8D0Y

Crystal Structure of HIV-1 BG505 SOSIPv8 Trimer in Complex with CD4bs targeting antibody 21N13 and interface targeting antibody 35O22 at 4.7 Angstrom

PDB DOI: https://doi.org/10.2210/pdb8D0Y/pdb

Classification: VIRAL PROTEIN/IMMUNE SYSTEM
Organism(s): Macaca mulatta, Human immunodeficiency virus 1
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2022-05-26 Released: 2023-07-19
Deposition Author(s): Xian, Y., Wilson, A.
Funding Organization(s): International AIDS Vaccine Initiative, Consortia for HIV/AIDS Vaccine Development, Other private

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 4.70 Å
R-Value Free: 0.298
R-Value Work: 0.268
R-Value Observed: 0.270

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This is version 1.2 of the entry. See complete history.

Literature

The domain-swaped dimer of the HIV-1 CD4bs targeting antibody 21N13

Xian, Y., Wilson, A.

To be published.

Macromolecule Content

Total Structure Weight: 151.91 kDa
Atom Count: 10,622
Modelled Residue Count: 1,278
Deposited Residue Count: 1,278
Unique protein chains: 6

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
35O22scFv Heavy Chain Variable	A [auth D]	128	Macaca mulatta	Mutation(s): 0
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Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
35O22scFv Light Chain Variable	B [auth E]	111	Macaca mulatta	Mutation(s): 0
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Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
PGT124 Fab Heavy Chain	C [auth H]	225	Macaca mulatta	Mutation(s): 0
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Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
PGT124 Fab Light Chain	D [auth L]	213	Macaca mulatta	Mutation(s): 0
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
BG505SOSIPv8 gp120	E [auth G]	455	Human immunodeficiency virus 1	Mutation(s): 0
UniProt
Find proteins for Q2N0S6 (Human immunodeficiency virus 1) Explore Q2N0S6 Go to UniProtKB: Q2N0S6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q2N0S6
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Reference Sequence

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
BG505SOSIPv8 gp41	F [auth B]	146	Human immunodeficiency virus 1	Mutation(s): 0
UniProt
Find proteins for Q2N0S6 (Human immunodeficiency virus 1) Explore Q2N0S6 Go to UniProtKB: Q2N0S6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q2N0S6
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Reference Sequence

Oligosaccharides

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Entity ID: 7
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	G [auth A]	7		N-Glycosylation	Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
Glycosylation Resources
GlyTouCan: G55220VL GlyCosmos: G55220VL GlyGen: G55220VL

Entity ID: 8
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	H [auth C], L [auth K]	2		N-Glycosylation	Interactions Focus chain H [auth C] Focus chain L [auth K] Interactions & Density Focus chain H [auth C] Focus chain L [auth K]
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 9
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	I [auth F]	7		N-Glycosylation	Interactions Focus chain I [auth F] Interactions & Density Focus chain I [auth F]
Glycosylation Resources
GlyTouCan: G23799GS GlyCosmos: G23799GS GlyGen: G23799GS

Entity ID: 10
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	J [auth I]	6		N-Glycosylation	Interactions Focus chain J [auth I] Interactions & Density Focus chain J [auth I]
Glycosylation Resources
GlyTouCan: G34442SS GlyCosmos: G34442SS GlyGen: G34442SS

Entity ID: 11
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	K [auth J], M, N, O	5		N-Glycosylation	Interactions Focus chain K [auth J] Focus chain M Focus chain N Focus chain O Interactions & Density Focus chain K [auth J] Focus chain M Focus chain N Focus chain O
Glycosylation Resources
GlyTouCan: G22768VO GlyCosmos: G22768VO GlyGen: G22768VO

Entity ID: 12
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	P	4		N-Glycosylation	Interactions Focus chain P Interactions & Density Focus chain P
Glycosylation Resources
GlyTouCan: G81315DD GlyCosmos: G81315DD GlyGen: G81315DD

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain Q [auth G] SDF format, chain R [auth G] SDF format, chain S [auth G] SDF format, chain T [auth G] SDF format, chain U [auth G] SDF format, chain V [auth B] MOL2 format, chain Q [auth G] MOL2 format, chain R [auth G] MOL2 format, chain S [auth G] MOL2 format, chain T [auth G] MOL2 format, chain U [auth G] MOL2 format, chain V [auth B]	Q [auth G] R [auth G] S [auth G] T [auth G] U [auth G] Q [auth G], R [auth G], S [auth G], T [auth G], U [auth G], V [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain Q [auth G] Focus chain R [auth G] Focus chain S [auth G] Focus chain T [auth G] Focus chain U [auth G] Focus chain V [auth B] Interactions & Density Focus chain Q [auth G] Focus chain R [auth G] Focus chain S [auth G] Focus chain T [auth G] Focus chain U [auth G] Focus chain V [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 4.70 Å
R-Value Free: 0.298
R-Value Work: 0.268
R-Value Observed: 0.270
Space Group: P 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 264.672	α = 90
b = 264.672	β = 90
c = 264.672	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHASER	phasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Released Date: 2023-07-19

Deposition Author(s):

Xian, Y.

Wilson, A.

Funding Organization	Location	Grant Number
International AIDS Vaccine Initiative	United States	INV-008352/OPP1153692
Consortia for HIV/AIDS Vaccine Development	United States	CHAVD 1UM1 AI144462
Other private		P01 AI110657

Revision History (Full details and data files)

Version 1.0: 2023-07-19
Type: Initial release
Version 1.1: 2023-10-25
Changes: Data collection
Version 1.2: 2023-11-22
Changes: Source and taxonomy

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.

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8D0Y

Crystal Structure of HIV-1 BG505 SOSIPv8 Trimer in Complex with CD4bs targeting antibody 21N13 and interface targeting antibody 35O22 at 4.7 Angstrom

The domain-swaped dimer of the HIV-1 CD4bs targeting antibody 21N13

Entity ID: 1

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Entity ID: 2

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Entity ID: 3

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Entity ID: 4

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Entity ID: 5

UniProt

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Entity ID: 6

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Entity ID: 7

Glycosylation Resources

Entity ID: 8

Glycosylation Resources

Entity ID: 9

Glycosylation Resources

Entity ID: 10

Glycosylation Resources

Entity ID: 11

Glycosylation Resources

Entity ID: 12

Glycosylation Resources

Experimental Data

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Deposition Data

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