < 16Å [55]
  • ≥ 16Å and < 20Å [22]
  • ≥ 20Å and < 30Å [25]
  • ≥ 30Å [25]

Model molecular weight

  • 0-50 kDa [8]
  • 50-100 kDa [18]
  • 100-250 kDa [96]
  • 250-500 kDa [157]
  • 500-1000 kDa [324]
  • 1-2 MDa [714]
  • 2-5 MDa [1412]
  • 5-10 MDa [27]
  • > 10 MDa [9]

Release Date

  • 2026 [342]
  • 2025 [534]
  • 2024 [615]
  • 2023 [587]
  • 2022 [400]
  • 2021 [289]
  • 2020 [315]
  • 2019 [146]
  • 2018 [127]
  • 2017 [94]
  • 2016 [103]
  • 2015 [49]
  • 2014 [57]
  • 2013 [26]
  • 2012 [8]
  • 2011 [16]
  • 2010 [11]
  • 2009 [2]
  • 2008 [6]
  • 2007 [24]
  • 2006 [8]
  • 2005 [2]
  • 2004 [1]
  • 2003 [2]

Author by name

  • Beckmann R [289]
  • Williamson JR [274]
  • Lyumkis D [233]
  • Berninghausen O [205]
  • Sheng K [180]
  • Cheng J [175]
  • Klinge S [162]
  • Dong X [149]
  • Wilson DN [144]
  • Vanden Broeck A [136]
  • Frank J [128]
  • Rabuck-gibbons JN [119]
  • Ban N [108]
  • Spahn CMT [105]
  • Wang C [98]
  • Zhang Y [98]
  • Hurt E [95]
  • Korostelev AA [95]
  • Li N [94]
  • Becker T [88]
  • Zhang K [86]
  • Mielke T [84]
  • Lee J [83]
  • Pestova TV [82]
  • Demo G [79]
  • Loveland AB [79]
  • Lau B [78]
  • Li Y [78]
  • Amunts A [77]
  • Li X [77]
  • Ortega J [75]
  • Gao N [74]
  • Thoms M [73]
  • Brown ZP [72]
  • Aiyer S [71]
  • Wang J [71]
  • Zhang L [71]
  • Hellen CUT [70]
  • Rappsilber J [70]
  • Zhang J [68]
  • Ramakrishnan V [67]
  • Zheng W [66]
  • Leibundgut M [65]
  • Abaeva IS [63]
  • Boehringer D [63]
  • Buschauer R [63]
  • Myasnikov AG [63]
  • Burger J [62]
  • Hirst J [62]
  • Davis JH [61]
  • De S [61]
  • Rodnina MV [61]
  • Lin J [60]
  • Ameismeier M [59]
  • Ebright RH [58]
  • Aibara S [57]
  • Chen Y [57]
  • Guo R [57]
  • Nikolay R [57]
  • Larsson DSD [55]
  • Selmer M [55]
  • Xiong Y [54]
  • Xu C [54]
  • Yonath A [54]
  • Denk T [53]
  • Bashan A [52]
  • Hashem Y [52]
  • Blaha G [51]
  • Chai P [51]
  • Scaiola A [51]
  • Yusupov M [51]
  • Devarkar SC [50]
  • Lomakin IB [50]
  • Beckert B [49]
  • Wang S [49]
  • Fucini P [48]
  • Connell SR [47]
  • Lei J [47]
  • Marquardt S [47]
  • Takacs M [47]
  • Webster MW [47]
  • Weixlbaumer A [47]
  • Wiliamson JR [47]
  • Crowe-mcauliffe C [46]
  • Gu J [46]
  • Hillen HS [46]
  • Lauer S [46]
  • Lauer SM [46]
  • Liu T [46]
  • Richter-dennerlein R [46]
  • Yang M [46]
  • Fraser JS [45]
  • Gil-carton D [45]
  • Wu S [45]
  • Hou YM [44]
  • Loerke J [44]
  • Rahil H [44]
  • Shi Y [44]
  • Urlaub H [44]
  • Kaelber JT [43]

Author by ORCID

  • Lyumkis D [189]
  • Williamson JR [183]
  • Klinge S [158]
  • Beckmann R [158]
  • Vanden Broeck A [134]
  • Wilson DN [132]
  • Cheng J [113]
  • Korostelev AA [93]
  • Demo G [79]
  • Lau B [78]
  • Berninghausen O [77]
  • Thoms M [73]
  • Amunts A [73]
  • Pestova TV [71]
  • Frank J [70]
  • Gao N [70]
  • Rappsilber J [69]
  • Li N [65]
  • Hurt E [63]
  • Hellen CUT [61]
  • Ramakrishnan V [61]
  • Hirst J [60]
  • Spahn CMT [59]
  • Nikolay R [57]
  • Brown ZP [56]
  • Ortega J [53]
  • Denk T [52]
  • Larsson DSD [51]
  • Zhang K [51]
  • Chai P [51]
  • Burger J [51]
  • Selmer M [50]
  • Xiong Y [50]
  • Davis JH [50]
  • Becker T [49]
  • Wang S [48]
  • Zhang Y [48]
  • Aiyer S [47]
  • Webster MW [47]
  • Takacs M [47]
  • Loveland AB [47]
  • Sheng K [47]
  • Weixlbaumer A [47]
  • Dong X [47]
  • Wiliamson JR [47]
  • Lee J [47]
  • Gu J [46]
  • Lomakin IB [46]
  • Richter-dennerlein R [46]
  • Hillen HS [46]
  • Yang M [46]
  • Lauer SM [46]
  • Liu T [45]
  • Fraser JS [44]
  • Boehringer D [44]
  • Rodnina MV [44]
  • Hou YM [43]
  • Kaelber JT [43]
  • Loerke J [43]
  • Fucini P [43]
  • Ebright RH [42]
  • Molodtsov V [42]
  • Connell SR [41]
  • Ban N [41]
  • Bock LV [41]
  • Graziadei A [40]
  • Rabuck-gibbons JN [40]
  • Charles K [40]
  • Walter NG [40]
  • Saint-andre C [40]
  • Rahil H [40]
  • Chauvier A [40]
  • Rehling P [39]
  • Finke AF [39]
  • Itoh Y [39]
  • Paternoga H [39]
  • Wang J [39]
  • Boshnakovska A [39]
  • Jomaa A [38]
  • Taoka M [37]
  • Yin Z [37]
  • Yusupov M [36]
  • Scaiola A [35]
  • Scheerer P [34]
  • Sharma V [34]
  • Hauryliuk V [34]
  • Liu J [34]
  • Gil-carton D [34]
  • Hussain T [34]
  • Guo W [33]
  • Lin J [33]
  • Bailey EJ [33]
  • Remme J [33]
  • Atkinson GC [33]
  • Schedlbauer A [32]
  • Blaha G [32]
  • Bashan A [32]
  • Myasnikov AG [32]
  • Bridges HR [31]
  • Zdorevskyi O [31]

Journal

  • NAT COMMUN [720]
  • SCIENCE [395]
  • NATURE [340]
  • NUCLEIC ACIDS RES [307]
  • TO BE PUBLISHED [283]
  • NAT STRUCT MOL BIOL [222]
  • BIORXIV [187]
  • CELL [149]
  • MOL CELL [144]
  • PNAS [131]
  • ELIFE [130]
  • STRUCTURE [111]
  • EMBO J [106]
  • SCI ADV [78]
  • CELL REP [51]
  • ACTA CRYSTALLOGR D STRUCT BIOL [41]
  • CELL RES [33]
  • SCI REP [32]
  • RNA [31]
  • MBIO [25]
  • PLOS ONE [25]
  • J BIOL CHEM [24]
  • NAT CHEM BIOL [21]
  • EMBO REP [20]
  • INT J MOL SCI [19]
  • J MOL BIOL [19]
  • PLOS BIOL [18]
  • NAT METHODS [16]
  • PROTEIN CELL [14]
  • FUNDAM RES [13]
  • NAT MICROBIOL [13]
  • NAT PLANTS [10]
  • COMMUN BIOL [9]
  • PROTEIN SCI [9]
  • BIOMOLECULES [8]
  • LIFE SCI ALLIANCE [8]
  • J AM CHEM SOC [7]
  • ACS CHEM BIOL [6]
  • ANTIOXID REDOX SIGNAL [6]
  • BIOCHEMISTRY [6]
  • FEBS LETT [6]
  • HEMASPHERE [6]
  • ISCIENCE [6]
  • MOLECULES [6]
  • FRONT MOL BIOSCI [5]
  • MSPHERE [5]
  • NAT CHEM [5]
  • RES SQ [5]
  • ACS PHARMACOL TRANSL SCI [4]
  • CELL DISCOV [4]
  • J.BIOCHEM. [4]
  • NAT CATAL [4]
  • PLANT CELL [4]
  • PLANT COMMUN. [4]
  • PNAS NEXUS [4]
  • ACS CENT SCI [3]
  • ACTA CRYSTALLOGR F STRUCT BIOL COMMUN [3]
  • BIOCHEM J [3]
  • PROTEINS [3]
  • CANCER DISCOV [2]
  • CHEM MED CHEM [2]
  • FEBS J [2]
  • FRONT MICROBIOL [2]
  • INT J BIOL MACROMOL [2]
  • J VIS EXP [2]
  • JOURNAL OF THE AMERICAN CHEMICAL SOCIETY [2]
  • MICROBIOL SPECTR [2]
  • NAT BIOTECHNOL [2]
  • PHILOS.TRANS.R.SOC.LOND.B BIOL.SCI. [2]
  • PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES (PNAS) [2]
  • ACS CENTRAL SCIENCE [1]
  • BIOCHEM BIOPHYS RES COMMUN [1]
  • CELL METAB. [1]
  • DRUG RESIST UPDAT. [1]
  • EMERG MICROBES INFECT [1]
  • EUR.J.MED.CHEM. [1]
  • FEBS OPEN BIO [1]
  • IUCRJ [1]
  • J CELL BIOL [1]
  • J INVEST DERMATOL. [1]
  • J MED CHEM [1]
  • J STRUCT BIOL [1]
  • METHODS [1]
  • NAT CELL BIOL [1]
  • PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES USA [1]

Software

  • RELION [1337]
  • CRYOSPARC [958]
  • CTFFIND [216]
  • GCTF [174]
  • FREALIGN [148]
  • SPIDER [82]
  • WARP [81]
  • CISTEM [50]
  • COOT [36]
  • UCSF CHIMERAX [28]
  • XMIPP [27]
  • CRYODRGN [23]
  • UCSF CHIMERA [22]
  • CHIMERA [20]
  • APPION [18]
  • CTFTILT [18]
  • SPIDER, APPION [17]
  • EMAN [16]
  • M [15]
  • PHENIX [13]
  • PYTOM [11]
  • RELION, CTFFIND3 [11]
  • SIGNATURE, CTFFIND3, SPIDER, SPARX [11]
  • MDFF [10]
  • SPIDER, RELION [10]
  • CTFFIND3, RELION [8]
  • O [8]
  • SITUS [7]
  • GAP [6]
  • SPIDER, SPARX [6]
  • EMREADY [5]
  • IMAGIC [5]
  • IMAGIC, EMAN, FREALIGN, SPIDER, GAP [5]
  • SPIDER, PACKAGE [5]
  • CHIMERA, COOT [4]
  • CHIMERA, EMFIT, COOT [4]
  • EMAN2 [4]
  • NAMD [4]
  • XMIPP, FREALIGN [4]
  • CTFFIND3 [3]
  • CTFFIND3, RELION1.3 [3]
  • IMAGIC-5, SPIDER [3]
  • ISOLDE [3]
  • SPIDER AND GAP [3]
  • SPIDER PACKAGE [3]
  • URO [3]
  • CHIMERA, O, COOT [2]
  • CTFFIND3, EMAN2.1, RELION1.3 [2]
  • CTFFIND3, RELION, 1.2, 1.3 [2]
  • CTFFIND4 [2]
  • EMAN2, IMAGIC, FREALIGN, RSAMPLE, CTFFIND3 [2]
  • GROMACS [2]
  • IMOD [2]
  • PROGRAM O [2]
  • S2S, MODERNA, MODELLER, MDFF [2]
  • SITUS, LOCALFIT [2]
  • AMIRA 3.1, TGS SOFTWARE [1]
  • AV3 [1]
  • BKPR [1]
  • CCP4 PACKAGE [1]
  • CHIMERA, CNS [1]
  • CHIMERA, MDFF [1]
  • CHIMERA, ROSETTA [1]
  • CRYOLO [1]
  • CTFFIND3, RELION, 1.2 [1]
  • DIREX [1]
  • EM [1]
  • EMAN2, IMAGIC [1]
  • ESSENS [1]
  • EYE [1]
  • FLEX-EM [1]
  • FREALIGNX [1]
  • IMAGIC, FREALIGN, SPIDER, GAP [1]
  • IMAGIC-5 [1]
  • IMAGIC-5,SPIDER [1]
  • RELION1.3 [1]
  • RSREF, TNT [1]
  • SCIPION [1]
  • SIGNATURE, SPIDER, CHIMERA [1]
  • SPARX [1]
  • SPDER [1]
  • SPHIRE [1]
  • SPIDER, IMAGIC [1]
  • SPIDER, IMAGIC-5, CTFFIND3, RELION [1]
  • STOPGAP [1]
  • TOM TOOLBOX [1]

Microscope

  • FEI TITAN KRIOS [2325]
  • TFS KRIOS [712]
  • FEI TALOS ARCTICA [217]
  • FEI POLARA 300 [121]
  • FEI TECNAI F30 [116]
  • FEI TECNAI F20 [63]
  • TFS GLACIOS [42]
  • JEOL CRYO ARM 300 [27]
  • FEI TECNAI SPIRIT [17]
  • JEOL CRYO ARM 200 [16]
  • FEI TECNAI 20 [13]
  • FEI TECNAI ARCTICA [12]
  • FEI/PHILIPS CM200FEG [11]
  • JEOL 2010F [9]
  • JEOL 3200FSC [6]
  • FEI TECNAI 12 [5]
  • FEI TITAN [5]
  • TFS TALOS [5]
  • JEOL 2200FSC [2]
  • JEOL 3200FS [2]
  • JEOL KYOTO-3000SFF [2]
  • FEI/PHILIPS CM200FEG/ST [1]
  • FEI/PHILIPS CM200FEG/UT [1]
  • FEI/PHILIPS CM300FEG/T [1]
  • JEOL 1400/HR YPS FEG [1]

Electron Source

  • FIELD EMISSION GUN [3686]
  • LAB6 [23]
  • OTHER [6]
  • TUNGSTEN HAIRPIN [2]

Film or detector model

  • GATAN K2 SUMMIT 4K X 4K [1037]
  • GATAN K3 6K X 4K [866]
  • GATAN K3 BIOQUANTUM 6K X 4K [616]
  • FEI FALCON III 4K X 4K [318]
  • FEI FALCON II 4K X 4K [278]
  • FEI FALCON IV 4K X 4K [187]
  • GATAN K2 QUANTUM 4K X 4K [117]
  • KODAK SO-163 FILM [64]
  • TFS FALCON 4I 4K X 4K [36]
  • TVIPS TEMCAM-F416 4K X 4K [33]
  • FEI EAGLE 4K X 4K [30]
  • GATAN ULTRASCAN 4000 4K X 4K [28]
  • GATAN K3 BIOCONTINUUM 6K X 4K [24]
  • GATAN K2 4K X 4K [22]
  • GATAN K2 BASE 4K X 4K [20]
  • OTHER [13]
  • DIRECT ELECTRON DE-20 5K X 3K [10]
  • DIRECT ELECTRON DE-64 8K X 8K [7]
  • FEI FALCON I 4K X 4K [5]
  • GENERIC GATAN 4K X 4K [4]
  • FEI EAGLE 2K X 2K [2]
  • GENERIC CCD [2]
  • GENERIC TVIPS 4K X 4K [2]
  • TVIPS TEMCAM-F415 4K X 4K [2]
  • DECTRIS SINGLA 1K X 1K [1]
  • DIRECT ELECTRON DE-16 4K X 4K [1]
  • GATAN K2 IS 4K X 4K [1]
  • GATAN MULTISCAN [1]

EMPIAR Experiment type

  • EMDB [44]
  • EXCEPTION [1]
  • FIB-SEM [1]
  • SBF-SEM [1]

EMPIAR Image category

  • MICROGRAPHS - MULTIFRAME [38]
  • MICROGRAPHS - SINGLE FRAME [7]
  • PICKED PARTICLES - MULTIFRAME - PROCESSED [5]
  • RECONSTRUCTED VOLUMES [3]
  • PICKED PARTICLES - SINGLE FRAME - PROCESSED [2]
  • PICKED PARTICLES - MULTIFRAME - UNPROCESSED [1]
  • PICKED PARTICLES - SINGLE FRAME - UNPROCESSED [1]
  • TILT SERIES [1]

External links

  • PDB [3690]
  • UniProt [2713]
  • AlphaFold DB [2704]
  • PDBe-Kb [2688]
  • Gene Ontology [2457]
  • InterPro [2394]
  • Pfam [2338]
  • ChEBI [2118]
  • DrugBank [2104]
  • ChEMBL [1973]
  • Complex Portal [877]
  • EMPIAR [674]
  • SCOP2 [218]
  • CATH [71]
  • EMDB [44]