6OPO

Symmetric model of CD4- and 17-bound B41 HIV-1 Env SOSIP in complex with DDM

PDB DOI: https://doi.org/10.2210/pdb6OPO/pdb
EM Map EMD-20151: 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), Bill & Melinda Gates Foundation

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: 461.73 kDa
Atom Count: 21,441
Modelled Residue Count: 2,565
Deposited Residue Count: 3,984
Unique protein chains: 5

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein gp160	A, F [auth D], K [auth J]	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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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
17b Fab light chain	B [auth L], G [auth E], L [auth K]	214	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein gp41	C [auth B], H [auth F], M	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

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
T-cell surface glycoprotein CD4	D [auth C], I [auth G], N	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
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
17b Fab heavy chain	E [auth H], J [auth I], O	229	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: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	AA [auth a], CA [auth c], DA [auth d], EA [auth e], FA [auth f], AA [auth a], CA [auth c], DA [auth d], EA [auth e], FA [auth f], GA [auth g], HA [auth h], JA [auth j], KA [auth k], MA [auth m], NA [auth n], OA [auth o], P, PA [auth p], Q, QA [auth q], RA [auth r], S, T, U, V, W, X, Z	2		N-Glycosylation	Interactions Focus chain AA [auth a] Focus chain CA [auth c] Focus chain DA [auth d] Focus chain EA [auth e] Focus chain FA [auth f] Focus chain GA [auth g] Focus chain HA [auth h] Focus chain JA [auth j] Focus chain KA [auth k] Focus chain MA [auth m] Focus chain NA [auth n] Focus chain OA [auth o] Focus chain P Focus chain PA [auth p] Focus chain Q Focus chain QA [auth q] Focus chain RA [auth r] Focus chain S Focus chain T Focus chain U Focus chain V Focus chain W Focus chain X Focus chain Z Interactions & Density Focus chain AA [auth a] Focus chain CA [auth c] Focus chain DA [auth d] Focus chain EA [auth e] Focus chain FA [auth f] Focus chain GA [auth g] Focus chain HA [auth h] Focus chain JA [auth j] Focus chain KA [auth k] Focus chain MA [auth m] Focus chain NA [auth n] Focus chain OA [auth o] Focus chain P Focus chain PA [auth p] Focus chain Q Focus chain QA [auth q] Focus chain RA [auth r] Focus chain S Focus chain T Focus chain U Focus chain V Focus chain W Focus chain X Focus chain Z
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 7
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	BA [auth b], LA [auth l], R	5		N-Glycosylation	Interactions Focus chain BA [auth b] Focus chain LA [auth l] Focus chain R Interactions & Density Focus chain BA [auth b] Focus chain LA [auth l] Focus chain R
Glycosylation Resources
GlyTouCan: G42227JK GlyCosmos: G42227JK GlyGen: G42227JK

Entity ID: 8
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	IA [auth i], SA [auth s], Y	3		N-Glycosylation	Interactions Focus chain IA [auth i] Focus chain SA [auth s] Focus chain Y Interactions & Density Focus chain IA [auth i] Focus chain SA [auth s] Focus chain Y
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
LMT (Subject of Investigation/LOI) Query on LMT Download Ideal Coordinates CCD File SDF format, chain EB [auth F] SDF format, chain LB [auth M] SDF format, chain XA [auth B] MOL2 format, chain EB [auth F] MOL2 format, chain LB [auth M] MOL2 format, chain XA [auth B]	EB [auth F], LB [auth M], XA [auth B]	DODECYL-BETA-D-MALTOSIDE C₂₄ H₄₆ O₁₁ NLEBIOOXCVAHBD-QKMCSOCLSA-N		Interactions Focus chain EB [auth F] Focus chain LB [auth M] Focus chain XA [auth B] Interactions & Density Focus chain EB [auth F] Focus chain LB [auth M] Focus chain XA [auth B]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain AB [auth D] SDF format, chain BB [auth D] SDF format, chain CB [auth D] SDF format, chain DB [auth D] SDF format, chain FB [auth F] SDF format, chain GB [auth F] SDF format, chain HB [auth J] SDF format, chain IB [auth J] SDF format, chain JB [auth J] SDF format, chain KB [auth J] SDF format, chain MB [auth M] SDF format, chain NB [auth M] SDF format, chain TA [auth A] SDF format, chain UA [auth A] SDF format, chain VA [auth A] SDF format, chain WA [auth A] SDF format, chain YA [auth B] SDF format, chain ZA [auth B] MOL2 format, chain AB [auth D] MOL2 format, chain BB [auth D] MOL2 format, chain CB [auth D] MOL2 format, chain DB [auth D] MOL2 format, chain FB [auth F] MOL2 format, chain GB [auth F] MOL2 format, chain HB [auth J] MOL2 format, chain IB [auth J] MOL2 format, chain JB [auth J] MOL2 format, chain KB [auth J] MOL2 format, chain MB [auth M] MOL2 format, chain NB [auth M] MOL2 format, chain TA [auth A] MOL2 format, chain UA [auth A] MOL2 format, chain VA [auth A] MOL2 format, chain WA [auth A] MOL2 format, chain YA [auth B] MOL2 format, chain ZA [auth B]	AB [auth D] BB [auth D] CB [auth D] DB [auth D] FB [auth F] AB [auth D], BB [auth D], CB [auth D], DB [auth D], FB [auth F], GB [auth F], HB [auth J], IB [auth J], JB [auth J], KB [auth J], MB [auth M], NB [auth M], TA [auth A], UA [auth A], VA [auth A], WA [auth A], YA [auth B], ZA [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AB [auth D] Focus chain BB [auth D] Focus chain CB [auth D] Focus chain DB [auth D] Focus chain FB [auth F] Focus chain GB [auth F] Focus chain HB [auth J] Focus chain IB [auth J] Focus chain JB [auth J] Focus chain KB [auth J] Focus chain MB [auth M] Focus chain NB [auth M] Focus chain TA [auth A] Focus chain UA [auth A] Focus chain VA [auth A] Focus chain WA [auth A] Focus chain YA [auth B] Focus chain ZA [auth B] Interactions & Density Focus chain AB [auth D] Focus chain BB [auth D] Focus chain CB [auth D] Focus chain DB [auth D] Focus chain FB [auth F] Focus chain GB [auth F] Focus chain HB [auth J] Focus chain IB [auth J] Focus chain JB [auth J] Focus chain KB [auth J] Focus chain MB [auth M] Focus chain NB [auth M] Focus chain TA [auth A] Focus chain UA [auth A] Focus chain VA [auth A] Focus chain WA [auth A] Focus chain YA [auth B] Focus chain ZA [auth B]

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
MODEL REFINEMENT	Rosetta	3.10
MODEL REFINEMENT	Coot	0.9-pre
RECONSTRUCTION	cryoSPARC	2

Structure Validation

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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
Bill & Melinda Gates Foundation	United States	OPP1115782

Revision History (Full details and data files)

Version 1.0: 2020-10-21
Type: Initial release
Version 1.1: 2020-12-09
Changes: Database references

Prepare Data

Validate Data

Deposit Data

Help and Resources

6OPO

Symmetric model of CD4- and 17-bound B41 HIV-1 Env SOSIP in complex with DDM

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Entity ID: 2

Entity Groups

Sequence Annotations

Expand

Entity ID: 3

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 4

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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Entity ID: 5

Entity Groups

Sequence Annotations

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Entity ID: 6

Glycosylation Resources

Entity ID: 7

Glycosylation Resources

Entity ID: 8

Glycosylation Resources

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)