RCSB PDB: Search

6ZXN	Download File View File

Cryo-EM structure of the SARS-CoV-2 spike protein bound to neutralizing nanobodies (Ty1)

(2020) Nat Commun 11: 4420-4420

Released	2020-09-23
Method	ELECTRON MICROSCOPY 2.93 Å
Organisms	Severe acute respiratory syndrome coronavirus 2 Vicugna pacos
Macromolecule	Nanobody Ty1 (protein) Spike glycoprotein (protein)
Unique Ligands	NAG
Unique branched monosaccharides	NAG

7A25	Download File View File

Cryo-EM structure of the SARS-CoV-2 spike protein bound to neutralizing sybodies (Sb23)

(2020) Nat Commun 11: 5588-5588

Released	2020-11-25
Method	ELECTRON MICROSCOPY 3.06 Å
Organisms	Severe acute respiratory syndrome coronavirus 2 synthetic construct
Macromolecule	Spike glycoprotein (protein) Sybody 23 (protein)
Unique Ligands	NAG
Unique branched monosaccharides	NAG

7A29	Download File View File

Cryo-EM structure of the SARS-CoV-2 spike protein bound to neutralizing sybodies (Sb23) 2-up conformation

(2020) Nat Commun 11: 5588-5588

Released	2020-10-21
Method	ELECTRON MICROSCOPY 2.94 Å
Organisms	Severe acute respiratory syndrome coronavirus 2 synthetic construct
Macromolecule	Neutralising sybody (Sb23) (protein) Spike glycoprotein (protein)
Unique Ligands	NAG
Unique branched monosaccharides	NAG

7B14	Download File View File

Nanobody E bound to Spike-RBD in a localized reconstruction

(2021) Science 371:

Released	2021-04-28
Method	ELECTRON MICROSCOPY 3.79 Å
Organisms	Camelus bactrianus Severe acute respiratory syndrome coronavirus 2
Macromolecule	Nanobody against SARS-CoV-2 (protein) Spike protein S1 (protein)
Unique Ligands	NAG

7B17	Download File View File

SARS-CoV-spike RBD bound to two neutralising nanobodies.

(2021) Science 371:

Released	2021-02-10
Method	ELECTRON MICROSCOPY 4.01 Å
Organisms	Lama glama Severe acute respiratory syndrome coronavirus 2 Vicugna pacos
Macromolecule	SARS-CoV-2 neutralizing biparatopic nanobody VE,nanobody E from Lama glama,SARS-CoV-2 neutralizing biparatopic nanobody VE,nanobody E from Lama glama (protein) Spike protein S1 (protein)
Unique Ligands	NAG

7B18	Download File View File

SARS-CoV-spike bound to two neutralising nanobodies

(2021) Science 371:

Released	2021-04-28
Method	ELECTRON MICROSCOPY 2.62 Å
Organisms	Lama glama Severe acute respiratory syndrome coronavirus 2 Vicugna pacos
Macromolecule	Nanobody against SARS-CoV-2 VHH E (protein) Nanobody against spike glycoprotein VHH V (protein) Spike glycoprotein (protein)
Unique Ligands	NAG
Unique branched monosaccharides	NAG

7KN5	Download File View File

Crystal structure of SARS-CoV-2 receptor binding domain complexed with nanobodies VHH E and U

Liu, H., Yuan, M., Zhu, X., Wu, N.C., Wilson, I.A.

(2021) Science 371:

Released	2021-01-20
Method	X-RAY DIFFRACTION 1.87 Å
Organisms	Severe acute respiratory syndrome coronavirus 2 Vicugna pacos
Macromolecule	Spike protein S1 (protein) VHH E (protein) VHH U (protein)
Unique Ligands	EDO, NAG
Unique branched monosaccharides	NAG

7KN6	Download File View File

Crystal structure of SARS-CoV-2 receptor binding domain complexed with nanobody VHH V and antibody Fab CC12.3

Liu, H., Yuan, M., Zhu, X., Wu, N.C., Wilson, I.A.

(2021) Science 371:

Released	2021-01-20
Method	X-RAY DIFFRACTION 2.55 Å
Organisms	Homo sapiens Severe acute respiratory syndrome coronavirus 2 Vicugna pacos
Macromolecule	CC12.3 Fab heavy chain (protein) CC12.3 Fab light chain (protein) Spike protein S1 (protein) VHH V (protein)
Unique Ligands	NAG

7KN7	Download File View File

Crystal structure of SARS-CoV-2 receptor binding domain complexed with nanobody VHH W and antibody Fab CC12.3

Liu, H., Yuan, M., Zhu, X., Wu, N.C., Wilson, I.A.

(2021) Science 371:

Released	2021-01-20
Method	X-RAY DIFFRACTION 2.73 Å
Organisms	Homo sapiens Severe acute respiratory syndrome coronavirus 2 Vicugna pacos
Macromolecule	CC12.3 Fab heavy chain (protein) CC12.3 Fab light chain (protein) Spike protein S1 (protein) VHH W (protein)
Unique Ligands	NAG

7KSG	Download File View File

SARS-CoV-2 spike in complex with nanobodies E

(2021) Science 371:

Released	2021-01-20
Method	ELECTRON MICROSCOPY 3.33 Å
Organisms	Lama glama Severe acute respiratory syndrome coronavirus 2
Macromolecule	Nanobody against SARS-CoV-2 glycoprotein (protein) Spike glycoprotein (protein)
Unique Ligands	NAG

7NLL	Download File View File

SARS-CoV-2 Spike RBD (dimer) in complex with two Fu2 nanobodies

(2022) Nat Commun 13: 155-155

Released	2022-02-02
Method	ELECTRON MICROSCOPY 2.89 Å
Organisms	Severe acute respiratory syndrome coronavirus 2 Vicugna pacos
Macromolecule	Nanobody Fu2 (protein) Spike protein S1 (protein)
Unique Ligands	NAG

7NS6	Download File View File

SARS-CoV-2 Spike (dimers) in complex with six Fu2 nanobodies

(2022) Nat Commun 13: 155-155

Released	2022-02-02
Method	ELECTRON MICROSCOPY 3.18 Å
Organisms	Severe acute respiratory syndrome coronavirus 2 Tequatrovirus T4 Vicugna pacos
Macromolecule	Fu2 nanobody (protein) Spike glycoprotein,Fibritin (protein)
Unique Ligands	NAG
Unique branched monosaccharides	BMA, NAG

7PZP	Download File View File

Mitochondrial DNA dependent RNA polymerase homodimer.

(2022) Cell 185: 2309

Released	2022-09-28
Method	ELECTRON MICROSCOPY 3.5 Å
Organisms	Homo sapiens
Macromolecule	DNA-directed RNA polymerase, mitochondrial (protein)

7PZR	Download File View File

Cryo-EM structure of POLRMT in free form.

(2022) Cell 185: 2309-2323.e24

Released	2022-11-16
Method	ELECTRON MICROSCOPY 3 Å
Organisms	Homo sapiens
Macromolecule	DNA-directed RNA polymerase, mitochondrial (protein)

7ZC4	Download File View File

Cryo-EM structure of POLRMT mutant.

(2022) Cell 185: 2309-2323.e24

Released	2023-02-01
Method	ELECTRON MICROSCOPY 3.24 Å
Organisms	Homo sapiens
Macromolecule	DNA-directed RNA polymerase, mitochondrial (protein)

8A94	Download File View File

SARS CoV2 Spike in the 2-up state in complex with Fab47.

(2023) Immunity 56: 193-206.e7

Released	2023-05-03
Method	ELECTRON MICROSCOPY 2.4 Å
Organisms	Homo sapiens Severe acute respiratory syndrome coronavirus
Macromolecule	Fab47 (Heavy chain Variable domain) (protein) Fab47 (Light chain Variable domain) (protein) SARS-CoV2 Spike in 2-up conformation in complex with Fab47 (protein)
Unique Ligands	NAG
Unique branched monosaccharides	NAG

8A95	Download File View File

SARS Cov2 Spike RBD in complex with Fab47

(2023) Immunity 56: 193-206.e7

Released	2023-08-16
Method	ELECTRON MICROSCOPY 2.64 Å
Organisms	Homo sapiens Severe acute respiratory syndrome coronavirus
Macromolecule	Fab47 (Heavy chain variable domain) (protein) Fab47 (Light chain variable domain) (protein) SARS-CoV2 Trimeric Spike in 1-up conformation in complex with three Fab47 (protein)
Unique Ligands	NAG
Unique branched monosaccharides	NAG

8A96	Download File View File

SARS Cov2 Spike RBD in complex with Fab47

(2023) Immunity 56: 193-206.e7

Released	2023-05-03
Method	ELECTRON MICROSCOPY 2.7 Å
Organisms	Homo sapiens Severe acute respiratory syndrome coronavirus
Macromolecule	Fab47 Heavy chain (variable domain) (protein) Fab47 Light chain (variable domain) (protein) Spike protein S1 (protein)

8A99	Download File View File

SARS Cov2 Spike in 1-up conformation complex with Fab47

(2023) Immunity 56: 193-206.e7

Released	2023-05-10
Method	ELECTRON MICROSCOPY 2.5 Å
Organisms	Homo sapiens Severe acute respiratory syndrome coronavirus 2
Macromolecule	Fab47 (Heavy chain variable domain) (protein) Fab47 (Light chain Variable domain) (protein) SARS-CoV2 spike 1-up conformation in complex with Fab47 (protein)
Unique Ligands	NAG
Unique branched monosaccharides	NAG

8C0Y	Download File View File

SARS-CoV2 Omicron BA.1 RBD in complex with CAB-A17 antibody

(2024) Cell Rep Med 5: 101577-101577

Released	2024-06-19
Method	ELECTRON MICROSCOPY 2.68 Å
Organisms	Homo sapiens Severe acute respiratory syndrome coronavirus 2
Macromolecule	CAB-A17 antibody (variable) (protein) Spike protein S2' (protein)

8C2R	Download File View File

SARS-CoV2 Omicron BA.1 spike in complex with CAB-A17 antibody

(2024) Cell Rep Med 5: 101577-101577

Released	2024-05-22
Method	ELECTRON MICROSCOPY 2.56 Å
Organisms	Homo sapiens Severe acute respiratory syndrome coronavirus 2
Macromolecule	CAB-A17 antibody (HC) (protein) CAB-A17 antibody (LC) (protein) Spike glycoprotein (protein)
Unique Ligands	NAG
Unique branched monosaccharides	NAG

8P5M	Download File View File

SARS-CoV-2 Spike RBD in complex with Mab-23 (Fab)

(2024) Nat Commun 15: 6338-6338

Released	2024-06-05
Method	ELECTRON MICROSCOPY 2.8 Å
Organisms	Homo sapiens Severe acute respiratory syndrome coronavirus 2
Macromolecule	Mab-23 (Heavy chain variable domain) (protein) Mab-23 (Light chain variable domain) (protein) Spike protein S1 (protein)

8Q5Y	Download File View File

cryoEM structure of SARS-CoV2 Spike trimer in complex with Fab23

Hallberg, M., Das, H.

(2024) Nat Commun 15: 6338-6338

Released	2024-07-17
Method	ELECTRON MICROSCOPY 2.6 Å
Organisms	Homo sapiens Severe acute respiratory syndrome coronavirus 2
Macromolecule	Monoclonal antibody Mab 23 (Heavy Chain) (protein) Monoclonal antibody Mab 23 (Light chain) (protein) Spike glycoprotein (protein)

8V4F	Download File View File

Model and map from local refinement of a CAB-A17 - Omicron Ba.1 spike complex