Cryo-EM structure of the SARS-CoV-2 Omicron spike protein
Resolution: 2.79 Å
EM Method: Single-particle
Fitted PDBs: 7t9j
Q-score: 0.366
Mannar D, Saville JW, Zhu X, Srivastava SS, Berezuk AM, Tuttle KS, Marquez AC, Sekirov I, Subramaniam S
Science (2022) 375 pp. 760-764 [ Pubmed: 35050643 DOI: doi:10.1126/science.abn7760 ]
Cryo-EM structure of SARS-CoV-2 Omicron spike protein in complex with human ACE2
Resolution: 2.45 Å
EM Method: Single-particle
Fitted PDBs: 7t9k
Q-score: 0.323
Mannar D, Saville JW, Zhu X, Srivastava SS, Berezuk AM, Tuttle KS, Marquez AC, Sekirov I, Subramaniam S
Science (2022) 375 pp. 760-764 [ Pubmed: 35050643 DOI: doi:10.1126/science.abn7760 ]
- Sars-cov-2 omicron spike protein (Complex from Severe acute respiratory syndrome coronavirus 2)
- Spike glycoprotein (142 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Sars-cov-2 omicron spike protein in complex with human ace2 (Complex from Severe acute respiratory syndrome coronavirus 2)
- Human ace2 (Complex from Homo sapiens)
- Processed angiotensin-converting enzyme 2 (70 kDa, Protein from Homo sapiens)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
Resolution: 2.66 Å
EM Method: Single-particle
Fitted PDBs: 7t9l
Q-score: 0.52
Mannar D, Saville JW, Zhu X, Srivastava SS, Berezuk AM, Tuttle KS, Marquez AC, Sekirov I, Subramaniam S
Science (2022) 375 pp. 760-764 [ Pubmed: 35050643 DOI: doi:10.1126/science.abn7760 ]
- Sars-cov-2 omicron spike protein (Complex from Severe acute respiratory syndrome coronavirus 2)
- Spike glycoprotein (142 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Sars-cov-2 omicron spike protein in complex with human ace2 (Complex from Severe acute respiratory syndrome coronavirus 2)
- Human ace2 (Complex from Homo sapiens)
- Processed angiotensin-converting enzyme 2 (70 kDa, Protein from Homo sapiens)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
The cryo-EM structure of A. thaliana Pol IV-RDR2 backtracked complex
Resolution: 3.16 Å
EM Method: Single-particle
Fitted PDBs: 7eu0
Q-score: 0.487
Huang K, Wu XX, Fang CL, Xu ZG, Zhang HW, Gao J, Zhou CM, You LL, Gu ZX, Mu WH, Feng Y, Wang JW, Zhang Y
Science (2021) 374 pp. 1579-1586 [ DOI: doi:10.1126/science.abj9184 Pubmed: 34941388 ]
- Dna-directed rna polymerases ii, iv and v subunit 11 (13 kDa, Protein from thale cress)
- Dna-directed rna polymerases ii, iv and v subunit 8b (16 kDa, Protein from thale cress)
- Dna (5'-d(*cp*tp*gp*tp*gp*cp*tp*tp*ap*tp*cp*gp*gp*tp*ap*gp*ap*gp*tp*g)-3') (6 kDa, DNA from synthetic construct)
- Dna (33-mer) (9 kDa, DNA from synthetic construct)
- Rna (5'-r(*cp*cp*gp*a)-3') (1 kDa, RNA from synthetic construct)
- Dna-directed rna polymerases ii, iv and v subunit 6a (16 kDa, Protein from thale cress)
- Dna-directed rna polymerase iv subunit 1 (169 kDa, Protein from Mouse-ear cress)
- Dna-directed rna polymerases ii, iv and v subunit 10 (8 kDa, Protein from thale cress)
- Dna-directed rna polymerases ii, iv and v subunit 12 (5 kDa, Protein from thale cress)
- Rna-dependent rna polymerase 2 (129 kDa, Protein from thale cress)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerases ii, iv and v subunit 3 (35 kDa, Protein from thale cress)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerases ii and iv subunit 5a (24 kDa, Protein from thale cress)
- Dna-directed rna polymerases iv and v subunit 2 (132 kDa, Protein from thale cress)
- Rna (39-mer) (12 kDa, RNA from synthetic construct)
- A. thaliana pol iv-rdr2 backtracked complex (550 kDa, Complex from Arabidopsis thaliana)
- Dna-directed rna polymerases ii, iv and v subunit 9a (13 kDa, Protein from thale cress)
The cryo-EM structure of A. thaliana Pol IV-RDR2 holoenzyme
Resolution: 3.86 Å
EM Method: Single-particle
Fitted PDBs: 7eu1
Q-score: 0.434
Huang K, Wu XX, Fang CL, Xu ZG, Zhang HW, Gao J, Zhou CM, You LL, Gu ZX, Mu WH, Feng Y, Wang JW, Zhang Y
Science (2021) 374 pp. 1579-1586 [ DOI: doi:10.1126/science.abj9184 Pubmed: 34941388 ]
- Dna-directed rna polymerases iv and v subunit 2 (132 kDa, Protein from Mouse-ear cress)
- Dna-directed rna polymerases ii, iv and v subunit 10 (8 kDa, Protein from Mouse-ear cress)
- Dna-directed rna polymerases ii, iv and v subunit 8b (16 kDa, Protein from Mouse-ear cress)
- Zinc ion (65 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- A. thaliana pol iv-rdr2 holoenzyme (Complex from Arabidopsis thaliana)
- Rna-dependent rna polymerase 2 (129 kDa, Protein from Mouse-ear cress)
- Dna-directed rna polymerases ii, iv and v subunit 6a (16 kDa, Protein from Mouse-ear cress)
- Dna-directed rna polymerases ii and iv subunit 5a (24 kDa, Protein from Mouse-ear cress)
- Dna-directed rna polymerases ii, iv and v subunit 9a (13 kDa, Protein from Mouse-ear cress)
- Dna-directed rna polymerases ii, iv and v subunit 3 (35 kDa, Protein from Mouse-ear cress)
- Dna-directed rna polymerases ii, iv and v subunit 11 (13 kDa, Protein from Mouse-ear cress)
- Dna-directed rna polymerase iv subunit 1 (169 kDa, Protein from Arabidopsis thaliana)
- Dna-directed rna polymerases ii, iv and v subunit 12 (5 kDa, Protein from Mouse-ear cress)
Barley photosystem I-LHCI-Lhca5 supercomplex
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 7ew6
Q-score: 0.466
Shen L, Tang K, Wang W, Wang C, Wu H, Mao Z, An S, Chang S, Kuang T, Shen JR, Han G, Zhang X
Nature (2022) 601 pp. 649-654 [ DOI: doi:10.1038/s41586-021-04277-6 Pubmed: 34879391 ]
- Photosystem i reaction center subunit xi, chloroplastic (22 kDa, Protein from Hordeum vulgare subsp. spontaneum)
- Digalactosyl diacyl glycerol (dgdg) (949 Da, Ligand)
- Photosystem i reaction center subunit psak, chloroplastic (13 kDa, Protein from Hordeum vulgare subsp. spontaneum)
- (3s,5r,6s,3's,5'r,6's)-5,6,5',6'-diepoxy-5,6,5',6'- tetrahydro-beta,beta-carotene-3,3'-diol (600 Da, Ligand)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Chlorophyll a (893 Da, Ligand)
- Chlorophyll a-b binding protein lhca5 (27 kDa, Protein from Hordeum vulgare subsp. spontaneum)
- Psi-lhci-lhca5 supercomplex of barley (Complex from Hordeum vulgare subsp. spontaneum)
- Chlorophyll a-b binding protein, chloroplastic (29 kDa, Protein from Hordeum vulgare subsp. spontaneum)
- Phylloquinone (450 Da, Ligand)
- Photosystem i reaction center subunit viii (4 kDa, Protein from Hordeum vulgare subsp. spontaneum)
- 1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
- Photosystem i iron-sulfur center (8 kDa, Protein from Hordeum vulgare subsp. spontaneum)
- Chlorophyll a-b binding protein, chloroplastic (27 kDa, Protein from Hordeum vulgare subsp. spontaneum)
- Chlorophyll a-b binding protein lhca1 (26 kDa, Protein from Hordeum vulgare subsp. spontaneum)
- Chlorophyll b (907 Da, Ligand)
- Photosystem i reaction center subunit iv, chloroplastic (15 kDa, Protein from Hordeum vulgare subsp. spontaneum)
- Photosystem i p700 chlorophyll a apoprotein a2 (82 kDa, Protein from Hordeum vulgare subsp. spontaneum)
- (3r,3'r,6s)-4,5-didehydro-5,6-dihydro-beta,beta-carotene-3,3'-diol (568 Da, Ligand)
- Iron/sulfur cluster (351 Da, Ligand)
- Beta-carotene (536 Da, Ligand)
- Photosystem i reaction center subunit iii, chloroplastic (24 kDa, Protein from Hordeum vulgare subsp. spontaneum)
- Photosystem i p700 chlorophyll a apoprotein a1 (83 kDa, Protein from Hordeum vulgare subsp. spontaneum)
- Chlorophyll a isomer (893 Da, Ligand)
- Photosystem i reaction center subunit vi, chloroplastic (14 kDa, Protein from Hordeum vulgare subsp. spontaneum)
- Photosystem i reaction center subunit ii, chloroplastic (21 kDa, Protein from Hordeum vulgare subsp. spontaneum)
- Photosystem i reaction center subunit ix (4 kDa, Protein from Hordeum vulgare subsp. spontaneum)
PSI-NDH supercomplex of Barley
Resolution: 4.5 Å
EM Method: Single-particle
Fitted PDBs: 7f9o
Q-score: 0.153
Shen L, Tang K, Wang W, Wang C, Wu H, Mao Z, An S, Chang S, Kuang T, Shen JR, Han G, Zhang X
Nature (2022) 601 pp. 649-654 [ DOI: doi:10.1038/s41586-021-04277-6 Pubmed: 34879391 ]
- Nad(p)h-quinone oxidoreductase subunit n, chloroplastic (25 kDa, Protein from Hordeum vulgare subsp. spontaneum)
- Nadh-plastoquinone oxidoreductase subunit 5 (87 kDa, Protein from Hordeum vulgare subsp. spontaneum)
- Photosystem i reaction center subunit xi, chloroplastic (22 kDa, Protein from Hordeum vulgare subsp. spontaneum)
- Digalactosyl diacyl glycerol (dgdg) (949 Da, Ligand)
- Photosystem i reaction center subunit psak, chloroplastic (13 kDa, Protein from Hordeum vulgare subsp. spontaneum)
- Nad(p)h-quinone oxidoreductase subunit k, chloroplastic (27 kDa, Protein from Hordeum vulgare subsp. spontaneum)
- (3s,5r,6s,3's,5'r,6's)-5,6,5',6'-diepoxy-5,6,5',6'- tetrahydro-beta,beta-carotene-3,3'-diol (600 Da, Ligand)
- Photosynthetic ndh subunit of subcomplex b4 (9 kDa, Protein from Hordeum vulgare subsp. spontaneum)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Chlorophyll a (893 Da, Ligand)
- Nad(p)h-quinone oxidoreductase subunit m, chloroplastic (24 kDa, Protein from Hordeum vulgare subsp. spontaneum)
- Chlorophyll a-b binding protein lhca5 (27 kDa, Protein from Hordeum vulgare subsp. spontaneum)
- Photosynthetic ndh subunit of subcomplex l1 (17 kDa, Protein from Hordeum vulgare subsp. spontaneum)
- Nad(p)h-quinone oxidoreductase subunit h, chloroplastic (44 kDa, Protein from Hordeum vulgare subsp. spontaneum)
- Photosynthetic ndh subunit of subcomplex l2 (23 kDa, Protein from Hordeum vulgare subsp. spontaneum)
- Chlorophyll a-b binding protein, chloroplastic (29 kDa, Protein from Hordeum vulgare subsp. spontaneum)
- Phylloquinone (450 Da, Ligand)
- Photosystem i reaction center subunit viii (4 kDa, Protein from Hordeum vulgare subsp. spontaneum)
- 1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
- Photosynthetic ndh subunit of subcomplex l5 (25 kDa, Protein from Hordeum vulgare subsp. spontaneum)
- Photosystem i iron-sulfur center (8 kDa, Protein from Hordeum vulgare subsp. spontaneum)
- Chlorophyll a-b binding protein, chloroplastic (27 kDa, Protein from Hordeum vulgare subsp. spontaneum)
- Nad(p)h-quinone oxidoreductase chain 4, chloroplastic (56 kDa, Protein from Hordeum vulgare subsp. spontaneum)
- Photosynthetic ndh subunit of subcomplex b1 (51 kDa, Protein from Hordeum vulgare subsp. spontaneum)
- Photosynthetic ndh subunit of subcomplex l4 (13 kDa, Protein from Hordeum vulgare subsp. spontaneum)
- Psi-ndh supercomplex of barley (Complex from Hordeum vulgare subsp. spontaneum)
- Photosynthetic ndh subunit of subcomplex l2 (24 kDa, Protein from Hordeum vulgare subsp. spontaneum)
- Chlorophyll a-b binding protein, chloroplastic (23 kDa, Protein from Hordeum vulgare subsp. spontaneum)
- Chlorophyll a-b binding protein lhca1 (26 kDa, Protein from Hordeum vulgare subsp. spontaneum)
- Nad(p)h-quinone oxidoreductase subunit 1, chloroplastic (38 kDa, Protein from Hordeum vulgare subsp. spontaneum)
- Nad(p)h-quinone oxidoreductase subunit i, chloroplastic (19 kDa, Protein from Hordeum vulgare subsp. spontaneum)
- Chlorophyll b (907 Da, Ligand)
- Photosynthetic ndh subunit of subcomplex b2 (38 kDa, Protein from Hordeum vulgare subsp. spontaneum)
- Photosystem i reaction center subunit iv, chloroplastic (15 kDa, Protein from Hordeum vulgare subsp. spontaneum)
- Unidentified stromal protein (5 kDa, Protein from Hordeum vulgare subsp. spontaneum)
- Photosystem i p700 chlorophyll a apoprotein a2 (82 kDa, Protein from Hordeum vulgare subsp. spontaneum)
- 1,2-di-o-acyl-3-o-[6-deoxy-6-sulfo-alpha-d-glucopyranosyl]-sn-glycerol (795 Da, Ligand)
- Nad(p)h-quinone oxidoreductase subunit 2, chloroplastic (53 kDa, Protein from Hordeum vulgare subsp. spontaneum)
- Chlorophyll a-b binding protein lhca4 (21 kDa, Protein from Hordeum vulgare subsp. spontaneum)
- Nad(p)h-quinone oxidoreductase subunit 6, chloroplastic (19 kDa, Protein from Hordeum vulgare subsp. spontaneum)
- Nad(p)h-quinone oxidoreductase subunit l, chloroplastic (22 kDa, Protein from Hordeum vulgare subsp. spontaneum)
- (3r,3'r,6s)-4,5-didehydro-5,6-dihydro-beta,beta-carotene-3,3'-diol (568 Da, Ligand)
- Nad(p)h-quinone oxidoreductase subunit j, chloroplastic (18 kDa, Protein from Hordeum vulgare subsp. spontaneum)
- Nad(p)h-quinone oxidoreductase subunit 4l, chloroplastic (11 kDa, Protein from Hordeum vulgare subsp. spontaneum)
- Iron/sulfur cluster (351 Da, Ligand)
- Nad(p)h-quinone oxidoreductase subunit 3, chloroplastic (13 kDa, Protein from Hordeum vulgare subsp. spontaneum)
- Photosynthetic ndh subunit of subcomplex b3 (13 kDa, Protein from Hordeum vulgare subsp. spontaneum)
- Photosynthetic ndh subunit of subcomplex b5 (18 kDa, Protein from Hordeum vulgare subsp. spontaneum)
- Beta-carotene (536 Da, Ligand)
- Photosystem i reaction center subunit iii, chloroplastic (24 kDa, Protein from Hordeum vulgare subsp. spontaneum)
- Photosystem i p700 chlorophyll a apoprotein a1 (83 kDa, Protein from Hordeum vulgare subsp. spontaneum)
- Chlorophyll a isomer (893 Da, Ligand)
- Photosystem i reaction center subunit vi, chloroplastic (14 kDa, Protein from Hordeum vulgare subsp. spontaneum)
- Photosystem i reaction center subunit ii, chloroplastic (21 kDa, Protein from Hordeum vulgare subsp. spontaneum)
- Photosystem i reaction center subunit ix (4 kDa, Protein from Hordeum vulgare subsp. spontaneum)
Cryo-EM structure of amyloid fibril formed by FUS low complexity domain
ATP-bound AMP-activated protein kinase
Resolution: 3.93 Å
EM Method: Single-particle
Fitted PDBs: 7m74
Q-score: 0.27
Yan Y, Mukherjee S, Harikumar KG, Strutzenberg TS, Zhou XE, Suino-Powell K, Xu TH, Sheldon RD, Lamp J, Brunzelle JS, Radziwon K, Ellis A, Novick SJ, Vega IE, Jones RG, Miller LJ, Xu HE, Griffin PR, Kossiakoff AA, Melcher K
Science (2021) 373 pp. 413-419 [ DOI: doi:10.1126/science.abe7565 Pubmed: 34437114 ]
- Maltose/maltodextrin abc transporter substrate-binding protein male (40 kDa, Protein from Escherichia coli)
- Nanobody (13 kDa, Protein from Lama glama)
- 5'-amp-activated protein kinase subunit beta-2 (22 kDa, Protein from Homo sapiens)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- 5'-amp-activated protein kinase catalytic subunit alpha-1 (56 kDa, Protein from Homo sapiens)
- Fab light chain (22 kDa, Protein from Homo sapiens)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Adenosine monophosphate (347 Da, Ligand)
- Fab heavy chain (24 kDa, Protein from Homo sapiens)
- 6-[4-(2-piperidin-1-ylethoxy)phenyl]-3-pyridin-4-ylpyrazolo[1,5-a]pyrimidine (399 Da, Ligand)
- Mbp-fused atp bound ampk in complex with c-compound stabilized by fab and a nanobody (Complex from Homo sapiens)
- 5'-amp-activated protein kinase subunit gamma-1 (34 kDa, Protein from Homo sapiens)
Structural basis of Integrator-mediated transcription regulation
Resolution: 3.6 Å
EM Method: Single-particle
Fitted PDBs: 7pks
Q-score: 0.278
Fianu I, Chen Y, Dienemann C, Dybkov O, Linden A, Urlaub H, Cramer P
Science (2021) 374 pp. 883-887 [ Pubmed: 34762484 DOI: doi:10.1126/science.abk0154 ]
- Zinc ion (65 Da, Ligand)
- Integrator complex subunit 4 (108 kDa, Protein from Homo sapiens)
- Unknown (2 kDa, Protein from Homo sapiens)
- Non-template dna (14 kDa, DNA from Human immunodeficiency virus 1)
- Serine/threonine-protein phosphatase 2a catalytic subunit alpha isoform (35 kDa, Protein from Homo sapiens)
- Serine/threonine-protein phosphatase 2a 65 kda regulatory subunit a alpha isoform (65 kDa, Protein from Homo sapiens)
- Non-template dna (Complex from Human immunodeficiency virus 1)
- Rpbi c-terminal domain peptide (1 kDa, Protein from domestic pig)
- Integrator complex subunit 6 (100 kDa, Protein from Homo sapiens)
- Integrator complex subunit 7 (106 kDa, Protein from Homo sapiens)
- Rna polymerase ii subunit d (16 kDa, Protein from domestic pig)
- Dna template (14 kDa, DNA from Human immunodeficiency virus 1)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from domestic pig)
- Negative elongation factor a (57 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from domestic pig)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from domestic pig)
- Integrator complex subunit 8 (113 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from domestic pig)
- Tar rna (5 kDa, RNA from Human immunodeficiency virus 1)
- Dsif (Complex from Homo sapiens)
- Pec-integrator-pp2a complex (1 MDa, Complex)
- Negative elongation factor b (68 kDa, Protein from Homo sapiens)
- Integrator complex subunit 5 (108 kDa, Protein from Homo sapiens)
- Integrator complex subunit 2 (134 kDa, Protein from Homo sapiens)
- Negative elongation factor e (1 kDa, Protein from Homo sapiens)
- Nelf (Complex from Homo sapiens)
- Rna (Complex from Human immunodeficiency virus 1)
- Rna polymerase ii subunit k (7 kDa, Protein from domestic pig)
- Magnesium ion (24 Da, Ligand)
- Integrator complex subunit 9 (73 kDa, Protein from Homo sapiens)
- Manganese (ii) ion (54 Da, Ligand)
- Integrator complex subunit 11 (67 kDa, Protein from Homo sapiens)
- Human integrator-pp2a complex (Complex from Homo sapiens)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from domestic pig)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from domestic pig)
- Negative elongation factor c/d (68 kDa, Protein from Homo sapiens)
- Rna_pol_l_2 domain-containing protein (13 kDa, Protein from domestic pig)
- Integrator complex subunit 1 (244 kDa, Protein from Homo sapiens)
- Transcription elongation factor spt5 (121 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit (217 kDa, Protein from domestic pig)
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from domestic pig)
- Template dna (Complex from Human immunodeficiency virus 1)
- Pol ii-ec (Complex from Sus scrofa domesticus)
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from domestic pig)