6CH8

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/pdb6CH8/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: 4.10 Å
R-Value Free: 0.274
R-Value Work: 0.229
R-Value Observed: 0.231

wwPDB Validation 3D Report Full Report

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

Macromolecule Content

Total Structure Weight: 186.61 kDa
Atom Count: 12,325
Modelled Residue Count: 1,474
Deposited Residue Count: 1,547
Unique protein chains: 6

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
35O22 Heavy Chain	B [auth D]	243	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
35O22 Light Chain	C [auth E]	216	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein gp120	D [auth G]	479	Human immunodeficiency virus 1	Mutation(s): 1 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

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
BG18 Heavy Chain	E [auth Q]	241	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 7
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	G [auth A], Q [auth O]	3		N-Glycosylation	Interactions Focus chain G [auth A] Focus chain Q [auth O] Interactions & Density Focus chain G [auth A] Focus chain Q [auth O]
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Entity ID: 8
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
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 C], L [auth J]	5		N-Glycosylation	Interactions Focus chain H [auth C] Focus chain L [auth J] Interactions & Density Focus chain H [auth C] Focus chain L [auth J]
Glycosylation Resources
GlyTouCan: G94626GC GlyCosmos: G94626GC GlyGen: G94626GC

Entity ID: 9
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-6)-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	I [auth F]	7		N-Glycosylation	Interactions Focus chain I [auth F] Interactions & Density Focus chain I [auth F]
Glycosylation Resources
GlyTouCan: G27658GQ GlyCosmos: G27658GQ GlyGen: G27658GQ

Entity ID: 10
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	J [auth H], U	5		N-Glycosylation	Interactions Focus chain J [auth H] Focus chain U Interactions & Density Focus chain J [auth H] Focus chain U
Glycosylation Resources
GlyTouCan: G22768VO GlyCosmos: G22768VO GlyGen: G22768VO

Entity ID: 11
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-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	K [auth I]	7		N-Glycosylation	Interactions Focus chain K [auth I] Interactions & Density Focus chain K [auth I]
Glycosylation Resources
GlyTouCan: G89970AS GlyCosmos: G89970AS GlyGen: G89970AS

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 K], T	4		N-Glycosylation	Interactions Focus chain M [auth K] Focus chain T Interactions & Density Focus chain M [auth K] Focus chain T
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	N [auth L]	4		N-Glycosylation	Interactions Focus chain N [auth L] Interactions & Density Focus chain N [auth L]
Glycosylation Resources
GlyTouCan: G22573RC GlyCosmos: G22573RC GlyGen: G22573RC

Entity ID: 14
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	O [auth M]	7		N-Glycosylation	Interactions Focus chain O [auth M] Interactions & Density Focus chain O [auth M]
Glycosylation Resources
GlyTouCan: G55220VL GlyCosmos: G55220VL GlyGen: G55220VL

Entity ID: 15
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-(1-6)-[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	P [auth N]	8		N/A	Interactions Focus chain P [auth N] Interactions & Density Focus chain P [auth N]
Glycosylation Resources
GlyTouCan: G89353OJ GlyCosmos: G89353OJ GlyGen: G89353OJ

Entity ID: 16
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	R [auth P]	6		N-Glycosylation	Interactions Focus chain R [auth P] Interactions & Density Focus chain R [auth P]
Glycosylation Resources
GlyTouCan: G34442SS GlyCosmos: G34442SS GlyGen: G34442SS

Entity ID: 17
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	S	8		N/A	Interactions Focus chain S Interactions & Density Focus chain S
Glycosylation Resources
GlyTouCan: G80966KZ GlyCosmos: G80966KZ GlyGen: G80966KZ

Entity ID: 18
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[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	V	9		N-Glycosylation	Interactions Focus chain V Interactions & Density Focus chain V
Glycosylation Resources
GlyTouCan: G96715HA GlyCosmos: G96715HA GlyGen: G96715HA

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 W [auth B] SDF format, chain X [auth G] SDF format, chain Y [auth G] SDF format, chain Z [auth G] MOL2 format, chain W [auth B] MOL2 format, chain X [auth G] MOL2 format, chain Y [auth G] MOL2 format, chain Z [auth G]	W [auth B], 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 W [auth B] Focus chain X [auth G] Focus chain Y [auth G] Focus chain Z [auth G] Interactions & Density Focus chain W [auth B] 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: 4.10 Å
R-Value Free: 0.274
R-Value Work: 0.229
R-Value Observed: 0.231
Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 239.223	α = 90
b = 239.223	β = 90
c = 355.266	γ = 120

Software Package:

Software Name	Purpose
BUSTER	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

View Full Validation Report

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: 2019-02-20
Changes: Author supporting evidence, Data collection
Version 1.2: 2019-12-18
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
Version 2.1: 2023-10-04
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.

Prepare Data

Validate Data

Deposit Data

Help and Resources

6CH8

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

Entity Groups

Sequence Annotations

Expand

Entity ID: 2

Entity Groups

Sequence Annotations

Expand

Entity ID: 3

Entity Groups

Sequence Annotations

Expand

Entity ID: 4

UniProt

Entity Groups

Sequence Annotations

Expand

Entity ID: 5

Entity Groups

Sequence Annotations

Expand

Entity ID: 6

Entity Groups

Sequence Annotations

Expand

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: 13

Glycosylation Resources

Entity ID: 14

Glycosylation Resources

Entity ID: 15

Glycosylation Resources

Entity ID: 16

Glycosylation Resources

Entity ID: 17

Glycosylation Resources

Entity ID: 18

Glycosylation Resources

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)