5I8H

Crystal Structure of HIV-1 BG505 SOSIP.664 Prefusion Env Trimer in Complex with V3 Loop-targeting Antibody PGT122 Fab and Fusion Peptide-targeting Antibody VRC34.01 Fab

PDB DOI: https://doi.org/10.2210/pdb5I8H/pdb

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

Deposited: 2016-02-18 Released: 2016-05-25
Deposition Author(s): Xu, K., Zhou, T., Kwong, P.D.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 4.30 Å
R-Value Free: 0.309
R-Value Work: 0.281
R-Value Observed: 0.282

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.0 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 354.77 kDa
Atom Count: 23,938
Modelled Residue Count: 2,915
Deposited Residue Count: 3,028
Unique protein chains: 6

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BG505 SOSIP.664 gp120	A, C	481	Human immunodeficiency virus 1	Mutation(s): 0 Gene Names: env
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
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
BG505 SOSIP.664 gp41	B, H [auth D]	153	Human immunodeficiency virus 1	Mutation(s): 0 Gene Names: env
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
Sequence Annotations Expand
Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
PGT122 Fab light chain	D [auth L], K [auth J]	210	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: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
VRC34.01 Fab heavy chain	E, G	223	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: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
VRC34.01 Fab light chain	F, I [auth H]	212	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
PGT122 Fab heavy chain	J [auth I], L [auth K]	235	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-(1-3)-[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	M, Z	7		N-Glycosylation	Interactions Focus chain M Focus chain Z Interactions & Density Focus chain M Focus chain Z
Glycosylation Resources
GlyTouCan: G55220VL GlyCosmos: G55220VL GlyGen: G55220VL

Entity ID: 8
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	AA [auth a], N	5		N-Glycosylation	Interactions Focus chain AA [auth a] Focus chain N Interactions & Density Focus chain AA [auth a] Focus chain N
Glycosylation Resources
GlyTouCan: G22768VO GlyCosmos: G22768VO GlyGen: G22768VO

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	BA [auth b], CA [auth c], DA [auth d], FA [auth f], GA [auth g], BA [auth b], CA [auth c], DA [auth d], FA [auth f], GA [auth g], IA [auth i], JA [auth j], O, P, Q, T, V, W, X	2		N-Glycosylation	Interactions Focus chain BA [auth b] Focus chain CA [auth c] Focus chain DA [auth d] Focus chain FA [auth f] Focus chain GA [auth g] Focus chain IA [auth i] Focus chain JA [auth j] Focus chain O Focus chain P Focus chain Q Focus chain T Focus chain V Focus chain W Focus chain X Interactions & Density Focus chain BA [auth b] Focus chain CA [auth c] Focus chain DA [auth d] Focus chain FA [auth f] Focus chain GA [auth g] Focus chain IA [auth i] Focus chain JA [auth j] Focus chain O Focus chain P Focus chain Q Focus chain T Focus chain V Focus chain W Focus chain X
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)-[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	EA [auth e], R	6		N-Glycosylation	Interactions Focus chain EA [auth e] Focus chain R Interactions & Density Focus chain EA [auth e] Focus chain R
Glycosylation Resources
GlyTouCan: G56014GC GlyCosmos: G56014GC GlyGen: G56014GC

Entity ID: 11
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	KA [auth k], LA [auth l], S, Y	3		N-Glycosylation	Interactions Focus chain KA [auth k] Focus chain LA [auth l] Focus chain S Focus chain Y Interactions & Density Focus chain KA [auth k] Focus chain LA [auth l] Focus chain S Focus chain Y
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

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-(1-2)-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	HA [auth h], U	10		N-Glycosylation	Interactions Focus chain HA [auth h] Focus chain U Interactions & Density Focus chain HA [auth h] Focus chain U
Glycosylation Resources
GlyTouCan: G91704UR GlyCosmos: G91704UR GlyGen: G91704UR

Entity ID: 13
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	MA [auth m]	4		N-Glycosylation	Interactions Focus chain MA [auth m] Interactions & Density Focus chain MA [auth m]
Glycosylation Resources
GlyTouCan: G81315DD GlyCosmos: G81315DD GlyGen: G81315DD

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 AB [auth D] SDF format, chain BB [auth I] SDF format, chain CB [auth K] SDF format, chain NA [auth A] SDF format, chain OA [auth A] SDF format, chain PA [auth A] SDF format, chain QA [auth A] SDF format, chain RA [auth B] SDF format, chain SA [auth B] SDF format, chain TA [auth B] SDF format, chain UA [auth C] SDF format, chain VA [auth C] SDF format, chain WA [auth C] SDF format, chain XA [auth C] SDF format, chain YA [auth C] SDF format, chain ZA [auth D] MOL2 format, chain AB [auth D] MOL2 format, chain BB [auth I] MOL2 format, chain CB [auth K] MOL2 format, chain NA [auth A] MOL2 format, chain OA [auth A] MOL2 format, chain PA [auth A] MOL2 format, chain QA [auth A] MOL2 format, chain RA [auth B] MOL2 format, chain SA [auth B] MOL2 format, chain TA [auth B] MOL2 format, chain UA [auth C] MOL2 format, chain VA [auth C] MOL2 format, chain WA [auth C] MOL2 format, chain XA [auth C] MOL2 format, chain YA [auth C] MOL2 format, chain ZA [auth D]	AB [auth D] BB [auth I] CB [auth K] NA [auth A] OA [auth A] AB [auth D], BB [auth I], CB [auth K], NA [auth A], OA [auth A], PA [auth A], QA [auth A], RA [auth B], SA [auth B], TA [auth B], UA [auth C], VA [auth C], WA [auth C], XA [auth C], YA [auth C], ZA [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AB [auth D] Focus chain BB [auth I] Focus chain CB [auth K] Focus chain NA [auth A] Focus chain OA [auth A] Focus chain PA [auth A] Focus chain QA [auth A] Focus chain RA [auth B] Focus chain SA [auth B] Focus chain TA [auth B] Focus chain UA [auth C] Focus chain VA [auth C] Focus chain WA [auth C] Focus chain XA [auth C] Focus chain YA [auth C] Focus chain ZA [auth D] Interactions & Density Focus chain AB [auth D] Focus chain BB [auth I] Focus chain CB [auth K] Focus chain NA [auth A] Focus chain OA [auth A] Focus chain PA [auth A] Focus chain QA [auth A] Focus chain RA [auth B] Focus chain SA [auth B] Focus chain TA [auth B] Focus chain UA [auth C] Focus chain VA [auth C] Focus chain WA [auth C] Focus chain XA [auth C] Focus chain YA [auth C] Focus chain ZA [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 4.30 Å
R-Value Free: 0.309
R-Value Work: 0.281
R-Value Observed: 0.282
Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 252.296	α = 90
b = 252.296	β = 90
c = 561.202	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data collection
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: 2016-05-25

Deposition Author(s):

Xu, K.

Zhou, T.

Kwong, P.D.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	--

Revision History (Full details and data files)

Version 1.0: 2016-05-25
Type: Initial release
Version 1.1: 2016-06-01
Changes: Derived calculations
Version 1.2: 2017-09-20
Changes: Author supporting evidence, Derived calculations
Version 1.3: 2019-12-11
Changes: Author supporting evidence
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, 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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5I8H

Crystal Structure of HIV-1 BG505 SOSIP.664 Prefusion Env Trimer in Complex with V3 Loop-targeting Antibody PGT122 Fab and Fusion Peptide-targeting Antibody VRC34.01 Fab

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UniProt

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Entity ID: 2

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Entity ID: 6

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Entity ID: 7

Glycosylation Resources

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Glycosylation Resources

Entity ID: 9

Glycosylation Resources

Entity ID: 10

Glycosylation Resources

Entity ID: 11

Glycosylation Resources

Entity ID: 12

Glycosylation Resources

Entity ID: 13

Glycosylation Resources

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)