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 
- 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. 
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Envelope glycoprotein gp41 | 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 AnnotationsExpand | |||||
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Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Envelope glycoprotein gp120 | 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 | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by:
(by identity cutoff) | 3D Structure
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 AnnotationsExpand | |||||
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Find similar proteins by:
(by identity cutoff) | 3D Structure
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 | ||||
Sequence AnnotationsExpand | |||||
|
Find similar proteins by:
(by identity cutoff) | 3D Structure
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 AnnotationsExpand | |||||
|
Find similar proteins by:
(by identity cutoff) | 3D Structure
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 AnnotationsExpand | |||||
|
Oligosaccharides
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 | ||
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 | ||
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 | ||
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 | ||
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 | ||
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 | ||
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 | ||
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 | AB [auth D] BB [auth D] CB [auth D] DB [auth D] EB [auth D] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N |
Experimental Data & Validation
Experimental Data
- Method: ELECTRON MICROSCOPY
- Resolution: 3.28 Å
- Aggregation State: PARTICLE 
- Reconstruction Method: SINGLE PARTICLE 
Task | Software Package | Version |
---|---|---|
RECONSTRUCTION | RELION | 3.0 |
MODEL REFINEMENT | PHENIX | 1.14 |
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