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PDB: 1212 results
8G7A
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BU of 8g7a by Molmil
SARS-CoV-2 spike/Nb3 complex with 2 RBDs up and 3 Nb3 (local refinement)
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, Nanosota-3, Spike glycoprotein
Authors:Ye, G, Bu, F, Liu, B, Li, F.
Deposit date:2023-02-16
Release date:2024-02-21
Method:ELECTRON MICROSCOPY (3.3 Å)
Cite:SARS-CoV-2 spike/Nb3 complex with 2 RBDs up and 3 Nb3 (local refinement)
To Be Published
8GDR
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BU of 8gdr by Molmil
SARS-Cov2 S protein structure in complex with neutralizing monoclonal antibody 002-S21B10
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Monoclonal antibody 002-S21B10 heavy chain variable domain, ...
Authors:Patel, A, Ortlund, E.A.
Deposit date:2023-03-06
Release date:2024-03-13
Method:ELECTRON MICROSCOPY (3.6 Å)
Cite:Elucidating the mechanism of SARS-CoV-2 Omicron variant escape from a RBD class-3 human antibody
To Be Published
8GB0
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BU of 8gb0 by Molmil
SARS-CoV-2 Spike H655Y variant, One RBD Open
Descriptor: Spike glycoprotein
Authors:Egri, S.B, Shen, K, Luban, J.
Deposit date:2023-02-24
Release date:2023-04-26
Method:ELECTRON MICROSCOPY (4.1 Å)
Cite:S:D614G and S:H655Y are gateway mutations that act epistatically to promote SARS-CoV-2 variant fitness.
Biorxiv, 2023
7RW2
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BU of 7rw2 by Molmil
Cryo-EM structure of NTD-directed neutralizing antibody 5-7 in complex with prefusion SARS-CoV-2 spike glycoprotein
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, 5-7 heavy chain, ...
Authors:Cerutti, G, Shapiro, L.
Deposit date:2021-08-19
Release date:2021-09-01
Last modified:2022-11-30
Method:ELECTRON MICROSCOPY (3.5 Å)
Cite:Neutralizing antibody 5-7 defines a distinct site of vulnerability in SARS-CoV-2 spike N-terminal domain.
Cell Rep, 37, 2021
7S0C
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BU of 7s0c by Molmil
Structure of the SARS-CoV-2 S 6P trimer in complex with neutralizing antibody N-612-017
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, N-612-017 Fab Heavy Chain, ...
Authors:Barnes, C.O, Bjorkman, P.J.
Deposit date:2021-08-30
Release date:2021-10-06
Last modified:2022-03-16
Method:ELECTRON MICROSCOPY (3.25 Å)
Cite:Rapid identification of neutralizing antibodies against SARS-CoV-2 variants by mRNA display.
Cell Rep, 38, 2022
7R17
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BU of 7r17 by Molmil
Beta Variant SARS-CoV-2 Spike with 2 Erect RBDs
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Spike glycoprotein
Authors:Benton, D.J, Wrobel, A.G, Gamblin, S.J.
Deposit date:2022-02-02
Release date:2022-03-09
Last modified:2022-03-16
Method:ELECTRON MICROSCOPY (3.7 Å)
Cite:Evolution of the SARS-CoV-2 spike protein in the human host.
Nat Commun, 13, 2022
7R18
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BU of 7r18 by Molmil
Mink Variant SARS-CoV-2 Spike in Closed conformation
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose, ...
Authors:Benton, D.J, Wrobel, A.G, Gamblin, S.J.
Deposit date:2022-02-02
Release date:2022-03-09
Last modified:2022-03-16
Method:ELECTRON MICROSCOPY (3 Å)
Cite:Evolution of the SARS-CoV-2 spike protein in the human host.
Nat Commun, 13, 2022
7R1B
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BU of 7r1b by Molmil
Mink Variant SARS-CoV-2 Spike with 1 Erect RBD
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Spike glycoprotein
Authors:Benton, D.J, Wrobel, A.G, Gamblin, S.J.
Deposit date:2022-02-02
Release date:2022-03-09
Last modified:2022-03-16
Method:ELECTRON MICROSCOPY (2.8 Å)
Cite:Evolution of the SARS-CoV-2 spike protein in the human host.
Nat Commun, 13, 2022
7R16
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BU of 7r16 by Molmil
Beta Variant SARS-CoV-2 Spike with 1 Erect RBD
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Spike glycoprotein
Authors:Benton, D.J, Wrobel, A.G, Gamblin, S.J.
Deposit date:2022-02-02
Release date:2022-03-09
Last modified:2022-03-16
Method:ELECTRON MICROSCOPY (3.5 Å)
Cite:Evolution of the SARS-CoV-2 spike protein in the human host.
Nat Commun, 13, 2022
7R19
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BU of 7r19 by Molmil
Mink Variant SARS-CoV-2 Spike with 2 Erect RBDs
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Spike glycoprotein
Authors:Benton, D.J, Wrobel, A.G, Gamblin, S.J.
Deposit date:2022-02-02
Release date:2022-03-09
Last modified:2022-03-16
Method:ELECTRON MICROSCOPY (3.3 Å)
Cite:Evolution of the SARS-CoV-2 spike protein in the human host.
Nat Commun, 13, 2022
7R13
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BU of 7r13 by Molmil
Alpha Variant SARS-CoV-2 Spike in Closed conformation
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Spike glycoprotein
Authors:Benton, D.J, Wrobel, A.G, Gamblin, S.J.
Deposit date:2022-02-02
Release date:2022-03-09
Last modified:2022-03-16
Method:ELECTRON MICROSCOPY (3.6 Å)
Cite:Evolution of the SARS-CoV-2 spike protein in the human host.
Nat Commun, 13, 2022
7R14
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BU of 7r14 by Molmil
Alpha Variant SARS-CoV-2 Spike with 1 Erect RBD
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose, ...
Authors:Benton, D.J, Wrobel, A.G, Gamblin, S.J.
Deposit date:2022-02-02
Release date:2022-03-09
Last modified:2022-03-16
Method:ELECTRON MICROSCOPY (3.4 Å)
Cite:Evolution of the SARS-CoV-2 spike protein in the human host.
Nat Commun, 13, 2022
7R15
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BU of 7r15 by Molmil
Alpha Variant SARS-CoV-2 Spike with 2 Erect RBDs
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Spike glycoprotein
Authors:Benton, D.J, Wrobel, A.G, Gamblin, S.J.
Deposit date:2022-02-02
Release date:2022-03-02
Last modified:2022-03-16
Method:ELECTRON MICROSCOPY (4.1 Å)
Cite:Evolution of the SARS-CoV-2 spike protein in the human host.
Nat Commun, 13, 2022
8HHX
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BU of 8hhx by Molmil
SARS-CoV-2 Delta Spike in complex with FP-12A
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, FP-12A Fab heavy chain, ...
Authors:Chen, X, Wu, Y.-M.
Deposit date:2022-11-17
Release date:2023-02-01
Method:ELECTRON MICROSCOPY (3.62 Å)
Cite:Structural basis for a conserved neutralization epitope on the receptor-binding domain of SARS-CoV-2.
Nat Commun, 14, 2023
8HHZ
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BU of 8hhz by Molmil
SARS-CoV-2 Omicron BA.1 Spike in complex with IY-2A
Descriptor: IY-2A Fab heavy chain, IY-2A Fab light chain, Spike glycoprotein
Authors:Chen, X, Mohapatra, A, Wu, Y.-M.
Deposit date:2022-11-17
Release date:2023-02-01
Method:ELECTRON MICROSCOPY (4.28 Å)
Cite:Structural basis for a conserved neutralization epitope on the receptor-binding domain of SARS-CoV-2.
Nat Commun, 14, 2023
7R40
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BU of 7r40 by Molmil
Structure of the SARS-CoV-2 spike glycoprotein in complex with the 87G7 antibody Fab fragment
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, 87G7 heavy chain variable region, ...
Authors:Hurdiss, D.L.
Deposit date:2022-02-08
Release date:2022-04-20
Last modified:2023-12-13
Method:ELECTRON MICROSCOPY (2.9 Å)
Cite:An ACE2-blocking antibody confers broad neutralization and protection against Omicron and other SARS-CoV-2 variants of concern.
Sci Immunol, 7, 2022
7RQ6
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BU of 7rq6 by Molmil
Cryo-EM structure of SARS-CoV-2 spike in complex with non-neutralizing NTD-directed CV3-13 Fab isolated from convalescent individual
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, CV3-13 Fab heavy chain, ...
Authors:Chen, Y, Pozharski, E, Tolbert, W.D, Pazgier, M.
Deposit date:2021-08-05
Release date:2022-04-20
Last modified:2023-08-09
Method:ELECTRON MICROSCOPY (4.18 Å)
Cite:A Fc-enhanced NTD-binding non-neutralizing antibody delays virus spread and synergizes with a nAb to protect mice from lethal SARS-CoV-2 infection.
Cell Rep, 38, 2022
7RBV
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BU of 7rbv by Molmil
SARS-CoV-2 Spike in complex with PVI.V6-14 Fab
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, PVI.V6-14 Fab heavy chain, ...
Authors:Altomare, C.G, Bajic, G.
Deposit date:2021-07-06
Release date:2022-05-04
Last modified:2022-07-06
Method:ELECTRON MICROSCOPY (3.6 Å)
Cite:Structure of a Vaccine-Induced, Germline-Encoded Human Antibody Defines a Neutralizing Epitope on the SARS-CoV-2 Spike N-Terminal Domain.
Mbio, 13, 2022
8FU7
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BU of 8fu7 by Molmil
Structure of Covid Spike variant deltaN135 in fully closed form
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, Spike glycoprotein
Authors:Yu, X, Juraszek, J, Rutten, L, Bakkers, M.J.G, Blokland, S, Van den Broek, N.J.F, Verwilligen, A.Y.W, Abeywickrema, P, Vingerhoets, J, Neefs, J, Bakhash, S.A.M, Roychoudhury, P, Greninger, A, Sharma, S, Langedijk, J.P.M.
Deposit date:2023-01-16
Release date:2023-04-05
Last modified:2024-04-24
Method:ELECTRON MICROSCOPY (3.21 Å)
Cite:Convergence of immune escape strategies highlights plasticity of SARS-CoV-2 spike.
Plos Pathog., 19, 2023
7S0D
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BU of 7s0d by Molmil
Structure of the SARS-CoV-2 S 6P trimer in complex with neutralizing antibody N-612-014
Descriptor: N-612-014 Fab Heavy Chain, N-612-014 Light Chain, Spike glycoprotein
Authors:Barnes, C.O, Bjorkman, P.J.
Deposit date:2021-08-30
Release date:2021-10-06
Last modified:2022-03-16
Method:ELECTRON MICROSCOPY (3.5 Å)
Cite:Rapid identification of neutralizing antibodies against SARS-CoV-2 variants by mRNA display.
Cell Rep, 38, 2022
7S0E
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BU of 7s0e by Molmil
Structure of the SARS-CoV-2 S1 subunit in complex with antibody N-612-004
Descriptor: N-612-004 Fab heavy chain, N-612-004 Light Chain, Spike glycoprotein
Authors:Barnes, C.O, Bjorkman, P.J.
Deposit date:2021-08-30
Release date:2021-10-06
Last modified:2022-03-16
Method:ELECTRON MICROSCOPY (4.9 Å)
Cite:Rapid identification of neutralizing antibodies against SARS-CoV-2 variants by mRNA display.
Cell Rep, 38, 2022
8HHY
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BU of 8hhy by Molmil
SARS-CoV-2 Delta Spike in complex with IS-9A
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, IS-9A Fab heavy chain, ...
Authors:Mohapatra, A, Wu, Y.-M.
Deposit date:2022-11-17
Release date:2023-02-01
Method:ELECTRON MICROSCOPY (2.77 Å)
Cite:Structural basis for a conserved neutralization epitope on the receptor-binding domain of SARS-CoV-2.
Nat Commun, 14, 2023
7SBO
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BU of 7sbo by Molmil
One RBD-up 2 of pre-fusion SARS-CoV-2 Delta variant spike protein
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose, ...
Authors:Zhang, J, Xiao, T.S, Cai, Y.F, Peng, H.Q, Volloch, S.R, Chen, B.
Deposit date:2021-09-25
Release date:2021-11-03
Last modified:2021-12-22
Method:ELECTRON MICROSCOPY (3.44 Å)
Cite:Membrane fusion and immune evasion by the spike protein of SARS-CoV-2 Delta variant.
Science, 374, 2021
8HC4
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BU of 8hc4 by Molmil
SARS-CoV-2 wildtype spike trimer (6P) in complex with 3 YB9-258 Fabs and 3 R1-32 Fabs (3 RBD up)
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Heavy chain of R1-32 Fab, ...
Authors:Liu, B, Gao, X, Chen, Q, Li, Z, Su, M, He, J, Xiong, X.
Deposit date:2022-11-01
Release date:2023-01-25
Last modified:2023-05-03
Method:ELECTRON MICROSCOPY (3.54 Å)
Cite:Somatically hypermutated antibodies isolated from SARS-CoV-2 Delta infected patients cross-neutralize heterologous variants.
Nat Commun, 14, 2023
7SBP
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BU of 7sbp by Molmil
Closed state of pre-fusion SARS-CoV-2 Kappa variant spike protein
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose, ...
Authors:Zhang, J, Xiao, T.S, Cai, Y.F, Peng, H.Q, Volloch, S.R, Chen, B.
Deposit date:2021-09-25
Release date:2021-11-03
Last modified:2021-12-22
Method:ELECTRON MICROSCOPY (3.44 Å)
Cite:Membrane fusion and immune evasion by the spike protein of SARS-CoV-2 Delta variant.
Science, 374, 2021

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