8D50 | pdb_00008d50

Crystal Structure of Mosaic HIV-1 Envelope (MosM3.1) in Complex with antibodies PGT124 and 35O22 at 4.3 Angstrom

PDB DOI: https://doi.org/10.2210/pdb8D50/pdb

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

Deposited: 2022-06-03 Released: 2023-12-13
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: 4.32 Å
R-Value Free:
0.369 (Depositor), 0.362 (DCC)
R-Value Work:
0.323 (Depositor), 0.325 (DCC)
R-Value Observed:
0.325 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Structural and Antigenic Characterization of B Cell Mosaic Env Trimers

Xian, Y., Wilson, I.A.

To be published.

Macromolecule Content

Total Structure Weight: 146.46 kDa
Atom Count: 10,251
Modeled Residue Count: 1,252
Deposited Residue Count: 1,252
Unique protein chains: 6

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein gp120	A [auth G]	431	Human immunodeficiency virus 1	Mutation(s): 0

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein gp41	B	137	Human immunodeficiency virus 1	Mutation(s): 0

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
35O22 Fab heavy chain	C [auth D]	141	Homo sapiens	Mutation(s): 0

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
35O22 Fab light chain	D [auth E]	107	Homo sapiens	Mutation(s): 0

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| 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
PGT124 Fab light chain	E [auth L]	210	Homo sapiens	Mutation(s): 0

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| 3D Structure

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
PGT124 Fab heavy chain	F [auth H]	226	Homo sapiens	Mutation(s): 0

Oligosaccharides

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Entity ID: 7
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-2)-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 P]	5		N-Glycosylation	Interactions Focus chain G [auth P] Interactions & Density Focus chain G [auth P]
Glycosylation Resources
GlyTouCan: G42227JK GlyCosmos: G42227JK GlyGen: G42227JK

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

Entity ID: 9
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-3)-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	I [auth C]	6		N-Glycosylation	Interactions Focus chain I [auth C] Interactions & Density Focus chain I [auth C]
Glycosylation Resources
GlyTouCan: G42984ZU GlyCosmos: G42984ZU GlyGen: G42984ZU

Entity ID: 10
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
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	J [auth F]	4		N-Glycosylation	Interactions Focus chain J [auth F] Interactions & Density Focus chain J [auth F]
Glycosylation Resources
GlyTouCan: G22573RC GlyCosmos: G22573RC GlyGen: G22573RC

Entity ID: 11
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	K [auth I], L [auth J], O [auth N]	3		N-Glycosylation	Interactions Focus chain K [auth I] Focus chain L [auth J] Focus chain O [auth N] Interactions & Density Focus chain K [auth I] Focus chain L [auth J] Focus chain O [auth N]
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain P [auth G] 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 V [auth B] SDF format, chain W [auth B] MOL2 format, chain P [auth G] 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 V [auth B] MOL2 format, chain W [auth B] mmCIF format, chain P [auth G] mmCIF format, chain Q [auth G] mmCIF format, chain R [auth G] mmCIF format, chain S [auth G] mmCIF format, chain T [auth G] mmCIF format, chain V [auth B] mmCIF format, chain W [auth B]	P [auth G] Q [auth G] R [auth G] S [auth G] T [auth G] P [auth G], Q [auth G], R [auth G], S [auth G], T [auth G], V [auth B], W [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain P [auth G] Focus chain Q [auth G] Focus chain R [auth G] Focus chain S [auth G] Focus chain T [auth G] Focus chain V [auth B] Focus chain W [auth B] Interactions & Density Focus chain P [auth G] Focus chain Q [auth G] Focus chain R [auth G] Focus chain S [auth G] Focus chain T [auth G] Focus chain V [auth B] Focus chain W [auth B]
MAN Query on MAN Download:Ideal Coordinates CCD File SDF format, chain U [auth G] MOL2 format, chain U [auth G] mmCIF format, chain U [auth G]	U [auth G]	alpha-D-mannopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-PQMKYFCFSA-N		Interactions Focus chain U [auth G] Interactions & Density Focus chain U [auth G]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 4.32 Å
R-Value Free: 0.369 (Depositor), 0.362 (DCC)
R-Value Work: 0.323 (Depositor), 0.325 (DCC)
R-Value Observed: 0.325 (Depositor)

Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 132.189	α = 90
b = 132.189	β = 90
c = 315.415	γ = 120

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

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Entry History

& Funding Information

Deposition Data

Released Date: 2023-12-13

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		2 P01 AI110657