ACAD11 D220A with 4-hydroxyvaleryl-CoA
Resolution: 2.6 Å
EM Method: Single-particle
Fitted PDBs: 8v3u
Q-score: 0.637
Structure of S. cerevisiae Hop1 CBR bound to a nucleosome
Resolution: 2.74 Å
EM Method: Single-particle
Fitted PDBs: 8cww
Q-score: 0.574
Milano CR, Ur SN, Gu Y, Zhang J, Allison R, Brown G, Neale MJ, Tromer EC, Corbett KD, Hochwagen A
EMBO J (2024) 43 pp. 836-867 [ DOI: doi:10.1038/s44318-024-00034-3 Pubmed: 38332377 ]
- Meiosis-specific protein hop1 (24 kDa, Protein from Saccharomyces cerevisiae)
- Widom 601 dna (146-mer) (44 kDa, DNA from Escherichia coli)
- Zinc ion (65 Da, Ligand)
- Histone h2a (13 kDa, Protein from Xenopus laevis)
- Complex of hop1 cbr domain bound to nucleosome (223 kDa, Complex from Saccharomyces cerevisiae)
- Histone h2b (13 kDa, Protein from Xenopus laevis)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Widom 601 dna (146-mer) (45 kDa, DNA from Escherichia coli)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
Closed state of SARS-CoV-2 BA.2 variant spike protein
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 8d55
Q-score: 0.434
Unmethylated Mtb Ribosome 50S with SEQ-9
Resolution: 2.6 Å
EM Method: Single-particle
Fitted PDBs: 7sfr
Q-score: 0.468
Zhang J, Lair C, Roubert C, Amaning K, Barrio MB, Benedetti Y, Cui Z, Xing Z, Li X, Franzblau SG, Baurin N, Bordon-Pallier F, Cantalloube C, Sans S, Silve S, Blanc I, Fraisse L, Rak A, Jenner LB, Yusupova G, Yusupov M, Zhang J, Kaneko T, Yang TJ, Fotouhi N, Nuermberger E, Tyagi S, Betoudji F, Upton A, Sacchettini JC, Lagrange S
Cell (2023) 186 pp. 1013- [ Pubmed: 36827973 DOI: doi:10.1016/j.cell.2023.01.043 ]
- 50s ribosomal protein l21 (11 kDa, Protein from Mycobacterium tuberculosis)
- 50s ribosomal protein l13 (21 kDa, Protein from Mycobacterium tuberculosis)
- 30s ribosomal protein s12 (13 kDa, Protein from Mycobacterium tuberculosis)
- 50s ribosomal protein l31 (8 kDa, Protein from Mycobacterium tuberculosis)
- 30s ribosomal protein s5 (22 kDa, Protein from Mycobacterium tuberculosis)
- 50s ribosomal protein l14 (13 kDa, Protein from Mycobacterium tuberculosis)
- 30s ribosomal protein s8 (14 kDa, Protein from Mycobacterium tuberculosis)
- 50s ribosomal protein l20 (14 kDa, Protein from Mycobacterium tuberculosis)
- 50s ribosomal protein l24 (11 kDa, Protein from Mycobacterium tuberculosis)
- 30s ribosomal protein s10 (11 kDa, Protein from Mycobacterium tuberculosis)
- Unmethylated mth ribosome with seq-9 (Complex from Mycobacterium tuberculosis)
- 23s rrna (1 MDa, RNA from Mycobacterium tuberculosis)
- 50s ribosomal protein l2 (30 kDa, Protein from Mycobacterium tuberculosis)
- 50s ribosomal protein l34 (5 kDa, Protein from Mycobacterium tuberculosis)
- 30s ribosomal protein s11 (14 kDa, Protein from Mycobacterium tuberculosis)
- 50s ribosomal protein l22 (20 kDa, Protein from Mycobacterium tuberculosis)
- 30s ribosomal protein s16 (17 kDa, Protein from Mycobacterium tuberculosis)
- Magnesium ion (24 Da, Ligand)
- 50s ribosomal protein l5 (20 kDa, Protein from Mycobacterium tuberculosis)
- 50s ribosomal protein l9 (16 kDa, Protein from Mycobacterium tuberculosis)
- 50s ribosomal protein l16 (15 kDa, Protein from Mycobacterium tuberculosis)
- 30s ribosomal protein s17 (14 kDa, Protein from Mycobacterium tuberculosis)
- 50s ribosomal protein l19 (13 kDa, Protein from Mycobacterium tuberculosis)
- 30s ribosomal protein s15 (10 kDa, Protein from Mycobacterium tuberculosis)
- Peptide (2 kDa, Protein from Mycobacterium tuberculosis)
- 50s ribosomal protein l28 (6 kDa, Protein from Mycobacterium tuberculosis)
- 16s rrna (498 kDa, RNA from Mycobacterium tuberculosis)
- 30s ribosomal protein s3 (30 kDa, Protein from Mycobacterium tuberculosis)
- 50s ribosomal protein l25 (22 kDa, Protein from Mycobacterium tuberculosis)
- 30s ribosomal protein s20 (9 kDa, Protein from Mycobacterium tuberculosis)
- Sequanamycin 9 (1 kDa, Ligand)
- 30s ribosomal protein s6 (10 kDa, Protein from Mycobacterium tuberculosis)
- 30s ribosomal protein s13 (14 kDa, Protein from Mycobacterium tuberculosis)
- 30s ribosomal protein s9 (16 kDa, Protein from Mycobacterium tuberculosis)
- 30s ribosomal protein s19 (10 kDa, Protein from Mycobacterium tuberculosis)
- Zinc ion (65 Da, Ligand)
- 50s ribosomal protein l3 (22 kDa, Protein from Mycobacterium tuberculosis)
- 50s ribosomal protein l15 (15 kDa, Protein from Mycobacterium tuberculosis)
- 50s ribosomal protein l33 (6 kDa, Protein from Mycobacterium tuberculosis)
- 30s ribosomal protein s7 (17 kDa, Protein from Mycobacterium tuberculosis)
- 50s ribosomal protein l23 (10 kDa, Protein from Mycobacterium tuberculosis)
- 50s ribosomal protein l30 (7 kDa, Protein from Mycobacterium tuberculosis)
- 30s ribosomal protein s18 (9 kDa, Protein from Mycobacterium tuberculosis)
- 50s ribosomal protein l29 (8 kDa, Protein from Mycobacterium tuberculosis)
- 50s ribosomal protein l27 (8 kDa, Protein from Mycobacterium tuberculosis)
- 50s ribosomal protein l18 (13 kDa, Protein from Mycobacterium tuberculosis)
- 50s ribosomal protein l36 (4 kDa, Protein from Mycobacterium tuberculosis)
- 30s ribosomal protein s4 (23 kDa, Protein from Mycobacterium tuberculosis)
- 50s ribosomal protein l32 (6 kDa, Protein from Mycobacterium tuberculosis)
- 30s ribosomal protein s14 type z (6 kDa, Protein from Mycobacterium tuberculosis)
- 50s ribosomal protein l6 (19 kDa, Protein from Mycobacterium tuberculosis)
- 50s ribosomal protein l4 (22 kDa, Protein from Mycobacterium tuberculosis)
- 50s ribosomal protein l17 (19 kDa, Protein from Mycobacterium tuberculosis)
- 50s ribosomal protein l35 (7 kDa, Protein from Mycobacterium tuberculosis)
- 5s rrna (37 kDa, RNA from Mycobacterium tuberculosis)
Resolution: 2.7 Å
EM Method: Single-particle
Fitted PDBs: 7upw
Q-score: 0.464
Luo S, Zhang J, Kreutzberger AJB, Eaton A, Edwards RJ, Jing C, Dai HQ, Sempowski GD, Cronin K, Parks R, Ye AY, Mansouri K, Barr M, Pishesha N, Williams AC, Vieira Francisco L, Saminathan A, Peng H, Batra H, Bellusci L, Khurana S, Alam SM, Montefiori DC, Saunders KO, Tian M, Ploegh H, Kirchhausen T, Chen B, Haynes BF, Alt FW
Sci Immunol (2022) 7 pp. eadd5446-eadd5446 [ DOI: doi:10.1126/sciimmunol.add5446 Pubmed: 35951767 ]
- Sp1-77 fab heavy chain, sp1-77 fab light chain (Complex from Homo sapiens)
- Sp1-77 fab heavy chain (49 kDa, Protein from Homo sapiens)
- Spike glycoprotein (Complex from Severe acute respiratory syndrome coronavirus)
- Spike glycoprotein (144 kDa, Protein from Severe acute respiratory syndrome coronavirus)
- Three rbd-down state of sars-cov-2 d614g spike in complex with the sp1-77 neutralizing antibody fab fragment (650 kDa, Complex)
- Sp1-77 fab light chain (23 kDa, Protein from Homo sapiens)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
Cryo-EM structure of VWF D'D3 dimer complexed with D1D2 at 2.85 angstron resolution (1 unit)
Resolution: 2.85 Å
EM Method: Single-particle
Fitted PDBs: 7wpp
Q-score: 0.481
Zeng J, Shu Z, Liang Q, Zhang J, Wu W, Wang X, Zhou A
Blood (2022) 139 pp. 3314-3324 [ Pubmed: 35148377 DOI: doi:10.1182/blood.2021014729 ]
- Von willebrand factor (54 kDa, Protein from Homo sapiens)
- Vwf d'd3-d1d2 complex (1 unit) (Complex from Homo sapiens)
- Von willebrand antigen 2 (81 kDa, Protein from Homo sapiens)
- Calcium ion (40 Da, Ligand)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
Cryo-EM structure of the SARS-CoV-2 S-6P in complex with Fab30
Resolution: 2.76 Å
EM Method: Single-particle
Fitted PDBs: 7enf
Q-score: 0.485
Wang X, Hu A, Chen X, Zhang Y, Yu F, Yue S, Li A, Zhang J, Pan Z, Yang Y, Lin Y, Gao L, Zhou J, Zhao J, Li F, Shi Y, Huang F, Yang X, Peng Y, Tu L, Zhang H, Zheng H, He J, Zhang H, Xu L, Huang Q, Zhu Y, Deng K, Ye L
Signal Transduct Target Ther (2022) 7 pp. 114- [ DOI: doi:10.1038/s41392-022-00954-8 ]
- Light chain of fab30 (24 kDa, Protein from Homo sapiens)
- Spike glycoprotein (142 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Complex of sars-cov-2 spike glycoprotein and fab30 (Complex from Severe acute respiratory syndrome coronavirus 2)
- Fab30 (Complex)
- Sars-cov-2 spike glycoprotein (Complex from Homo sapiens)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Heavy chain of fab30 (24 kDa, Protein from Homo sapiens)
S protein of SARS-CoV-2 in complex with 2G1
Resolution: 2.7 Å
EM Method: Single-particle
Fitted PDBs: 7x08
Q-score: 0.458
Ma H, Guo Y, Tang H, Tseng CK, Wang L, Zong H, Wang Z, He Y, Chang Y, Wang S, Huang H, Ke Y, Yuan Y, Wu M, Zhang Y, Drelich A, Kempaiah KR, Peng BH, Wang A, Yang K, Yin H, Liu J, Yue Y, Xu W, Zhu S, Ji T, Zhang X, Wang Z, Li G, Liu G, Song J, Mu L, Xiang Z, Song Z, Chen H, Bian Y, Zhang B, Chen H, Zhang J, Liao Y, Zhang L, Yang L, Chen Y, Gilly J, Xiao X, Han L, Jiang H, Xie Y, Zhou Q, Zhu J
Cell Discov (2022) 8 pp. 16-16 [ Pubmed: 35169121 DOI: doi:10.1038/s41421-022-00381-7 ]
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- S protein of sars-cov-2 (Complex from Severe acute respiratory syndrome coronavirus)
- Light chain of 2g1 (22 kDa, Protein from Homo sapiens)
- S protein of sars-cov-2 in complex with 2g1 (Complex)
- Spike glycoprotein (142 kDa, Protein from Severe acute respiratory syndrome coronavirus)
- Linoleic acid (280 Da, Ligand)
- 2g1 (Complex from Homo sapiens)
- Heavy chain of 2g1 (49 kDa, Protein from Homo sapiens)
CryoEM structure of A2296-methylated Mycobacterium tuberculosis ribosome bound with SEQ-9
Resolution: 2.7 Å
EM Method: Single-particle
Fitted PDBs: 7kgb
Q-score: 0.576
Zhang J, Lair C, Roubert C, Amaning K, Barrio MB, Benedetti Y, Cui Z, Xing Z, Li X, Franzblau SG, Baurin N, Bordon-Pallier F, Cantalloube C, Sans S, Silve S, Blanc I, Fraisse L, Rak A, Jenner LB, Yusupova G, Yusupov M, Zhang J, Kaneko T, Yang TJ, Fotouhi N, Nuermberger E, Tyagi S, Betoudji F, Upton A, Sacchettini JC, Lagrange S
Cell (2023) [ Pubmed: 36827973 DOI: doi:10.1016/j.cell.2023.01.043 ]
- 30s ribosomal protein s13 (14 kDa, Protein from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
- 50s ribosomal protein l31 (8 kDa, Protein from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
- 50s ribosomal protein l33 2 (6 kDa, Protein from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
- 30s ribosomal protein s15 (10 kDa, Protein from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
- 30s ribosomal protein s17 (14 kDa, Protein from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
- 23s rrna (1 MDa, RNA from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
- 50s ribosomal protein l35 (7 kDa, Protein from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
- 50s ribosomal protein l28 (6 kDa, Protein from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
- 30s ribosomal protein s3 (30 kDa, Protein from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
- 30s ribosomal protein s19 (10 kDa, Protein from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
- Magnesium ion (24 Da, Ligand)
- 50s ribosomal protein l2 (30 kDa, Protein from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
- Trna-initiator met(cau) (24 kDa, RNA from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
- 50s ribosomal protein l22 (20 kDa, Protein from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
- 50s ribosomal protein l25 (22 kDa, Protein from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
- 50s ribosomal protein l18 (13 kDa, Protein from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
- 30s ribosomal protein s8 (14 kDa, Protein from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
- 50s ribosomal protein l17 (19 kDa, Protein from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
- 50s ribosomal protein l3 (23 kDa, Protein from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
- 50s ribosomal protein l32 (6 kDa, Protein from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
- 16s rrna (498 kDa, RNA from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
- 50s ribosomal protein l19 (13 kDa, Protein from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
- Sequanamycin 9 (1 kDa, Ligand)
- 50s ribosomal protein l14 (13 kDa, Protein from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
- 50s ribosomal protein l4 (23 kDa, Protein from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
- 50s ribosomal protein l9 (16 kDa, Protein from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
- 50s ribosomal protein l15 (15 kDa, Protein from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
- Zinc ion (65 Da, Ligand)
- 30s ribosomal protein s12 (13 kDa, Protein from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
- 50s ribosomal protein l5 (21 kDa, Protein from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
- 50s ribosomal protein l16 (15 kDa, Protein from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
- 30s ribosomal protein s11 (14 kDa, Protein from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
- 30s ribosomal protein s18 1 (9 kDa, Protein from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
- 30s ribosomal protein s10 (11 kDa, Protein from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
- 50s ribosomal protein l23 (10 kDa, Protein from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
- 50s ribosomal protein l30 (7 kDa, Protein from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
- 50s ribosomal protein l36 (4 kDa, Protein from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
- 50s ribosomal protein l24 (11 kDa, Protein from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
- 50s ribosomal protein l27 (8 kDa, Protein from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
- 50s ribosomal protein l20 (14 kDa, Protein from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
- A2296-methylated mycobacterium tuberculosis ribosome bound with seq-9 (Complex from Mycobacterium tuberculosis H37Rv)
- 30s ribosomal protein s5 (22 kDa, Protein from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
- 50s ribosomal protein l29 (8 kDa, Protein from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
- 30s ribosomal protein s6 (10 kDa, Protein from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
- 30s ribosomal protein s16 (17 kDa, Protein from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
- 50s ribosomal protein l37 (2 kDa, Protein from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
- 50s ribosomal protein l6 (19 kDa, Protein from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
- 50s ribosomal protein l34 (5 kDa, Protein from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
- 30s ribosomal protein s14 type z (6 kDa, Protein from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
- 30s ribosomal protein s9 (16 kDa, Protein from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
- 50s ribosomal protein l21 (11 kDa, Protein from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
- 30s ribosomal protein s4 (23 kDa, Protein from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
- 5s rrna (37 kDa, RNA from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
- 30s ribosomal protein s7 (17 kDa, Protein from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
- 30s ribosomal protein s20 (9 kDa, Protein from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
- 50s ribosomal protein l13 (21 kDa, Protein from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Structural basis for enhanced infectivity and immune evasion of SARS-CoV-2 variants
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 7n1q
Q-score: 0.472
Cai Y, Zhang J, Xiao T, Lavine CL, Rawson S, Peng H, Zhu H, Anand K, Tong P, Gautam A, Lu S, Sterling SM, Walsh Jr RM, Rits-Volloch S, Lu J, Wesemann DR, Yang W, Seaman MS, Chen B
Science (2021) 373 pp. 642-648 [ DOI: doi:10.1126/science.abi9745 Pubmed: 34168070 ]