6OKP

B41 SOSIP.664 in complex with the silent-face antibody SF12 and V3-targeting antibody 10-1074

PDB DOI: https://doi.org/10.2210/pdb6OKP/pdb
EM Map EMD-20100: EMDB EMDataResource

Classification: VIRAL PROTEIN/IMMUNE SYSTEM
Organism(s): Human immunodeficiency virus 1, Homo sapiens
Expression System: Cricetulus griseus, Homo sapiens
Mutation(s): No

Deposited: 2019-04-14 Released: 2019-06-05
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), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.28 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

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

Macromolecule Content

Total Structure Weight: 453.21 kDa
Atom Count: 22,857
Modelled Residue Count: 2,660
Deposited Residue Count: 3,824
Unique protein chains: 6

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein gp41	A, B, C	153	Human immunodeficiency virus 1	Mutation(s): 0 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: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein gp120	D, E, F	516	Human immunodeficiency virus 1	Mutation(s): 0 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
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Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
10-1074 Heavy Chain,10-1074 Heavy Chain	G [auth K]	244	Homo sapiens	Mutation(s): 0
UniProt
Find proteins for S6B291 (Homo sapiens) Explore S6B291 Go to UniProtKB: S6B291
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	S6B291
Sequence Annotations Expand
Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
10-1074 Light Chain,10-1074 Light Chain	H [auth L]	214	Homo sapiens	Mutation(s): 0
UniProt
Find proteins for Q8N5F4 (Homo sapiens) Explore Q8N5F4 Go to UniProtKB: Q8N5F4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8N5F4
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
SF12 Heavy Chain,SF12 Heavy Chain	I [auth M], K [auth O], M [auth Q]	241	Homo sapiens	Mutation(s): 0
UniProt
Find proteins for S6B291 (Homo sapiens) Explore S6B291 Go to UniProtKB: S6B291
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	S6B291
Sequence Annotations Expand
Reference Sequence

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
SF12 Light Chain,SF12 Light Chain	J [auth N], L [auth P], N [auth R]	212	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P01834 (Homo sapiens) Explore P01834 Go to UniProtKB: P01834
PHAROS: P01834
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P01834
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 7
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-2)-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	O [auth G]	8		N-Glycosylation	Interactions Focus chain O [auth G] Interactions & Density Focus chain O [auth G]
Glycosylation Resources
GlyTouCan: G80966KZ GlyCosmos: G80966KZ GlyGen: G80966KZ

Entity ID: 8
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-(1-3)-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 H], RA [auth r], SA [auth s]	9		N-Glycosylation	Interactions Focus chain P [auth H] Focus chain RA [auth r] Focus chain SA [auth s] Interactions & Density Focus chain P [auth H] Focus chain RA [auth r] Focus chain SA [auth s]
Glycosylation Resources
GlyTouCan: G52461YB GlyCosmos: G52461YB GlyGen: G52461YB

Entity ID: 9
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	IA [auth i], JA [auth j], Q [auth I], Z	7		N-Glycosylation	Interactions Focus chain IA [auth i] Focus chain JA [auth j] Focus chain Q [auth I] Focus chain Z Interactions & Density Focus chain IA [auth i] Focus chain JA [auth j] Focus chain Q [auth I] Focus chain Z
Glycosylation Resources
GlyTouCan: G55220VL GlyCosmos: G55220VL GlyGen: G55220VL

Entity ID: 10
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], DA [auth d], EA [auth e], FA [auth f], KA [auth k], BA [auth b], DA [auth d], EA [auth e], FA [auth f], KA [auth k], MA [auth m], OA [auth o], PA [auth p], QA [auth q], R [auth J], T, V, W, X, Y	2		N-Glycosylation	Interactions Focus chain BA [auth b] Focus chain DA [auth d] Focus chain EA [auth e] Focus chain FA [auth f] Focus chain KA [auth k] Focus chain MA [auth m] Focus chain OA [auth o] Focus chain PA [auth p] Focus chain QA [auth q] Focus chain R [auth J] Focus chain T Focus chain V Focus chain W Focus chain X Focus chain Y Interactions & Density Focus chain BA [auth b] Focus chain DA [auth d] Focus chain EA [auth e] Focus chain FA [auth f] Focus chain KA [auth k] Focus chain MA [auth m] Focus chain OA [auth o] Focus chain PA [auth p] Focus chain QA [auth q] Focus chain R [auth J] Focus chain T Focus chain V Focus chain W Focus chain X Focus chain Y
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

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	AA [auth a], CA [auth c], LA [auth l], NA [auth n], S, AA [auth a], CA [auth c], LA [auth l], NA [auth n], S, U	3		N-Glycosylation	Interactions Focus chain AA [auth a] Focus chain CA [auth c] Focus chain LA [auth l] Focus chain NA [auth n] Focus chain S Focus chain U Interactions & Density Focus chain AA [auth a] Focus chain CA [auth c] Focus chain LA [auth l] Focus chain NA [auth n] Focus chain S Focus chain U
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-(1-3)-[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	GA [auth g]	7		N-Glycosylation	Interactions Focus chain GA [auth g] Interactions & Density Focus chain GA [auth g]
Glycosylation Resources
GlyTouCan: G07617FP GlyCosmos: G07617FP GlyGen: G07617FP

Entity ID: 13
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	HA [auth h]	6		N-Glycosylation	Interactions Focus chain HA [auth h] Interactions & Density Focus chain HA [auth h]
Glycosylation Resources
GlyTouCan: G56014GC GlyCosmos: G56014GC GlyGen: G56014GC

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 D] SDF format, chain CB [auth D] SDF format, chain DB [auth D] SDF format, chain EB [auth D] SDF format, chain FB [auth D] SDF format, chain GB [auth D] SDF format, chain HB [auth D] SDF format, chain IB [auth E] SDF format, chain JB [auth E] SDF format, chain KB [auth E] SDF format, chain LB [auth E] SDF format, chain MB [auth E] SDF format, chain NB [auth E] SDF format, chain OB [auth E] SDF format, chain PB [auth E] SDF format, chain QB [auth E] SDF format, chain RB [auth F] SDF format, chain SB [auth F] SDF format, chain TA [auth A] SDF format, chain TB [auth F] SDF format, chain UA [auth A] SDF format, chain UB [auth F] SDF format, chain VA [auth B] SDF format, chain VB [auth F] SDF format, chain WA [auth B] SDF format, chain WB [auth F] SDF format, chain XA [auth C] SDF format, chain XB [auth F] SDF format, chain YA [auth C] SDF format, chain YB [auth F] SDF format, chain ZA [auth D] SDF format, chain ZB [auth F] 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 EB [auth D] MOL2 format, chain FB [auth D] MOL2 format, chain GB [auth D] MOL2 format, chain HB [auth D] MOL2 format, chain IB [auth E] MOL2 format, chain JB [auth E] MOL2 format, chain KB [auth E] MOL2 format, chain LB [auth E] MOL2 format, chain MB [auth E] MOL2 format, chain NB [auth E] MOL2 format, chain OB [auth E] MOL2 format, chain PB [auth E] MOL2 format, chain QB [auth E] MOL2 format, chain RB [auth F] MOL2 format, chain SB [auth F] MOL2 format, chain TA [auth A] MOL2 format, chain TB [auth F] MOL2 format, chain UA [auth A] MOL2 format, chain UB [auth F] MOL2 format, chain VA [auth B] MOL2 format, chain VB [auth F] MOL2 format, chain WA [auth B] MOL2 format, chain WB [auth F] MOL2 format, chain XA [auth C] MOL2 format, chain XB [auth F] MOL2 format, chain YA [auth C] MOL2 format, chain YB [auth F] MOL2 format, chain ZA [auth D] MOL2 format, chain ZB [auth F]	AB [auth D] BB [auth D] CB [auth D] DB [auth D] EB [auth D] AB [auth D], BB [auth D], CB [auth D], DB [auth D], EB [auth D], FB [auth D], GB [auth D], HB [auth D], IB [auth E], JB [auth E], KB [auth E], LB [auth E], MB [auth E], NB [auth E], OB [auth E], PB [auth E], QB [auth E], RB [auth F], SB [auth F], TA [auth A], TB [auth F], UA [auth A], UB [auth F], VA [auth B], VB [auth F], WA [auth B], WB [auth F], XA [auth C], XB [auth F], YA [auth C], YB [auth F], ZA [auth D], ZB [auth F]	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 EB [auth D] Focus chain FB [auth D] Focus chain GB [auth D] Focus chain HB [auth D] Focus chain IB [auth E] Focus chain JB [auth E] Focus chain KB [auth E] Focus chain LB [auth E] Focus chain MB [auth E] Focus chain NB [auth E] Focus chain OB [auth E] Focus chain PB [auth E] Focus chain QB [auth E] Focus chain RB [auth F] Focus chain SB [auth F] Focus chain TA [auth A] Focus chain TB [auth F] Focus chain UA [auth A] Focus chain UB [auth F] Focus chain VA [auth B] Focus chain VB [auth F] Focus chain WA [auth B] Focus chain WB [auth F] Focus chain XA [auth C] Focus chain XB [auth F] Focus chain YA [auth C] Focus chain YB [auth F] Focus chain ZA [auth D] Focus chain ZB [auth F] Interactions & Density Focus chain AB [auth D] Focus chain BB [auth D] Focus chain CB [auth D] Focus chain DB [auth D] Focus chain EB [auth D] Focus chain FB [auth D] Focus chain GB [auth D] Focus chain HB [auth D] Focus chain IB [auth E] Focus chain JB [auth E] Focus chain KB [auth E] Focus chain LB [auth E] Focus chain MB [auth E] Focus chain NB [auth E] Focus chain OB [auth E] Focus chain PB [auth E] Focus chain QB [auth E] Focus chain RB [auth F] Focus chain SB [auth F] Focus chain TA [auth A] Focus chain TB [auth F] Focus chain UA [auth A] Focus chain UB [auth F] Focus chain VA [auth B] Focus chain VB [auth F] Focus chain WA [auth B] Focus chain WB [auth F] Focus chain XA [auth C] Focus chain XB [auth F] Focus chain YA [auth C] Focus chain YB [auth F] Focus chain ZA [auth D] Focus chain ZB [auth F]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.28 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	3.0
MODEL REFINEMENT	PHENIX	1.14

Structure Validation

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Entry History & Funding Information

Deposition Data

Released Date: 2019-06-05

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
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	P50 GM082545-06

Revision History (Full details and data files)

Version 1.0: 2019-06-05
Type: Initial release
Version 1.1: 2019-07-03
Changes: Data collection, Database references
Version 1.2: 2019-12-18
Changes: Author supporting evidence, Other
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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Help and Resources

6OKP

B41 SOSIP.664 in complex with the silent-face antibody SF12 and V3-targeting antibody 10-1074

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 2

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 3

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 4

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 5

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 6

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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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

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)