8D0Y | pdb_00008d0y

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, I.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 (Depositor), 0.300 (DCC)
R-Value Work:
0.268 (Depositor), 0.270 (DCC)
R-Value Observed:
0.270 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

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

Xian, Y., Wilson, I.A.

To be published.

Macromolecule Content

Total Structure Weight: 151.91 kDa
Atom Count: 10,622
Modeled 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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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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 type 1) Explore Q2N0S6 Go to UniProtKB: Q2N0S6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q2N0S6
Glycosylation
Glycosylation Sites: 13	Glycosylation Focus chain E [auth G]
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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 type 1) Explore Q2N0S6 Go to UniProtKB: Q2N0S6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q2N0S6
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain F [auth B]
Sequence Annotations Expand
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 V [auth B] SDF format, chain U [auth G] SDF format, chain T [auth G] SDF format, chain S [auth G] SDF format, chain R [auth G] SDF format, chain Q [auth G] MOL2 format, chain V [auth B] MOL2 format, chain U [auth G] MOL2 format, chain T [auth G] MOL2 format, chain S [auth G] MOL2 format, chain R [auth G] MOL2 format, chain Q [auth G] mmCIF format, chain V [auth B] mmCIF format, chain U [auth G] mmCIF format, chain T [auth G] mmCIF format, chain S [auth G] mmCIF format, chain R [auth G] mmCIF format, chain Q [auth G]	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 (Depositor), 0.300 (DCC)
R-Value Work: 0.268 (Depositor), 0.270 (DCC)
R-Value Observed: 0.270 (Depositor)

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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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2023-07-19

Deposition Author(s):

Xian, Y.

Wilson, I.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