6OPN

CD4- and 17-bound HIV-1 Env B41 SOSIP in complex with small molecule GO35

PDB DOI: https://doi.org/10.2210/pdb6OPN/pdb
EM Map EMD-20150: EMDB EMDataResource

Classification: VIRAL PROTEIN/Immune System
Organism(s): Human immunodeficiency virus 1, Homo sapiens
Expression System: Homo sapiens
Mutation(s): Yes

Deposited: 2019-04-25 Released: 2020-10-21
Deposition Author(s): Ozorowski, G., Torres, J.L., Ward, A.B.
Funding Organization(s): Other private, National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.50 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 308.83 kDa
Atom Count: 14,241
Modelled Residue Count: 1,713
Deposited Residue Count: 2,655
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein gp160	A, D, G	524	Human immunodeficiency virus 1	Mutation(s): 5 Gene Names: env
UniProt
Find proteins for B3UES2 (Human immunodeficiency virus 1) Explore B3UES2 Go to UniProtKB: B3UES2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	B3UES2
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein gp41	B, E, H	153	Human immunodeficiency virus 1	Mutation(s): 2 Gene Names: env
UniProt
Find proteins for B3UEZ6 (Human immunodeficiency virus 1) Explore B3UEZ6 Go to UniProtKB: B3UEZ6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	B3UEZ6
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
T-cell surface glycoprotein CD4	C, F, I	208	Homo sapiens	Mutation(s): 0 Gene Names: CD4
UniProt & NIH Common Fund Data Resources
Find proteins for P01730 (Homo sapiens) Explore P01730 Go to UniProtKB: P01730
PHAROS: P01730 GTEx: ENSG00000010610
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P01730
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	J, L, N	2		N-Glycosylation	Interactions Focus chain J Focus chain L Focus chain N Interactions & Density Focus chain J Focus chain L Focus chain N
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
N07 (Subject of Investigation/LOI) Query on N07 Download Ideal Coordinates CCD File SDF format, chain IA [auth E] SDF format, chain SA [auth H] SDF format, chain Y [auth B] MOL2 format, chain IA [auth E] MOL2 format, chain SA [auth H] MOL2 format, chain Y [auth B]	IA [auth E], SA [auth H], Y [auth B]	[3'-(5-methyl-1,3,4-oxadiazol-2-yl)[1,1'-biphenyl]-3-yl](piperidin-1-yl)methanone C₂₁ H₂₁ N₃ O₂ IKHAJTCUSZHKAO-UHFFFAOYSA-N		Interactions Focus chain IA [auth E] Focus chain SA [auth H] Focus chain Y [auth B] Interactions & Density Focus chain IA [auth E] Focus chain SA [auth H] Focus chain Y [auth B]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain BA [auth D] SDF format, chain EA [auth D] SDF format, chain FA [auth D] SDF format, chain GA [auth D] SDF format, chain LA [auth G] SDF format, chain MA [auth G] SDF format, chain NA [auth G] SDF format, chain P [auth A] SDF format, chain R [auth A] SDF format, chain S [auth A] SDF format, chain T [auth A] SDF format, chain V [auth A] SDF format, chain W [auth A] SDF format, chain AA [auth D] SDF format, chain CA [auth D] SDF format, chain DA [auth D] SDF format, chain HA [auth D] SDF format, chain JA [auth G] SDF format, chain KA [auth G] SDF format, chain OA [auth G] SDF format, chain PA [auth G] SDF format, chain Q [auth A] SDF format, chain QA [auth G] SDF format, chain RA [auth G] SDF format, chain U [auth A] SDF format, chain X [auth A] SDF format, chain Z [auth D] MOL2 format, chain BA [auth D] MOL2 format, chain EA [auth D] MOL2 format, chain FA [auth D] MOL2 format, chain GA [auth D] MOL2 format, chain LA [auth G] MOL2 format, chain MA [auth G] MOL2 format, chain NA [auth G] MOL2 format, chain P [auth A] MOL2 format, chain R [auth A] MOL2 format, chain S [auth A] MOL2 format, chain T [auth A] MOL2 format, chain V [auth A] MOL2 format, chain W [auth A] MOL2 format, chain AA [auth D] MOL2 format, chain CA [auth D] MOL2 format, chain DA [auth D] MOL2 format, chain HA [auth D] MOL2 format, chain JA [auth G] MOL2 format, chain KA [auth G] MOL2 format, chain OA [auth G] MOL2 format, chain PA [auth G] MOL2 format, chain Q [auth A] MOL2 format, chain QA [auth G] MOL2 format, chain RA [auth G] MOL2 format, chain U [auth A] MOL2 format, chain X [auth A] MOL2 format, chain Z [auth D]	AA [auth D] BA [auth D] CA [auth D] DA [auth D] EA [auth D] AA [auth D], BA [auth D], CA [auth D], DA [auth D], EA [auth D], FA [auth D], GA [auth D], HA [auth D], JA [auth G], KA [auth G], LA [auth G], MA [auth G], NA [auth G], OA [auth G], P [auth A], PA [auth G], Q [auth A], QA [auth G], R [auth A], RA [auth G], S [auth A], T [auth A], U [auth A], V [auth A], W [auth A], X [auth A], Z [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth D] Focus chain BA [auth D] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain EA [auth D] Focus chain FA [auth D] Focus chain GA [auth D] Focus chain HA [auth D] Focus chain JA [auth G] Focus chain KA [auth G] Focus chain LA [auth G] Focus chain MA [auth G] Focus chain NA [auth G] Focus chain OA [auth G] Focus chain P [auth A] Focus chain PA [auth G] Focus chain Q [auth A] Focus chain QA [auth G] Focus chain R [auth A] Focus chain RA [auth G] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth A] Focus chain X [auth A] Focus chain Z [auth D] Interactions & Density Focus chain AA [auth D] Focus chain BA [auth D] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain EA [auth D] Focus chain FA [auth D] Focus chain GA [auth D] Focus chain HA [auth D] Focus chain JA [auth G] Focus chain KA [auth G] Focus chain LA [auth G] Focus chain MA [auth G] Focus chain NA [auth G] Focus chain OA [auth G] Focus chain P [auth A] Focus chain PA [auth G] Focus chain Q [auth A] Focus chain QA [auth G] Focus chain R [auth A] Focus chain RA [auth G] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth A] Focus chain X [auth A] Focus chain Z [auth D]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.50 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	2
MODEL REFINEMENT	Rosetta	3.10
MODEL REFINEMENT	Coot	0.9-pre

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2020-10-21

Deposition Author(s):

Ozorowski, G.

Torres, J.L.

Ward, A.B.

Funding Organization	Location	Grant Number
Other private	United States	109718-63-RKNT
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01GM069832