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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Citation Author = "Stephens, T."

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Search Summary

This query matches 101 Structures.

Refinements

Structure Determination Methodology

experimental (101)

Scientific Name of Source Organism

	Homo sapiens (54)
	Severe acute respiratory syndrome coronavirus 2 (34)
	Human immunodeficiency virus 1 (28)
	Macaca fascicularis (9)
	Mus musculus (8)
	Macaca mulatta (7)
	Western equine encephalitis virus (6)
	Human herpesvirus 4 strain B95-8 (4)
	Macaca (4)
	Venezuelan equine encephalitis virus (4)

More...

Taxonomy

	Eukaryota (84)
	Riboviria (81)
	Duplodnaviria (9)

Experimental Method

	ELECTRON MICROSCOPY (78)
	X-RAY DIFFRACTION (23)

Polymer Entity Type

Protein (101)

Refinement Resolution (Å)

	1.5 - 2.0 (4)
	2.0 - 2.5 (11)
	2.5 - 3.0 (17)
	3.0 - 3.5 (28)
	3.5 - 4.0 (23)
	4.0 - 4.5 (11)
	> 4.5 (7)

Release Date

	2015 - 2019 (6)
	2020 - 2024 (95)

Enzyme Classification Name

Hydrolases (15)

Membrane Protein Annotation

	mpstruc (13)
	MemProtMD (1)

Symmetry Type

	Asymmetric (62)
	Cyclic (37)
	Dihedral (1)
	Icosahedral (1)

SCOP Classification

	All beta proteins (8)
	Artifacts (5)
	Alpha and beta proteins (a+b) (2)

AllSelected

1 to 25 of 101 Structures

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6MTO \| pdb_00006mto	Download File View File

Crystal structure of VRC42.01 Fab in complex with T117-F MPER scaffold

Kwon, Y.D., Druz, A., Law, W.H., Peng, D., Zhang, B., Doria-Rose, N.A., Kwong, P.D.

(2019) Immunity 50: 677-691.e13

Released	2019-03-27
Method	X-RAY DIFFRACTION 2.634 Å
Organisms	Homo sapiens Human immunodeficiency virus 1
Macromolecule	Antibody VRC42.01 Fab heavy chain (protein) Antibody VRC42.01 Fab light chain (protein) VRC42 epitope T117-F scaffold (protein)

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6MTP \| pdb_00006mtp	Download File View File

Crystal structure of VRC42.04 Fab in complex with gp41 peptide

Kwon, Y.D., Druz, A., Law, W.H., Peng, D., Zhang, B., Doria-Rose, N.A., Kwong, P.D.

(2019) Immunity 50: 677-691.e13

Released	2019-03-27
Method	X-RAY DIFFRACTION 2.036 Å
Organisms	Homo sapiens Human immunodeficiency virus 1
Macromolecule	Antibody VRC42.04 Fab heavy chain (protein) Antibody VRC42.04 Fab light chain (protein) RV217 founder virus gp41 peptide (protein)

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6MTQ \| pdb_00006mtq	Download File View File

Crystal structure of VRC42.N1 Fab in complex with T117-F MPER scaffold

Kwon, Y.D., Law, W.H., Veradi, R., Doria-Rose, N.A., Kwong, P.D.

(2019) Immunity 50: 677-691.e13

Released	2019-03-27
Method	X-RAY DIFFRACTION 2.7 Å
Organisms	Homo sapiens Human immunodeficiency virus 1
Macromolecule	Antibody VRC42.N1 Fab heavy chain (protein) Antibody VRC42.N1 Fab light chain (protein) VRC42 epitope T117-F scaffold (protein)

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6MTR \| pdb_00006mtr	Download File View File

Crystal structure of VRC43.01 Fab

Kwon, Y.D., Druz, A., Law, W.H., Peng, D., Zhang, B., Doria-Rose, N.A., Kwong, P.D.

(2019) Immunity 50: 677-691.e13

Released	2019-03-27
Method	X-RAY DIFFRACTION 1.798 Å
Organisms	Homo sapiens
Macromolecule	Antibody VRC43.01 Fab heavy chain (protein) Antibody VRC43.01 Fab light chain (protein)

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6MTS \| pdb_00006mts	Download File View File

Crystal structure of VRC43.03 Fab

Kwon, Y.D., Druz, A., Law, W.H., Peng, D., Doria-Rose, N.A., Kwong, P.D.

(2019) Immunity 50: 677-691.e13

Released	2019-03-27
Method	X-RAY DIFFRACTION 2.437 Å
Organisms	Homo sapiens
Macromolecule	Antibody VRC43.03 Fab heavy chain (protein) Antibody VRC43.03 Fab light chain (protein)

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6MTT \| pdb_00006mtt	Download File View File

Crystal structure of VRC46.01 Fab in complex with gp41 peptide

Kwon, Y.D., Druz, A., Law, W.H., Peng, D., Veradi, R., Doria-Rose, N.A., Kwong, P.D.

(2019) Immunity 50: 677-691.e13

Released	2019-03-27
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Homo sapiens Human immunodeficiency virus 1
Macromolecule	Antibody VRC46.01 Fab heavy chain (protein) Antibody VRC46.01 Fb light chain (protein) RV217 founder virus gp41 peptide (protein)

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6XLU \| pdb_00006xlu	Download File View File

Structure of SARS-CoV-2 spike at pH 4.0

Zhou, T., Tsybovsky, Y., Olia, A., Kwong, P.D.

(2020) Cell Host Microbe 28: 867-879.e5

Released	2020-08-12
Method	ELECTRON MICROSCOPY 2.4 Å
Organisms	Severe acute respiratory syndrome coronavirus 2
Macromolecule	Spike glycoprotein (protein)
Unique Ligands	NAG
Unique branched monosaccharides	NAG

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6XM0 \| pdb_00006xm0	Download File View File

Consensus structure of SARS-CoV-2 spike at pH 5.5

Zhou, T., Tsybovsky, Y., Olia, A., Kwong, P.D.

(2020) Cell Host Microbe 28: 867-879.e5

Released	2020-08-12
Method	ELECTRON MICROSCOPY 2.7 Å
Organisms	Severe acute respiratory syndrome coronavirus 2
Macromolecule	Spike glycoprotein (protein)
Unique Ligands	NAG
Unique branched monosaccharides	NAG

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6XM3 \| pdb_00006xm3	Download File View File

Structure of SARS-CoV-2 spike at pH 5.5, single RBD up, conformation 1

Zhou, T., Tsybovsky, Y., Olia, A., Kwong, P.D.

(2020) Cell Host Microbe 28: 867-879.e5

Released	2020-08-12
Method	ELECTRON MICROSCOPY 2.9 Å
Organisms	Severe acute respiratory syndrome coronavirus 2
Macromolecule	Spike glycoprotein (protein)
Unique Ligands	NAG
Unique branched monosaccharides	NAG

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6XM4 \| pdb_00006xm4	Download File View File

Structure of SARS-CoV-2 spike at pH 5.5, single RBD up, conformation 2

Zhou, T., Tsybovsky, Y., Olia, A., Kwong, P.D.

(2020) Cell Host Microbe 28: 867-879.e5

Released	2020-08-12
Method	ELECTRON MICROSCOPY 2.9 Å
Organisms	Severe acute respiratory syndrome coronavirus 2
Macromolecule	Spike glycoprotein (protein)
Unique Ligands	NAG
Unique branched monosaccharides	NAG

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6XM5 \| pdb_00006xm5	Download File View File

Structure of SARS-CoV-2 spike at pH 5.5, all RBDs down

Zhou, T., Tsybovsky, Y., Olia, A., Kwong, P.D.

(2020) Cell Host Microbe 28: 867-879.e5

Released	2020-07-29
Method	ELECTRON MICROSCOPY 3.1 Å
Organisms	Severe acute respiratory syndrome coronavirus 2
Macromolecule	Spike glycoprotein (protein)
Unique Ligands	NAG
Unique branched monosaccharides	NAG

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6XSK \| pdb_00006xsk	Download File View File

Cryo-EM Structure of Vaccine-Elicited Rhesus Antibody 789-203-3C12 in Complex with Stabilized SI06 (A/Solomon Islands/3/06) Influenza Hemagglutinin Trimer

Cerutti, G., Gorman, J., Kwong, P.D., Shapiro, L.

(2022) Immunity 55: 2405-2418.e7

Released	2021-07-21
Method	ELECTRON MICROSCOPY 3.85 Å
Organisms	Influenza A virus (A/Solomon Islands/3/2006(H1N1)) Macaca mulatta
Macromolecule	789-203-3C12 Fab Heavy Chain (protein) 789-203-3C12 Fab Light Chain (protein) Hemagglutinin HA1 chain (protein) Hemagglutinin HA2 chain (protein)
Unique Ligands	NAG
Unique branched monosaccharides	BMA, NAG

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7JWY \| pdb_00007jwy	Download File View File

Structure of SARS-CoV-2 spike at pH 4.5

Zhou, T., Tsybovsky, Y., Kwong, P.D.

(2020) Cell Host Microbe 28: 867-879.e5

Released	2020-11-25
Method	ELECTRON MICROSCOPY 2.5 Å
Organisms	Severe acute respiratory syndrome coronavirus 2
Macromolecule	Spike glycoprotein (protein)
Unique Ligands	NAG
Unique branched monosaccharides	NAG

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7JZ1 \| pdb_00007jz1	Download File View File

Crystal structure of broadly Plasmodium RIFIN reactive LAIR1-inserted antibody MGC34

Xu, K., Kwong, P.D.

(2021) Nat Commun 12: 4226-4226

Released	2021-05-26
Method	X-RAY DIFFRACTION 3.37 Å
Organisms	Homo sapiens
Macromolecule	MGC34 heavy chain (protein) MGC34 light chain (protein)

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7JZ4 \| pdb_00007jz4	Download File View File

Crystal structure of broadly Plasmodium RIFIN reactive LAIR1-inserted antibody MGD21

Xu, K., Kwong, P.D.

(2021) Nat Commun 12: 4226-4226

Released	2021-05-26
Method	X-RAY DIFFRACTION 2.747 Å
Organisms	Homo sapiens
Macromolecule	MGD21 heavy chain (protein) MGD21 light chain (protein)
Unique Ligands	NAG, PO4

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7JZI \| pdb_00007jzi	Download File View File

Crystal structure of LAIR1 ectodomain (from MGD21) in complex with Plasmodium RIFIN (PF3D7_1040300) V2 domain

Xu, K., Kwong, P.D.

(2021) Nat Commun 12: 4226-4226

Released	2021-05-26
Method	X-RAY DIFFRACTION 2.707 Å
Organisms	Homo sapiens Plasmodium falciparum NF54
Macromolecule	LAIR1 ectodomain from antibody MGD21 (protein) Rifin (protein)
Unique Ligands	PT

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7JZK \| pdb_00007jzk	Download File View File

Crystal structure of LAIR1 ectodomain (from MGD21) in complex with Plasmodium RIFIN (PF3D7_0401300) V2 domain

Xu, K., Kwong, P.D.

(2021) Nat Commun 12: 4226-4226

Released	2021-05-26
Method	X-RAY DIFFRACTION 2.457 Å
Organisms	Homo sapiens Plasmodium falciparum NF54
Macromolecule	LAIR1 ecotodomain from MGD21 antibody (protein) Rifin (protein)
Unique branched monosaccharides	BMA, NAG

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7KMB \| pdb_00007kmb	Download File View File

ACE2-RBD Focused Refinement Using Symmetry Expansion of Applied C3 for Triple ACE2-bound SARS-CoV-2 Trimer Spike at pH 7.4

Gorman, J., Kwong, P.D., Shapiro, L.

(2020) Cell Host Microbe 28: 867-879.e5

Released	2020-12-09
Method	ELECTRON MICROSCOPY 3.39 Å
Organisms	Homo sapiens Severe acute respiratory syndrome coronavirus 2
Macromolecule	Angiotensin-converting enzyme 2 (protein) Spike glycoprotein (protein)
Unique Ligands	NAG
Unique branched monosaccharides	NAG

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7KMS \| pdb_00007kms	Download File View File

Cryo-EM structure of triple ACE2-bound SARS-CoV-2 trimer spike at pH 7.4

Gorman, J., Kwong, P.D., Shapiro, L.

(2020) Cell Host Microbe 28: 867-879.e5

Released	2020-12-09
Method	ELECTRON MICROSCOPY 3.64 Å
Organisms	Homo sapiens Severe acute respiratory syndrome coronavirus 2
Macromolecule	Angiotensin-converting enzyme 2 (protein) Spike glycoprotein (protein)
Unique Ligands	NAG
Unique branched monosaccharides	NAG

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7KMZ \| pdb_00007kmz	Download File View File

Cryo-EM structure of double ACE2-bound SARS-CoV-2 trimer Spike at pH 7.4

Gorman, J., Kwong, P.D., Shapiro, L.

(2020) Cell Host Microbe 28: 867-879.e5

Released	2020-12-09
Method	ELECTRON MICROSCOPY 3.62 Å
Organisms	Homo sapiens Severe acute respiratory syndrome coronavirus 2
Macromolecule	Angiotensin-converting enzyme 2 (protein) Spike glycoprotein (protein)
Unique Ligands	NAG
Unique branched monosaccharides	NAG

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7KNB \| pdb_00007knb	Download File View File

Cryo-EM structure of single ACE2-bound SARS-CoV-2 trimer spike at pH 7.4

Gorman, J., Kwong, P.D., Shapiro, L.

(2020) Cell Host Microbe 28: 867-879.e5

Released	2020-12-09
Method	ELECTRON MICROSCOPY 3.93 Å
Organisms	Homo sapiens Severe acute respiratory syndrome coronavirus 2
Macromolecule	Angiotensin-converting enzyme 2 (protein) Spike glycoprotein (protein)
Unique Ligands	NAG
Unique branched monosaccharides	NAG

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7KNE \| pdb_00007kne	Download File View File

Cryo-EM structure of single ACE2-bound SARS-CoV-2 trimer spike at pH 5.5

Gorman, J., Rapp, M., Kwong, P.D., Shapiro, L.

(2020) Cell Host Microbe 28: 867-879.e5

Released	2020-12-16
Method	ELECTRON MICROSCOPY 3.85 Å
Organisms	Homo sapiens Severe acute respiratory syndrome coronavirus 2
Macromolecule	Angiotensin-converting enzyme 2 (protein) Spike glycoprotein (protein)
Unique Ligands	NAG
Unique branched monosaccharides	NAG

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7KNH \| pdb_00007knh	Download File View File

Cryo-EM Structure of Double ACE2-Bound SARS-CoV-2 Trimer Spike at pH 5.5

Gorman, J., Rapp, M., Kwong, P.D., Shapiro, L.

(2020) Cell Host Microbe 28: 867-879.e5

Released	2020-12-16
Method	ELECTRON MICROSCOPY 3.74 Å
Organisms	Homo sapiens Severe acute respiratory syndrome coronavirus 2
Macromolecule	Angiotensin-converting enzyme 2 (protein) Spike glycoprotein (protein)
Unique Ligands	NAG
Unique branched monosaccharides	NAG

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7KNI \| pdb_00007kni	Download File View File

Cryo-EM structure of Triple ACE2-bound SARS-CoV-2 Trimer Spike at pH 5.5

Gorman, J., Rapp, M., Kwong, P.D., Shapiro, L.

(2020) Cell Host Microbe 28: 867-879.e5

Released	2020-12-16
Method	ELECTRON MICROSCOPY 3.91 Å
Organisms	Homo sapiens Severe acute respiratory syndrome coronavirus 2
Macromolecule	Angiotensin-converting enzyme 2 (protein) Spike glycoprotein (protein)
Unique Ligands	NAG
Unique branched monosaccharides	NAG

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7LRS \| pdb_00007lrs	Download File View File

Cryo-EM structure of SARS-CoV-2 spike in complex with neutralizing antibody A23-58.1 that targets the receptor-binding domain

Zhou, T., Tsybovsky, Y.

(2021) Science 373:

Released	2021-07-14
Method	ELECTRON MICROSCOPY 3.89 Å
Organisms	Homo sapiens Severe acute respiratory syndrome coronavirus 2
Macromolecule	Spike glycoprotein (protein) antibody A23-58.1 heavy chain (protein) antibody A23-58.1 light chain (protein)
Unique branched monosaccharides	BMA, MAN, NAG

1 to 25 of 101 Structures

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Structure Determination Methodology

Scientific Name of Source Organism

Taxonomy

Experimental Method

Polymer Entity Type

Refinement Resolution (Å)

Release Date

Enzyme Classification Name

Membrane Protein Annotation

Symmetry Type

SCOP Classification

6MTO | pdb_00006mto

6MTP | pdb_00006mtp

6MTQ | pdb_00006mtq

6MTR | pdb_00006mtr

6MTS | pdb_00006mts

6MTT | pdb_00006mtt

6XLU | pdb_00006xlu

6XM0 | pdb_00006xm0

6XM3 | pdb_00006xm3

6XM4 | pdb_00006xm4

6XM5 | pdb_00006xm5

6XSK | pdb_00006xsk

7JWY | pdb_00007jwy

7JZ1 | pdb_00007jz1

7JZ4 | pdb_00007jz4

7JZI | pdb_00007jzi

7JZK | pdb_00007jzk

7KMB | pdb_00007kmb

7KMS | pdb_00007kms

7KMZ | pdb_00007kmz

7KNB | pdb_00007knb

7KNE | pdb_00007kne

7KNH | pdb_00007knh

7KNI | pdb_00007kni

7LRS | pdb_00007lrs