6IEQ

Crystal Structure of HIV-1 Env ConM SOSIP.v7 in Complex with bNAb PGT124 and 35O22

PDB DOI: https://doi.org/10.2210/pdb6IEQ/pdb

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

Deposited: 2018-09-16 Released: 2019-05-22
Deposition Author(s): Han, B.W., Wilson, I.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.90 Å
R-Value Free: 0.296
R-Value Work: 0.247
R-Value Observed: 0.250

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Ligand Structure Quality Assessment

This is version 2.2 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 180.56 kDa
Atom Count: 11,846
Modelled Residue Count: 1,453
Deposited Residue Count: 1,556
Unique protein chains: 6

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein gp160	A [auth G]	497	Human immunodeficiency virus 1	Mutation(s): 0
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Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein gp160	B	153	Human immunodeficiency virus 1	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 Light Chain	C [auth L]	214	Homo sapiens	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 Heavy Chain	D [auth H]	236	Homo sapiens	Mutation(s): 0
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
35O22 Fab Heavy Chain	E [auth D]	240	Homo sapiens	Mutation(s): 0
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Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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Reference Sequence

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
35O22 Fab Light Chain	F [auth E]	216	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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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-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	G [auth A]	6		N-Glycosylation	Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
Glycosylation Resources
GlyTouCan: G09724ZC GlyCosmos: G09724ZC GlyGen: G09724ZC

Entity ID: 8
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	H [auth C]	4		N-Glycosylation	Interactions Focus chain H [auth C] Interactions & Density Focus chain H [auth C]
Glycosylation Resources
GlyTouCan: G81315DD GlyCosmos: G81315DD GlyGen: G81315DD

Entity ID: 9
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	I [auth F], M, O	2		N-Glycosylation	Interactions Focus chain I [auth F] Focus chain M Focus chain O Interactions & Density Focus chain I [auth F] Focus chain M Focus chain O
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 10
Molecule	Chains	Length	2D Diagram	Glycosylation	3D 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	J [auth I], L [auth K], N	5		N/A	Interactions Focus chain J [auth I] Focus chain L [auth K] Focus chain N Interactions & Density Focus chain J [auth I] Focus chain L [auth K] Focus chain N
Glycosylation Resources
GlyTouCan: G42227JK GlyCosmos: G42227JK GlyGen: G42227JK

Entity ID: 11
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose	K [auth J]	2		N/A	Interactions Focus chain K [auth J] Interactions & Density Focus chain K [auth J]
Glycosylation Resources
GlyTouCan: G77384RA GlyCosmos: G77384RA GlyGen: G77384RA

Entity ID: 12
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-2)-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	P	8		N/A	Interactions Focus chain P Interactions & Density Focus chain P
Glycosylation Resources
GlyTouCan: G81980VO GlyCosmos: G81980VO GlyGen: G81980VO

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 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] SDF format, chain W [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] MOL2 format, chain W [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], W [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] Focus chain W [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] Focus chain W [auth B]
MAN Query on MAN Download Ideal Coordinates CCD File SDF format, chain X [auth L] SDF format, chain Y [auth H] MOL2 format, chain X [auth L] MOL2 format, chain Y [auth H]	X [auth L], Y [auth H]	alpha-D-mannopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-PQMKYFCFSA-N		Interactions Focus chain X [auth L] Focus chain Y [auth H] Interactions & Density Focus chain X [auth L] Focus chain Y [auth H]

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 11
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900118 Query on PRD_900118	K [auth J]	6alpha-alpha-mannobiose	Oligosaccharide / Metabolism		Interactions Focus chain K [auth J] Interactions & Density Focus chain K [auth J]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.90 Å
R-Value Free: 0.296
R-Value Work: 0.247
R-Value Observed: 0.250
Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 127.59	α = 90
b = 127.59	β = 90
c = 315.507	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2019-05-22

Deposition Author(s):

Han, B.W.

Wilson, I.A.

Revision History (Full details and data files)

Version 1.0: 2019-05-22
Type: Initial release
Version 1.1: 2019-06-12
Changes: Data collection, Database references
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Source and taxonomy, Structure summary
Version 2.1: 2023-11-22
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
Version 2.2: 2024-03-20
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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6IEQ

Crystal Structure of HIV-1 Env ConM SOSIP.v7 in Complex with bNAb PGT124 and 35O22

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

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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

Entity ID: 11

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)