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natural_source_ncbi_code:"311400"

Filter By

Current Database

  • EMDB [36]

Current status

  • REL [36]

Sample type

  • Complex [36]
  • Protein [10]
  • Ligand [6]
  • RNA [4]
  • DNA [2]
  • Sample [2]

Organism

  • Thermococcus kodakarensis [36]
  • Synthetic construct [4]
  • Pyrococcus furiosus [1]

EM Method

  • Single-particle [36]

Resolution

  • ≥ 2Å and < 3Å [10]
  • ≥ 3Å and < 4Å [17]
  • ≥ 4Å and < 5Å [1]
  • ≥ 6Å and < 8Å [4]
  • ≥ 8Å and < 12Å [3]
  • ≥ 16Å and < 20Å [1]

Model molecular weight

  • 100-250 kDa [3]
  • 250-500 kDa [5]
  • 500-1000 kDa [2]
  • 2-5 MDa [2]

Release Date

  • 2025 [1]
  • 2024 [25]
  • 2023 [2]
  • 2021 [2]
  • 2020 [4]
  • 2013 [1]
  • 2012 [1]

Author by name

  • Gilbert RJC [19]
  • Li M [19]
  • Li Q [19]
  • Lu Y [19]
  • Ma J [19]
  • Macgregor-chatwin C [19]
  • Sheng Y [19]
  • Wang D [19]
  • Ye M [19]
  • Yi G [19]
  • Zhang P [19]
  • Santangelo TJ [8]
  • Ebright RH [6]
  • Firlar E [6]
  • Kaelber JT [6]
  • Kuznedelov K [6]
  • Marshall CJ [6]
  • Miao X [6]
  • Molodtsov V [6]
  • Sanders TJ [6]
  • Ulisse P [6]
  • Wang C [6]
  • Wenck BR [6]
  • You L [6]
  • Anger AM [2]
  • Armache J-P [2]
  • Beckmann R [2]
  • Berninghausen O [2]
  • Bowerman S [2]
  • Briney CA [2]
  • Bryson KM [2]
  • Burkhart BW [2]
  • Florens L [2]
  • Fuchs RT [2]
  • Gamage ST [2]
  • Hartmann J [2]
  • Ishino S [2]
  • Ishino Y [2]
  • Isobe T [2]
  • Iwasaki K [2]
  • Kohda D [2]
  • Levy MJ [2]
  • Liman GLS [2]
  • Lin Q [2]
  • Luger K [2]
  • Matzov D [2]
  • Mayanagi K [2]
  • Meier JL [2]
  • Miyazaki N [2]
  • Morikawa K [2]
  • Nance KD [2]
  • Nir R [2]
  • Nobe Y [2]
  • Oki K [2]
  • Robb GB [2]
  • Sas-chen A [2]
  • Schwartz S [2]
  • Shachar R [2]
  • Shalev-benami M [2]
  • Sharma S [2]
  • Shirai T [2]
  • Taoka M [2]
  • Thomas JM [2]
  • Thomm M [2]
  • Washburn MP [2]
  • Wereszczynski J [2]
  • Yamagami T [2]
  • Anshari ZR [1]
  • Armache JP [1]
  • Arnold GJ [1]
  • Becker T [1]
  • Colucci E [1]
  • Daberkow I [1]
  • Franckenberg S [1]
  • Frankenberg S [1]
  • Froehlich T [1]
  • Green R [1]
  • Guskov A [1]
  • Hamaguchi T [1]
  • Himiyama T [1]
  • Hopfner K-P [1]
  • Hopfner KP [1]
  • Karcher A [1]
  • Marquez V [1]
  • Nakamura T [1]
  • Naz Z [1]
  • Nemchinova M [1]
  • Patino-ruiz MF [1]
  • Rahman M [1]
  • Rashid N [1]
  • Rathore I [1]
  • Saleem M [1]
  • Shoemaker CJ [1]
  • Sieber H [1]
  • Slotboom DJ [1]
  • Ungewickell C [1]
  • Villa E [1]
  • Whittaker J [1]
  • Whittaker JJ [1]
  • Wickles S [1]

Author by ORCID

  • Ye M [19]
  • Gilbert RJC [19]
  • Wang D [19]
  • Li M [19]
  • Lu Y [19]
  • Li Q [19]
  • Zhang P [19]
  • Sheng Y [19]
  • Yi G [19]
  • Ebright RH [6]
  • Kaelber JT [6]
  • Wang C [6]
  • Kuznedelov K [6]
  • Molodtsov V [6]
  • Santangelo TJ [6]
  • Miao X [6]
  • Luger K [2]
  • Taoka M [2]
  • Washburn MP [2]
  • Briney CA [2]
  • Sharma S [2]
  • Sas-chen A [2]
  • Gamage ST [2]
  • Lin Q [2]
  • Wereszczynski J [2]
  • Robb GB [2]
  • Schwartz S [2]
  • Nance KD [2]
  • Bowerman S [2]
  • Liman GLS [2]
  • Shachar R [2]
  • Himiyama T [1]
  • Yonekura K [1]
  • Whittaker J [1]
  • Armache J-P [1]
  • Armache JP [1]
  • Saleem M [1]
  • Rashid N [1]
  • Hopfner KP [1]
  • Froehlich T [1]
  • Wlodawer A [1]
  • Slotboom DJ [1]
  • Anshari ZR [1]
  • Guskov A [1]
  • Rathore I [1]
  • Colucci E [1]
  • Wilson DN [1]
  • Nemchinova M [1]
  • Villa E [1]
  • Naz Z [1]

Journal

  • NAT COMMUN [20]
  • NATURE [9]
  • ELIFE [2]
  • TO BE PUBLISHED [2]
  • BIOCONJUG.CHEM. [1]
  • BIOMOLECULES [1]
  • NUCLEIC ACIDS RES [1]

Software

  • CRYOSPARC [9]
  • RELION [4]
  • GCTF [2]
  • SPIDER [2]
  • CTFFIND [1]
  • MDFF [1]
  • UCSF CHIMERA [1]

Microscope

  • FEI TITAN KRIOS [30]
  • FEI TALOS ARCTICA [2]
  • FEI TECNAI 20 [2]
  • FEI TECNAI 12 [1]
  • JEOL CRYO ARM 300 [1]

Electron Source

  • FIELD EMISSION GUN [35]
  • LAB6 [1]

Film or detector model

  • FEI FALCON IV 4K X 4K [12]
  • GATAN K3 BIOQUANTUM 6K X 4K [11]
  • GATAN K3 6K X 4K [7]
  • FEI FALCON III 4K X 4K [3]
  • FEI EAGLE 4K X 4K [1]
  • FEI FALCON II 4K X 4K [1]
  • TVIPS TEMCAM-F416 4K X 4K [1]

External links

  • PDB [12]
  • AlphaFold DB [6]
  • ChEBI [6]
  • ChEMBL [6]
  • DrugBank [6]
  • Gene Ontology [6]
  • InterPro [6]
  • Pfam [6]
  • UniProt [6]
  • PDBe-Kb [5]
  • SCOP2 [2]
Sort by: Download
Showing 1 - 10 of 36. Page 1 of 4
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EMD-47167
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3D View
Cryo-EM structure of phosphoglucomutase from Thermococcus kodakarensis
Release date: April 16, 2025
Resolution: 2.45 Å
EM Method: Single-particle
Fitted PDBs: 9du5
Q-score: 0.593

Naz Z, Rathore I, Saleem M, Rahman M, Wlodawer A, Rashid N

Biomolecules (2025) 15 [ DOI: doi:10.3390/biom15030319 Pubmed: 40149855 ]

EMD-44438
Composite map
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Cryo-EM structure of Thermococcus kodakarensis FttA-dependent transcription pre-termination complex containing 44 nt RNA
Release date: July 31, 2024
Resolution: 2.5 Å
EM Method: Single-particle
Fitted PDBs: 9bct
Q-score: 0.554

You L, Wang C, Molodtsov V, Kuznedelov K, Miao X, Wenck BR, Ulisse P, Sanders TJ, Marshall CJ, Firlar E, Kaelber JT, Santangelo TJ, Ebright RH

Nature (2024) 635 pp. 229-236 [ Pubmed: 39322680 DOI: doi:10.1038/s41586-024-07979-9 ]

EMD-44439
Composite map
Download Map
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Cryo-EM structure of Thermococcus kodakarensis FttA-dependent transcription pre-termination complex containing 52 nt RNA
Release date: July 31, 2024
Resolution: 2.2 Å
EM Method: Single-particle
Fitted PDBs: 9bcu
Q-score: 0.613

You L, Wang C, Molodtsov V, Kuznedelov K, Miao X, Wenck BR, Ulisse P, Sanders TJ, Marshall CJ, Firlar E, Kaelber JT, Santangelo TJ, Ebright RH

Nature (2024) 635 pp. 229-236 [ Pubmed: 39322680 DOI: doi:10.1038/s41586-024-07979-9 ]

EMD-44454
Download Map
3D View
Cryo-EM structure of Thermococcus kodakarensis FttA-dependent transcription pre-termination complex containing 44 nt RNA
Release date: July 31, 2024
Resolution: 2.5 Å
EM Method: Single-particle

You L, Wang C, Molodtsov V, Kuznedelov K, Miao X, Wenck BR, Ulisse P, Sanders TJ, Marshall CJ, Firlar E, Kaelber JT, Santangelo TJ, Ebright RH

Nature (2024) 635 pp. 229-236 [ Pubmed: 39322680 DOI: doi:10.1038/s41586-024-07979-9 ]

EMD-44455
Download Map
3D View
Cryo-EM structure of Thermococcus kodakarensis FttA-dependent transcription pre-termination complex containing 52 nt RNA
Release date: July 31, 2024
Resolution: 2.2 Å
EM Method: Single-particle

You L, Wang C, Molodtsov V, Kuznedelov K, Miao X, Wenck BR, Ulisse P, Sanders TJ, Marshall CJ, Firlar E, Kaelber JT, Santangelo TJ, Ebright RH

Nature (2024) 635 pp. 229-236 [ Pubmed: 39322680 DOI: doi:10.1038/s41586-024-07979-9 ]

EMD-44649
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Cryo-EM structure of Thermococcus kodakarensis FttA-dependent transcription pre-termination complex containing 44 nt RNA local refinement map
Release date: July 31, 2024
Resolution: 2.67 Å
EM Method: Single-particle

You L, Wang C, Molodtsov V, Kuznedelov K, Miao X, Wenck BR, Ulisse P, Sanders TJ, Marshall CJ, Firlar E, Kaelber JT, Santangelo TJ, Ebright RH

Nature (2024) 635 pp. 229-236 [ Pubmed: 39322680 DOI: doi:10.1038/s41586-024-07979-9 ]

EMD-44650
Download Map
3D View
Cryo-EM structure of Thermococcus kodakarensis FttA-dependent transcription pre-termination complex containing 52 nt RNA local refinement map
Release date: July 31, 2024
Resolution: 2.34 Å
EM Method: Single-particle

You L, Wang C, Molodtsov V, Kuznedelov K, Miao X, Wenck BR, Ulisse P, Sanders TJ, Marshall CJ, Firlar E, Kaelber JT, Santangelo TJ, Ebright RH

Nature (2024) 635 pp. 229-236 [ Pubmed: 39322680 DOI: doi:10.1038/s41586-024-07979-9 ]

EMD-38109
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3D View
MCM in the Apo state.
Release date: Jan. 17, 2024
Resolution: 3.26 Å
EM Method: Single-particle
Fitted PDBs: 8x7t
Q-score: 0.374

Ma J, Yi G, Ye M, MacGregor-Chatwin C, Sheng Y, Lu Y, Li M, Li Q, Wang D, Gilbert RJC, Zhang P

Nat Commun (2024) 15 pp. 10304-10304 [ Pubmed: 39604363 DOI: doi:10.1038/s41467-024-53745-w ]

EMD-38110
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Structure of MCM_apo before local refinement
Release date: Jan. 17, 2024
Resolution: 3.26 Å
EM Method: Single-particle

Ma J, Yi G, Ye M, MacGregor-Chatwin C, Sheng Y, Lu Y, Li M, Li Q, Wang D, Gilbert RJC, Zhang P

Nat Commun (2024) 15 pp. 10304-10304 [ Pubmed: 39604363 DOI: doi:10.1038/s41467-024-53745-w ]

EMD-38111
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3D View
MCM in complex with dsDNA in presence of ATP.
Release date: Jan. 17, 2024
Resolution: 3.57 Å
EM Method: Single-particle
Fitted PDBs: 8x7u
Q-score: 0.347

Ma J, Yi G, Ye M, MacGregor-Chatwin C, Sheng Y, Lu Y, Li M, Li Q, Wang D, Gilbert RJC, Zhang P

Nat Commun (2024) 15 pp. 10304-10304 [ Pubmed: 39604363 DOI: doi:10.1038/s41467-024-53745-w ]

Sort by: Download
Showing 1 - 10 of 36. Page 1 of 4
Display:
Statistics
×

Download











































Preview first 10
Download

Filter By

Current Database

  • EMDB [36]

Current status

  • REL [36]

Sample type

  • Complex [36]
  • Protein [10]
  • Ligand [6]
  • RNA [4]
  • DNA [2]
  • Sample [2]

Organism

  • Thermococcus kodakarensis [36]
  • Synthetic construct [4]
  • Pyrococcus furiosus [1]

EM Method

  • Single-particle [36]

Resolution

  • ≥ 2Å and < 3Å [10]
  • ≥ 3Å and < 4Å [17]
  • ≥ 4Å and < 5Å [1]
  • ≥ 6Å and < 8Å [4]
  • ≥ 8Å and < 12Å [3]
  • ≥ 16Å and < 20Å [1]

Model molecular weight

  • 100-250 kDa [3]
  • 250-500 kDa [5]
  • 500-1000 kDa [2]
  • 2-5 MDa [2]

Release Date

  • 2025 [1]
  • 2024 [25]
  • 2023 [2]
  • 2021 [2]
  • 2020 [4]
  • 2013 [1]
  • 2012 [1]

Author by name

  • Gilbert RJC [19]
  • Li M [19]
  • Li Q [19]
  • Lu Y [19]
  • Ma J [19]
  • Macgregor-chatwin C [19]
  • Sheng Y [19]
  • Wang D [19]
  • Ye M [19]
  • Yi G [19]
  • Zhang P [19]
  • Santangelo TJ [8]
  • Ebright RH [6]
  • Firlar E [6]
  • Kaelber JT [6]
  • Kuznedelov K [6]
  • Marshall CJ [6]
  • Miao X [6]
  • Molodtsov V [6]
  • Sanders TJ [6]
  • Ulisse P [6]
  • Wang C [6]
  • Wenck BR [6]
  • You L [6]
  • Anger AM [2]
  • Armache J-P [2]
  • Beckmann R [2]
  • Berninghausen O [2]
  • Bowerman S [2]
  • Briney CA [2]
  • Bryson KM [2]
  • Burkhart BW [2]
  • Florens L [2]
  • Fuchs RT [2]
  • Gamage ST [2]
  • Hartmann J [2]
  • Ishino S [2]
  • Ishino Y [2]
  • Isobe T [2]
  • Iwasaki K [2]
  • Kohda D [2]
  • Levy MJ [2]
  • Liman GLS [2]
  • Lin Q [2]
  • Luger K [2]
  • Matzov D [2]
  • Mayanagi K [2]
  • Meier JL [2]
  • Miyazaki N [2]
  • Morikawa K [2]
  • Nance KD [2]
  • Nir R [2]
  • Nobe Y [2]
  • Oki K [2]
  • Robb GB [2]
  • Sas-chen A [2]
  • Schwartz S [2]
  • Shachar R [2]
  • Shalev-benami M [2]
  • Sharma S [2]
  • Shirai T [2]
  • Taoka M [2]
  • Thomas JM [2]
  • Thomm M [2]
  • Washburn MP [2]
  • Wereszczynski J [2]
  • Yamagami T [2]
  • Anshari ZR [1]
  • Armache JP [1]
  • Arnold GJ [1]
  • Becker T [1]
  • Colucci E [1]
  • Daberkow I [1]
  • Franckenberg S [1]
  • Frankenberg S [1]
  • Froehlich T [1]
  • Green R [1]
  • Guskov A [1]
  • Hamaguchi T [1]
  • Himiyama T [1]
  • Hopfner K-P [1]
  • Hopfner KP [1]
  • Karcher A [1]
  • Marquez V [1]
  • Nakamura T [1]
  • Naz Z [1]
  • Nemchinova M [1]
  • Patino-ruiz MF [1]
  • Rahman M [1]
  • Rashid N [1]
  • Rathore I [1]
  • Saleem M [1]
  • Shoemaker CJ [1]
  • Sieber H [1]
  • Slotboom DJ [1]
  • Ungewickell C [1]
  • Villa E [1]
  • Whittaker J [1]
  • Whittaker JJ [1]
  • Wickles S [1]

Author by ORCID

  • Ye M [19]
  • Gilbert RJC [19]
  • Wang D [19]
  • Li M [19]
  • Lu Y [19]
  • Li Q [19]
  • Zhang P [19]
  • Sheng Y [19]
  • Yi G [19]
  • Ebright RH [6]
  • Kaelber JT [6]
  • Wang C [6]
  • Kuznedelov K [6]
  • Molodtsov V [6]
  • Santangelo TJ [6]
  • Miao X [6]
  • Luger K [2]
  • Taoka M [2]
  • Washburn MP [2]
  • Briney CA [2]
  • Sharma S [2]
  • Sas-chen A [2]
  • Gamage ST [2]
  • Lin Q [2]
  • Wereszczynski J [2]
  • Robb GB [2]
  • Schwartz S [2]
  • Nance KD [2]
  • Bowerman S [2]
  • Liman GLS [2]
  • Shachar R [2]
  • Himiyama T [1]
  • Yonekura K [1]
  • Whittaker J [1]
  • Armache J-P [1]
  • Armache JP [1]
  • Saleem M [1]
  • Rashid N [1]
  • Hopfner KP [1]
  • Froehlich T [1]
  • Wlodawer A [1]
  • Slotboom DJ [1]
  • Anshari ZR [1]
  • Guskov A [1]
  • Rathore I [1]
  • Colucci E [1]
  • Wilson DN [1]
  • Nemchinova M [1]
  • Villa E [1]
  • Naz Z [1]

Journal

  • NAT COMMUN [20]
  • NATURE [9]
  • ELIFE [2]
  • TO BE PUBLISHED [2]
  • BIOCONJUG.CHEM. [1]
  • BIOMOLECULES [1]
  • NUCLEIC ACIDS RES [1]

Software

  • CRYOSPARC [9]
  • RELION [4]
  • GCTF [2]
  • SPIDER [2]
  • CTFFIND [1]
  • MDFF [1]
  • UCSF CHIMERA [1]

Microscope

  • FEI TITAN KRIOS [30]
  • FEI TALOS ARCTICA [2]
  • FEI TECNAI 20 [2]
  • FEI TECNAI 12 [1]
  • JEOL CRYO ARM 300 [1]

Electron Source

  • FIELD EMISSION GUN [35]
  • LAB6 [1]

Film or detector model

  • FEI FALCON IV 4K X 4K [12]
  • GATAN K3 BIOQUANTUM 6K X 4K [11]
  • GATAN K3 6K X 4K [7]
  • FEI FALCON III 4K X 4K [3]
  • FEI EAGLE 4K X 4K [1]
  • FEI FALCON II 4K X 4K [1]
  • TVIPS TEMCAM-F416 4K X 4K [1]

External links

  • PDB [12]
  • AlphaFold DB [6]
  • ChEBI [6]
  • ChEMBL [6]
  • DrugBank [6]
  • Gene Ontology [6]
  • InterPro [6]
  • Pfam [6]
  • UniProt [6]
  • PDBe-Kb [5]
  • SCOP2 [2]