Loading
PDBj
English日本語简体中文繁體中文한국어
✖
MenuPDBj@FacebookPDBj@X(formerly Twitter)PDBj@BlueSkyPDBj@YouTubewwPDB FoundationwwPDBDonate
RCSB PDBPDBeBMRBAdv. SearchSearch help
9K75
DownloadVisualize
BU of 9k75 by Molmil
SARS-CoV-2 related bat coronavirus BANAL-103 spike in the closed state
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, Spike glycoprotein
Authors:Qingqing, L, Xiao, C, Xiaoning, L, Yibing, Z, Ru, L, Zirui, K, Didi, W, Jiaxu, W, Lili, L, Junxia, Y, Jianxiang, S, Shuiling, J, Ying, P, Na, Z, Yushun, W, Jian, S.
Deposit date:2024-10-23
Release date:2025-07-16
Last modified:2026-02-04
Method:ELECTRON MICROSCOPY (3.11 Å)
Cite:Structural and functional constraints on spike activation and host protease utilization limit cell entry of SARS-CoV-2-related bat coronaviruses.
J.Virol., 99, 2025
8ZY2
DownloadVisualize
BU of 8zy2 by Molmil
Sarbecovirus BANAL-20-52 Spike Trimer in a Locked 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, BILIVERDINE IX ALPHA, ...
Authors:Wang, J, Xiong, X.
Deposit date:2024-06-16
Release date:2025-02-05
Last modified:2025-07-23
Method:ELECTRON MICROSCOPY (2.9 Å)
Cite:SARS-related coronavirus S-protein structures reveal synergistic RBM interactions underpinning high-affinity human ACE2 binding.
Sci Adv, 11, 2025
8ZY3
DownloadVisualize
BU of 8zy3 by Molmil
Sarbecovirus BANAL-20-236 Spike Trimer in a Locked 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:Wang, J, Xiong, X.
Deposit date:2024-06-16
Release date:2025-02-05
Last modified:2025-07-23
Method:ELECTRON MICROSCOPY (3.3 Å)
Cite:SARS-related coronavirus S-protein structures reveal synergistic RBM interactions underpinning high-affinity human ACE2 binding.
Sci Adv, 11, 2025
7SL5
DownloadVisualize
BU of 7sl5 by Molmil
Crystal Structure of VP12E7 Fab in complex with SARS-CoV-2 S fusion peptide
Descriptor: Heavy chain VP12E7 Fab, Light chain VP12E7 Fab, PRO-SER-LYS-ARG-SER-PHE-ILE-GLU-ASP-LEU-LEU-PHE-ASN
Authors:Tortorici, M.A, Veesler, D, Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Deposit date:2021-10-22
Release date:2022-07-20
Last modified:2024-11-20
Method:X-RAY DIFFRACTION (2.5 Å)
Cite:ACE2-binding exposes the SARS-CoV-2 fusion peptide to broadly neutralizing coronavirus antibodies.
Science, 377, 2022
7SKZ
DownloadVisualize
BU of 7skz by Molmil
Crystal Structure of VN01H1 Fab in complex with SARS-CoV-2 S fusion peptide
Descriptor: Heavy chain of VN01H1 Fab, Light chain of VN01H1 Fab, PRO-SER-LYS-ARG-SER-PHE-ILE-GLU-ASP-LEU-LEU-PHE-ASN
Authors:Tortorici, M.A, Veesler, D, Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Deposit date:2021-10-22
Release date:2022-07-20
Last modified:2024-11-20
Method:X-RAY DIFFRACTION (1.86 Å)
Cite:ACE2-binding exposes the SARS-CoV-2 fusion peptide to broadly neutralizing coronavirus antibodies.
Science, 377, 2022
7T5O
DownloadVisualize
BU of 7t5o by Molmil
VFLIP Spike Trimer with GAR03
Descriptor: GAR03 Fab heavy chain, GAR03 Fab light chain, Spike glycoprotein
Authors:Sobti, M, Stewart, A.G, Rouet, R, Langley, D.B.
Deposit date:2021-12-12
Release date:2023-01-25
Last modified:2025-05-21
Method:ELECTRON MICROSCOPY (3.39 Å)
Cite:Broadly neutralizing SARS-CoV-2 antibodies through epitope-based selection from convalescent patients.
Nat Commun, 14, 2023
7TGE
DownloadVisualize
BU of 7tge by Molmil
SARS-CoV-2 Omicron 1-RBD down Spike Protein Trimer without the P986-P987 stabilizing mutations (S-GSAS-Omicron)
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:Stalls, V, Acharya, P.
Deposit date:2022-01-07
Release date:2022-03-09
Last modified:2025-05-28
Method:ELECTRON MICROSCOPY (3.68 Å)
Cite:Structural diversity of the SARS-CoV-2 Omicron spike.
Mol.Cell, 82, 2022
36AZ
DownloadVisualize
BU of 36az by Molmil
Structure of BA.1-S-RBD/2130WT/2196-S93Y
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2130WT heavy chain, 2130WT light chain, ...
Authors:Du, J, Pallesen, J.
Deposit date:2026-05-28
Release date:2026-07-15
Method:ELECTRON MICROSCOPY (3.9 Å)
Cite:Structure-Guided Design of Therapeutic Antibodies Targeting SARS-CoV-2 Omicron Variants.
Res Sq, 2026
27KE
DownloadVisualize
BU of 27ke by Molmil
Cryo-EM structure of Black swan ACE2 complexed with SARS-CoV-2 RBD
Descriptor: Black swan ACE2, Spike protein S1
Authors:Gao, F.G, Liu, S.
Deposit date:2026-06-04
Release date:2026-06-17
Method:ELECTRON MICROSCOPY (3.3 Å)
Cite:Cryo-EM structure of Black swan ACE2 complexed with SARS-CoV-2 RBD
To Be Published
27KF
DownloadVisualize
BU of 27kf by Molmil
Cryo-EM structure of Tundra swan ACE2 complexed with SARS-CoV-2 RBD
Descriptor: Spike protein S1, Tundra swan ACE2
Authors:Gao, F.G, Liu, S.
Deposit date:2026-06-04
Release date:2026-06-17
Method:ELECTRON MICROSCOPY (3.4 Å)
Cite:Cryo-EM structure of Tundra swan ACE2 complexed with SARS-CoV-2 RBD
To Be Published
9ZT7
DownloadVisualize
BU of 9zt7 by Molmil
SARS-CoV-2 S2 in complex with COV2-2509
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, COV2-2509 Fab-Heavy chain, ...
Authors:Park, S, Ward, A.B.
Deposit date:2025-12-23
Release date:2026-03-11
Method:ELECTRON MICROSCOPY (3.11 Å)
Cite:The buried S2 apex of SARS-CoV-2 spike elicits an immunodominant germline-restricted public antibody response.
Biorxiv, 2026
9Z12
DownloadVisualize
BU of 9z12 by Molmil
SARS-CoV-2 spike S2 in complex with antibody B3-1
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, Antibody B3-1 Heavy Chain, Antibody B3-1 Light Chain, ...
Authors:Zhou, L, Hsieh, C, McLellan, J.S.
Deposit date:2025-11-03
Release date:2026-07-08
Method:ELECTRON MICROSCOPY (3.2 Å)
Cite:SARS-CoV-2 spike S2 in complex with antibody B3-1
To Be Published
9ZT6
DownloadVisualize
BU of 9zt6 by Molmil
SARS-CoV-2 S2 in complex with polyclonal Fab-B_Donor8
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Human polyclonal Fab model with polyalanine backbone - Heavy chain, ...
Authors:Park, S, Ward, A.B.
Deposit date:2025-12-23
Release date:2026-03-11
Method:ELECTRON MICROSCOPY (2.83 Å)
Cite:The buried S2 apex of SARS-CoV-2 spike elicits an immunodominant germline-restricted public antibody response.
Biorxiv, 2026
9Z18
DownloadVisualize
BU of 9z18 by Molmil
SARS-CoV-2 spike S2 in complex with antibody N6-2
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, Antibody N6-2 Heavy Chain, Antibody N6-2 Light Chain, ...
Authors:Zhou, L, Hsieh, C, McLellan, J.S.
Deposit date:2025-11-03
Release date:2026-07-08
Method:ELECTRON MICROSCOPY (2.9 Å)
Cite:SARS-CoV-2 spike S2 in complex with antibody N6-2
To Be Published
9ZT8
DownloadVisualize
BU of 9zt8 by Molmil
Stabilized SARS-CoV-2 S2 apo
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 protein S2
Authors:Park, S, Ward, A.B.
Deposit date:2025-12-23
Release date:2026-03-11
Method:ELECTRON MICROSCOPY (2.75 Å)
Cite:The buried S2 apex of SARS-CoV-2 spike elicits an immunodominant germline-restricted public antibody response.
Biorxiv, 2026
9YJI
DownloadVisualize
BU of 9yji by Molmil
Crystal structure of SARS-CoV-2 spike stem helix peptide in complex with monoclonal antibody CC65.1
Descriptor: CC65.1 heavy chain, CC65.1 light chain, Stem helix peptide of Spike protein S2'
Authors:Yuan, M, Wilson, I.A.
Deposit date:2025-10-03
Release date:2026-07-15
Method:X-RAY DIFFRACTION (2.05 Å)
Cite:Neutralizing antibodies targeting betacoronavirus S2 stem helix
To Be Published
9ZT5
DownloadVisualize
BU of 9zt5 by Molmil
SARS-CoV-2 S2 in complex with polyclonal Fab-B_Donor3
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Human polyclonal Fab model with polyalanine backbone - Heavy chain, ...
Authors:Park, S, Ward, A.B.
Deposit date:2025-12-23
Release date:2026-03-11
Method:ELECTRON MICROSCOPY (3.21 Å)
Cite:The buried S2 apex of SARS-CoV-2 spike elicits an immunodominant germline-restricted public antibody response.
Biorxiv, 2026
7A29
DownloadVisualize
BU of 7a29 by Molmil
Cryo-EM structure of the SARS-CoV-2 spike protein bound to neutralizing sybodies (Sb23) 2-up 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, Neutralising sybody (Sb23), ...
Authors:Hallberg, B.M, Das, H.
Deposit date:2020-08-16
Release date:2020-10-21
Last modified:2025-07-02
Method:ELECTRON MICROSCOPY (2.94 Å)
Cite:Selection, biophysical and structural analysis of synthetic nanobodies that effectively neutralize SARS-CoV-2.
Nat Commun, 11, 2020
7A4N
DownloadVisualize
BU of 7a4n by Molmil
Cryo-EM structure of a prefusion stabilized SARS-CoV-2 Spike (D614N, R682S, R685G, A892P, A942P and V987P)(S-closed trimer)
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,Fibritin
Authors:Rutten, L, Renault, L.L.R, Juraszek, J, Langedijk, J.P.M.
Deposit date:2020-08-20
Release date:2020-11-04
Last modified:2024-10-23
Method:ELECTRON MICROSCOPY (2.75 Å)
Cite:Stabilizing the closed SARS-CoV-2 spike trimer.
Nat Commun, 12, 2021
7A5R
DownloadVisualize
BU of 7a5r by Molmil
Complex of SARS-CoV-2 spike and CR3022 Fab (Non-Uniform Refinement)
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, CR3022 Fab Heavy Chain, CR3022 Fab Light Chain, ...
Authors:Wrobel, A.G, Benton, D.J, Rosenthal, P.B, Gamblin, S.J.
Deposit date:2020-08-21
Release date:2020-09-16
Last modified:2024-11-20
Method:ELECTRON MICROSCOPY (3.7 Å)
Cite:Antibody-mediated disruption of the SARS-CoV-2 spike glycoprotein.
Nat Commun, 11, 2020
7A5S
DownloadVisualize
BU of 7a5s by Molmil
Complex of SARS-CoV-2 spike and CR3022 Fab (Homogeneous Refinement)
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, CR3022 Fab Heavy Chain, CR3022 Fab Light Chain, ...
Authors:Wrobel, A.G, Benton, D.J, Rosenthal, P.B, Gamblin, S.J.
Deposit date:2020-08-21
Release date:2020-09-16
Last modified:2024-10-23
Method:ELECTRON MICROSCOPY (3.9 Å)
Cite:Antibody-mediated disruption of the SARS-CoV-2 spike glycoprotein.
Nat Commun, 11, 2020
7A25
DownloadVisualize
BU of 7a25 by Molmil
Cryo-EM structure of the SARS-CoV-2 spike protein bound to neutralizing sybodies (Sb23)
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:Hallberg, B.M, Das, H.
Deposit date:2020-08-16
Release date:2020-11-25
Last modified:2025-07-09
Method:ELECTRON MICROSCOPY (3.06 Å)
Cite:Selection, biophysical and structural analysis of synthetic nanobodies that effectively neutralize SARS-CoV-2.
Nat Commun, 11, 2020
7A93
DownloadVisualize
BU of 7a93 by Molmil
SARS-CoV-2 Spike Glycoprotein with 2 RBDs Erect
Descriptor: Spike glycoprotein
Authors:Benton, D.J, Wrobel, A.G, Rosenthal, P.B, Gamblin, S.J.
Deposit date:2020-09-01
Release date:2020-09-16
Last modified:2024-10-16
Method:ELECTRON MICROSCOPY (5.9 Å)
Cite:Receptor binding and priming of the spike protein of SARS-CoV-2 for membrane fusion.
Nature, 588, 2020
9FCM
DownloadVisualize
BU of 9fcm by Molmil
Single-domain antibody binding the SARS-COV2 S2
Descriptor: CHLORIDE ION, Single-domain antibody R3DC23, Spike protein S2'
Authors:Vann Molle, I, Remaut, H.
Deposit date:2024-05-15
Release date:2025-05-21
Last modified:2025-06-11
Method:X-RAY DIFFRACTION (1.94 Å)
Cite:Ultrapotent SARS coronavirus-neutralizing single-domain antibodies that clamp the spike at its base.
Nat Commun, 16, 2025
9FGR
DownloadVisualize
BU of 9fgr by Molmil
SARS-CoV-2 (wuhan variant) Spike protein in complex with the single chain fragment scFv76-77 (focused refinement)
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, Spike glycoprotein, scFv76-77 single chain fragment
Authors:Berlinguer, M, Chaves-Sanjuan, A, Milazzo, F.M, Minenkova, O, De Santis, R, Bolognesi, M.
Deposit date:2024-05-25
Release date:2024-06-05
Last modified:2024-10-09
Method:ELECTRON MICROSCOPY (4 Å)
Cite:Structure of scFv76-77 in complex with SARS-CoV-2 Spike protein
To Be Published

257179

PDB entries from 2026-07-29

PDB statisticsPDBj update infoContact PDBjnumon