6MET
Structural basis of coreceptor recognition by HIV-1 envelope spike
- PDB DOI: https://doi.org/10.2210/pdb6MET/pdb
- EM Map EMD-9109: EMDB EMDataResource
- Classification: MEMBRANE PROTEIN
- Organism(s): Human immunodeficiency virus 1, Homo sapiens
- Expression System: Homo sapiens
- Mutation(s): No 
- Membrane Protein: Yes  PDBTMMemProtMD
- Deposited: 2018-09-07 Released: 2018-12-12 
- Funding Organization(s): National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)
Experimental Data Snapshot
- Method: ELECTRON MICROSCOPY
- Resolution: 4.50 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 gp160 | A [auth G] | 461 | Human immunodeficiency virus 1 | Mutation(s): 0  Gene Names: env Membrane Entity: Yes  | |
UniProt | |||||
Find proteins for Q70145 (Human immunodeficiency virus 1) Explore Q70145  Go to UniProtKB:  Q70145 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | Q70145 | ||||
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 |
T-cell surface glycoprotein CD4 | B [auth A] | 363 | Homo sapiens | Mutation(s): 0  Gene Names: CD4 Membrane Entity: Yes  | |
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 AnnotationsExpand | |||||
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Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 3 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
C-C chemokine receptor type 5 | C [auth B] | 313 | Homo sapiens | Mutation(s): 0  Gene Names: CCR5, CMKBR5 Membrane Entity: Yes  | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P51681 (Homo sapiens) Explore P51681  Go to UniProtKB:  P51681 | |||||
PHAROS:  P51681 GTEx:  ENSG00000160791  | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P51681 | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
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 | D [auth C], G [auth F], H, I, K, D [auth C], G [auth F], H, I, K, L | 2 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT |
Entity ID: 5 | |||||
---|---|---|---|---|---|
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 | E [auth D], J | 3 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G15407YE GlyCosmos:  G15407YE GlyGen:  G15407YE |
Entity ID: 6 | |||||
---|---|---|---|---|---|
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 | F [auth E] | 6 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G56014GC GlyCosmos:  G56014GC GlyGen:  G56014GC |
Small Molecules
Ligands 2 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
A2G Query on A2G | T [auth B] | 2-acetamido-2-deoxy-alpha-D-galactopyranose C8 H15 N O6 OVRNDRQMDRJTHS-CBQIKETKSA-N | |||
NAG Query on NAG | M [auth G] N [auth G] O [auth G] P [auth G] Q [auth G] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N |
Modified Residues 1 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Type | Formula | 2D Diagram | Parent |
TYS Query on TYS | C [auth B] | L-PEPTIDE LINKING | C9 H11 N O6 S | TYR |
Experimental Data & Validation
Experimental Data
- Method: ELECTRON MICROSCOPY
- Resolution: 4.50 Å
- Aggregation State: PARTICLE 
- Reconstruction Method: SINGLE PARTICLE 
Task | Software Package | Version |
---|---|---|
MODEL REFINEMENT | PHENIX | |
RECONSTRUCTION | RELION | 2.1 |
Entry History & Funding Information
Deposition Data
- Released Date: 2018-12-12  Deposition Author(s): Shaik, M.M., Chen, B.
Funding Organization | Location | Grant Number |
---|---|---|
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI) | United States | AI141002 |
Revision History (Full details and data files)
- Version 1.0: 2018-12-12
Type: Initial release - Version 1.1: 2018-12-26
Changes: Data collection, Database references - Version 1.2: 2019-01-16
Changes: Data collection, Database references - Version 1.3: 2019-12-18
Changes: Author supporting evidence, Data collection - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary