5JS9

Uncleaved prefusion optimized gp140 trimer with an engineered 8-residue HR1 turn bound to broadly neutralizing antibodies 8ANC195 and PGT128

PDB DOI: https://doi.org/10.2210/pdb5JS9/pdb

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

Deposited: 2016-05-07 Released: 2016-07-13
Deposition Author(s): Kong, L., Wilson, I.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 6.92 Å
R-Value Free: 0.322
R-Value Work: 0.284
R-Value Observed: 0.288

wwPDB Validation 3D Report Full Report

This is version 2.1 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 179.4 kDa
Atom Count: 12,007
Modelled Residue Count: 1,447
Deposited Residue Count: 1,523
Unique protein chains: 6

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
broadly neutralizing antibody PGT128 heavy chain	A	239	Homo sapiens	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: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
broadly neutralizing antibody PGT128 light chain	B	211	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: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
gp120	C	480	Human immunodeficiency virus 1	Mutation(s): 0
UniProt
Find proteins for Q2N0S6 (Human immunodeficiency virus 1) Explore Q2N0S6 Go to UniProtKB: Q2N0S6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q2N0S6
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Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
gp41	D	140	Human immunodeficiency virus 1	Mutation(s): 0
UniProt
Find proteins for Q2N0S6 (Human immunodeficiency virus 1) Explore Q2N0S6 Go to UniProtKB: Q2N0S6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q2N0S6
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
broadly neutralizing antibody 8ANC195 heavy chain	E	238	Homo sapiens	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: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
broadly neutralizing antibody 8ANC195 light chain	F	215	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
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	G, H, I, J	2		N-Glycosylation	Interactions Focus chain G Focus chain H Focus chain I Focus chain J Interactions & Density Focus chain G Focus chain H Focus chain I Focus chain J
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 8
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[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	K	8		N-Glycosylation	Interactions Focus chain K Interactions & Density Focus chain K
Glycosylation Resources
GlyTouCan: G80966KZ GlyCosmos: G80966KZ GlyGen: G80966KZ

Entity ID: 9
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-(1-2)-alpha-D-mannopyranose-(1-6)-[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	10		N-Glycosylation	Interactions Focus chain L Interactions & Density Focus chain L
Glycosylation Resources
GlyTouCan: G40702WU GlyCosmos: G40702WU GlyGen: G40702WU

Entity ID: 10
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-(1-3)-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	M	8		N-Glycosylation	Interactions Focus chain M Interactions & Density Focus chain M
Glycosylation Resources
GlyTouCan: G83582BK GlyCosmos: G83582BK GlyGen: G83582BK

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	N	5		N-Glycosylation	Interactions Focus chain N Interactions & Density Focus chain N
Glycosylation Resources
GlyTouCan: G22768VO GlyCosmos: G22768VO GlyGen: G22768VO

Entity ID: 12
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	O	5		N-Glycosylation	Interactions Focus chain O Interactions & Density Focus chain O
Glycosylation Resources
GlyTouCan: G42227JK GlyCosmos: G42227JK GlyGen: G42227JK

Entity ID: 13
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	P, Q, R	3		N-Glycosylation	Interactions Focus chain P Focus chain Q Focus chain R Interactions & Density Focus chain P Focus chain Q Focus chain R
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Entity ID: 14
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-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-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	S	11		N-Glycosylation	Interactions Focus chain S Interactions & Density Focus chain S
Glycosylation Resources
GlyTouCan: G60230HH GlyCosmos: G60230HH GlyGen: G60230HH

Entity ID: 15
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	T	4		N-Glycosylation	Interactions Focus chain T Interactions & Density Focus chain T
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 U [auth C] SDF format, chain W [auth C] SDF format, chain X [auth D] SDF format, chain V [auth C] MOL2 format, chain U [auth C] MOL2 format, chain W [auth C] MOL2 format, chain X [auth D] MOL2 format, chain V [auth C]	U [auth C], V [auth C], W [auth C], X [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth D] Interactions & Density Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 6.92 Å
R-Value Free: 0.322
R-Value Work: 0.284
R-Value Observed: 0.288
Space Group: I 2 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 261.955	α = 90
b = 261.955	β = 90
c = 261.955	γ = 90

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2016-07-13

Deposition Author(s):

Kong, L.

Wilson, I.A.

Revision History (Full details and data files)

Version 1.0: 2016-07-13
Type: Initial release
Version 1.1: 2018-03-21
Changes: Derived calculations
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2023-09-27
Changes: Data collection, Database references, Refinement description, Structure summary

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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5JS9

Uncleaved prefusion optimized gp140 trimer with an engineered 8-residue HR1 turn bound to broadly neutralizing antibodies 8ANC195 and PGT128

Entity ID: 1

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Entity ID: 2

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Entity ID: 3

UniProt

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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

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Glycosylation Resources

Entity ID: 10

Glycosylation Resources

Entity ID: 11

Glycosylation Resources

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Glycosylation Resources

Entity ID: 13

Glycosylation Resources

Entity ID: 14

Glycosylation Resources

Entity ID: 15

Glycosylation Resources

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)