8D53 | pdb_00008d53

Crystal Structure of Mosaic HIV-1 Envelope (MosM3.3) in Complex with antibodies PGT124 and 35O22 at 3.25 Angstrom

PDB DOI: https://doi.org/10.2210/pdb8D53/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: 2024-07-24
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: 3.24 Å
R-Value Free:
0.331 (Depositor), 0.310 (DCC)
R-Value Work:
0.317 (Depositor), 0.320 (DCC)
R-Value Observed:
0.318 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 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: 147.71 kDa
Atom Count: 10,333
Modelled Residue Count: 1,243
Deposited Residue Count: 1,243
Unique protein chains: 6

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein gp120	A [auth G]	446	Human immunodeficiency virus 1	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Glycosylation
Glycosylation Sites: 15	Glycosylation Focus chain A [auth G]
Sequence Annotations Expand
Reference Sequence LOADING

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein gp41	B	132	Human immunodeficiency virus 1	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain B
Sequence Annotations Expand
Reference Sequence LOADING

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
PGT124 Fab Light Chain	C [auth L]	212	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence LOADING

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
PGT124 Fab Heavy Chain	D [auth H]	229	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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Reference Sequence LOADING

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
35O22scFV Heavy chain variable	E [auth D]	117	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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Reference Sequence LOADING

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
35O22scFv Light Chain Variable	F [auth E]	107	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence LOADING

Oligosaccharides

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Entity ID: 7
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	G [auth A], H [auth C], L [auth K], M, Q, G [auth A], H [auth C], L [auth K], M, Q, R	2	N/A	N-Glycosylation	Interactions Focus chain G [auth A] Focus chain H [auth C] Focus chain L [auth K] Focus chain M Focus chain Q Focus chain R Interactions & Density Focus chain G [auth A] Focus chain H [auth C] Focus chain L [auth K] Focus chain M Focus chain Q Focus chain R

Entity ID: 8
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-6)-[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	I [auth F]	9	N/A	N-Glycosylation	Interactions Focus chain I [auth F] Interactions & Density Focus chain I [auth F]

Entity ID: 9
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	J [auth I], P, S	3	N/A	N-Glycosylation	Interactions Focus chain J [auth I] Focus chain P Focus chain S Interactions & Density Focus chain J [auth I] Focus chain P Focus chain S

Entity ID: 10
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	K [auth J]	4	N/A	N-Glycosylation	Interactions Focus chain K [auth J] Interactions & Density Focus chain K [auth J]

Entity ID: 11
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(5-4)-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	N	6	N/A	N-Glycosylation	Interactions Focus chain N Interactions & Density Focus chain N

Entity ID: 12
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-alpha-D-mannopyranose-(6-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	O	5	N/A	N-Glycosylation	Interactions Focus chain O Interactions & Density Focus chain O

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 T [auth G] SDF format, chain U [auth G] SDF format, chain V [auth G] SDF format, chain W [auth G] SDF format, chain X [auth B] MOL2 format, chain T [auth G] MOL2 format, chain U [auth G] MOL2 format, chain V [auth G] MOL2 format, chain W [auth G] MOL2 format, chain X [auth B] mmCIF format, chain T [auth G] mmCIF format, chain U [auth G] mmCIF format, chain V [auth G] mmCIF format, chain W [auth G] mmCIF format, chain X [auth B]	T [auth G], U [auth G], V [auth G], W [auth G], X [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain T [auth G] Focus chain U [auth G] Focus chain V [auth G] Focus chain W [auth G] Focus chain X [auth B] Interactions & Density Focus chain T [auth G] Focus chain U [auth G] Focus chain V [auth G] Focus chain W [auth G] Focus chain X [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.24 Å
R-Value Free: 0.331 (Depositor), 0.310 (DCC)
R-Value Work: 0.317 (Depositor), 0.320 (DCC)
R-Value Observed: 0.318 (Depositor)

Space Group: P 3 1 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 139.266	α = 90
b = 139.266	β = 90
c = 320.332	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data scaling
PHENIX	refinement
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: 2024-07-24

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