6CH7

XFEL crystal structure of a natively-glycosylated BG505 SOSIP.664 HIV-1 Envelope Trimer in complex with the broadly-neutralizing antibodies BG18 and 35O22

PDB DOI: https://doi.org/10.2210/pdb6CH7/pdb

Classification: IMMUNE SYSTEM
Organism(s): Human immunodeficiency virus 1, Homo sapiens
Expression System: Cricetulus griseus, Homo sapiens
Mutation(s): Yes

Deposited: 2018-02-22 Released: 2018-05-02
Deposition Author(s): Barnes, C.O., Bjorkman, P.J.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), Bill & Melinda Gates Foundation, National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.80 Å
R-Value Free: 0.262
R-Value Work: 0.232
R-Value Observed: 0.234

wwPDB Validation 3D Report Full Report

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

Macromolecule Content

Total Structure Weight: 184.32 kDa
Atom Count: 12,160
Modelled Residue Count: 1,467
Deposited Residue Count: 1,547
Unique protein chains: 6

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein gp41	A [auth B]	153	Human immunodeficiency virus 1	Mutation(s): 1 Gene Names: env
UniProt
Find proteins for Q2N0S5 (Human immunodeficiency virus 1) Explore Q2N0S5 Go to UniProtKB: Q2N0S5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q2N0S5
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Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
35O22 Heavy Chain	B [auth D]	243	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
35O22 Light Chain	C [auth E]	216	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
Envelope glycoprotein gp120	D [auth G]	479	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
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
BG18 Heavy Chain	E [auth Q]	241	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
BG18 Light Chain	F [auth R]	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
alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	G [auth A]	5		N-Glycosylation	Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
Glycosylation Resources
GlyTouCan: G00395TQ GlyCosmos: G00395TQ GlyGen: G00395TQ

Entity ID: 8
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	H [auth C]	8		N-Glycosylation	Interactions Focus chain H [auth C] Interactions & Density Focus chain H [auth C]
Glycosylation Resources
GlyTouCan: G61334IA GlyCosmos: G61334IA GlyGen: G61334IA

Entity ID: 9
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(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)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	I [auth F]	8		N-Glycosylation	Interactions Focus chain I [auth F] Interactions & Density Focus chain I [auth F]
Glycosylation Resources
GlyTouCan: G17140UR GlyCosmos: G17140UR GlyGen: G17140UR

Entity ID: 10
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 H], L [auth J], O [auth M]	3		N-Glycosylation	Interactions Focus chain J [auth H] Focus chain L [auth J] Focus chain O [auth M] Interactions & Density Focus chain J [auth H] Focus chain L [auth J] Focus chain O [auth M]
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Entity ID: 11
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	K [auth I]	4		N-Glycosylation	Interactions Focus chain K [auth I] Interactions & Density Focus chain K [auth I]
Glycosylation Resources
GlyTouCan: G22573RC GlyCosmos: G22573RC GlyGen: G22573RC

Entity ID: 12
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
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	M [auth K]	7		N-Glycosylation	Interactions Focus chain M [auth K] Interactions & Density Focus chain M [auth K]
Glycosylation Resources
GlyTouCan: G84881ST GlyCosmos: G84881ST GlyGen: G84881ST

Entity ID: 13
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
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	N [auth L]	6		N-Glycosylation	Interactions Focus chain N [auth L] Interactions & Density Focus chain N [auth L]
Glycosylation Resources
GlyTouCan: G34442SS GlyCosmos: G34442SS GlyGen: G34442SS

Entity ID: 14
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	P [auth N]	2		N-Glycosylation	Interactions Focus chain P [auth N] Interactions & Density Focus chain P [auth N]
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 15
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	Q [auth O]	7		N-Glycosylation	Interactions Focus chain Q [auth O] Interactions & Density Focus chain Q [auth O]
Glycosylation Resources
GlyTouCan: G55220VL GlyCosmos: G55220VL GlyGen: G55220VL

Entity ID: 16
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-6)-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	R [auth P]	7		N-Glycosylation	Interactions Focus chain R [auth P] Interactions & Density Focus chain R [auth P]
Glycosylation Resources
GlyTouCan: G51771NH GlyCosmos: G51771NH GlyGen: G51771NH

Entity ID: 17
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-2)-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	S	6		N-Glycosylation	Interactions Focus chain S Interactions & Density Focus chain S
Glycosylation Resources
GlyTouCan: G60415BS GlyCosmos: G60415BS GlyGen: G60415BS

Entity ID: 18
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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	T	9		N-Glycosylation	Interactions Focus chain T Interactions & Density Focus chain T
Glycosylation Resources
GlyTouCan: G64261IK GlyCosmos: G64261IK GlyGen: G64261IK

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.80 Å
R-Value Free: 0.262
R-Value Work: 0.232
R-Value Observed: 0.234
Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 238.944	α = 90
b = 238.944	β = 90
c = 354.014	γ = 120

Software Package:

Software Name	Purpose
BUSTER	refinement
cctbx.xfel	data reduction
cctbx.prime	data scaling
PHASER	phasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Released Date: 2018-05-02

Deposition Author(s):

Barnes, C.O.

Bjorkman, P.J.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	P01 AI100148
Bill & Melinda Gates Foundation	United States	OPP1124068
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	P41GM103393

Revision History (Full details and data files)

Version 1.0: 2018-05-02
Type: Initial release
Version 1.1: 2018-11-28
Changes: Data collection
Version 1.2: 2019-02-20
Changes: Author supporting evidence, Data collection
Version 1.3: 2019-12-18
Changes: Author supporting evidence, Data collection
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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6CH7

XFEL crystal structure of a natively-glycosylated BG505 SOSIP.664 HIV-1 Envelope Trimer in complex with the broadly-neutralizing antibodies BG18 and 35O22

Entity ID: 1

UniProt

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Glycosylation Resources

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Glycosylation Resources

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Glycosylation Resources

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Glycosylation Resources

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Glycosylation Resources

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Glycosylation Resources

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Glycosylation Resources

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Glycosylation Resources

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Glycosylation Resources

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Glycosylation Resources

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Glycosylation Resources

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Glycosylation Resources

Experimental Data

Structure Validation

Deposition Data

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