8D4R | pdb_00008d4r

Crystal Structure of Mosaic HIV-1 Envelope (MosM3.2) in Complex with antibodies PGT124 and 35O22 at 3.8 Angstrom

PDB DOI: https://doi.org/10.2210/pdb8D4R/pdb

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

Deposited: 2022-06-02 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: 3.81 Å
R-Value Free:
0.296 (Depositor), 0.290 (DCC)
R-Value Work:
0.277 (Depositor), 0.280 (DCC)
R-Value Observed:
0.279 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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, I.A.

To be published.

Macromolecule Content

Total Structure Weight: 161.92 kDa
Atom Count: 11,327
Modeled Residue Count: 1,373
Deposited Residue Count: 1,373
Unique protein chains: 6

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein gp120	A [auth G]	427	Human immunodeficiency virus 1	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Glycosylation
Glycosylation Sites: 17	Glycosylation Focus chain A [auth G]
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein gp41	B	131	Human immunodeficiency virus 1	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain B
Sequence Annotations Expand
Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
35O22 Fab heavy chain	C [auth D]	187	Homo sapiens	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: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
35O22 Fab light chain	D [auth E]	192	Homo sapiens	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: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
PGT124 Fab light chain	E [auth L]	210	Homo sapiens	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: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
PGT124 Fab heavy chain	F [auth H]	226	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 7
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose	G [auth U]	3		N/A	Interactions Focus chain G [auth U] Interactions & Density Focus chain G [auth U]
Glycosylation Resources
GlyTouCan: G25559RS GlyCosmos: G25559RS GlyGen: G25559RS

Entity ID: 8
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
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	H [auth T]	6		N-Glycosylation	Interactions Focus chain H [auth T] Interactions & Density Focus chain H [auth T]
Glycosylation Resources
GlyTouCan: G94106MV GlyCosmos: G94106MV GlyGen: G94106MV

Entity ID: 9
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	I [auth A]	7		N-Glycosylation	Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]
Glycosylation Resources
GlyTouCan: G55220VL GlyCosmos: G55220VL GlyGen: G55220VL

Entity ID: 10
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	J [auth C], K [auth F], N [auth K], P [auth N], Q [auth O], J [auth C], K [auth F], N [auth K], P [auth N], Q [auth O], R [auth P], S [auth Q], T [auth R], U [auth S]	2		N-Glycosylation	Interactions Focus chain J [auth C] Focus chain K [auth F] Focus chain N [auth K] Focus chain P [auth N] Focus chain Q [auth O] Focus chain R [auth P] Focus chain S [auth Q] Focus chain T [auth R] Focus chain U [auth S] Interactions & Density Focus chain J [auth C] Focus chain K [auth F] Focus chain N [auth K] Focus chain P [auth N] Focus chain Q [auth O] Focus chain R [auth P] Focus chain S [auth Q] Focus chain T [auth R] Focus chain U [auth S]
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

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	L [auth I]	5		N-Glycosylation	Interactions Focus chain L [auth I] Interactions & Density Focus chain L [auth I]
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	M [auth J]	4		N-Glycosylation	Interactions Focus chain M [auth J] Interactions & Density Focus chain M [auth J]
Glycosylation Resources
GlyTouCan: G81315DD GlyCosmos: G81315DD GlyGen: G81315DD

Entity ID: 13
Molecule	Chains	Length	2D Diagram	Glycosylation	3D 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	O [auth M]	4		N-Glycosylation	Interactions Focus chain O [auth M] Interactions & Density Focus chain O [auth M]
Glycosylation Resources
GlyTouCan: G22573RC GlyCosmos: G22573RC GlyGen: G22573RC

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.81 Å
R-Value Free: 0.296 (Depositor), 0.290 (DCC)
R-Value Work: 0.277 (Depositor), 0.280 (DCC)
R-Value Observed: 0.279 (Depositor)

Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 125.474	α = 90
b = 125.474	β = 90
c = 315.834	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

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