6MEO

Structural basis of coreceptor recognition by HIV-1 envelope spike


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.9 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural basis of coreceptor recognition by HIV-1 envelope spike.

Shaik, M.M.Peng, H.Lu, J.Rits-Volloch, S.Xu, C.Liao, M.Chen, B.

(2018) Nature 565: 318-323

  • DOI: 10.1038/s41586-018-0804-9
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • HIV-1 envelope glycoprotein (Env), which consists of trimeric (gp160) <sub>3 </sub> cleaved to (gp120 and gp41) <sub>3 </sub>, interacts with the primary receptor CD4 and a coreceptor (such as chemokine receptor CCR5) to fuse viral and target-cell me ...

    HIV-1 envelope glycoprotein (Env), which consists of trimeric (gp160) 3 cleaved to (gp120 and gp41) 3 , interacts with the primary receptor CD4 and a coreceptor (such as chemokine receptor CCR5) to fuse viral and target-cell membranes. The gp120-coreceptor interaction has previously been proposed as the most crucial trigger for unleashing the fusogenic potential of gp41. Here we report a cryo-electron microscopy structure of a full-length gp120 in complex with soluble CD4 and unmodified human CCR5, at 3.9 Å resolution. The V3 loop of gp120 inserts into the chemokine-binding pocket formed by seven transmembrane helices of CCR5, and the N terminus of CCR5 contacts the CD4-induced bridging sheet of gp120. CCR5 induces no obvious allosteric changes in gp120 that can propagate to gp41; it does bring the Env trimer close to the target membrane. The N terminus of gp120, which is gripped by gp41 in the pre-fusion or CD4-bound Env, flips back in the CCR5-bound conformation and may irreversibly destabilize gp41 to initiate fusion. The coreceptor probably functions by stabilizing and anchoring the CD4-induced conformation of Env near the cell membrane. These results advance our understanding of HIV-1 entry into host cells and may guide the development of vaccines and therapeutic agents.


    Organizational Affiliation

    Department of Cell Biology, Harvard Medical School, Boston, MA, USA.,Cryo-EM Core Facility, University of Massachusetts Medical School, Worcester, MA, USA.,Division of Molecular Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA. bchen@crystal.harvard.edu.,Codex BioSolutions, Gaithersburg, MD, USA.,Xiamen Amoytop Biotech, Xiamen, China.,Division of Molecular Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.,Department of Pediatrics, Harvard Medical School, Boston, MA, USA.,Department of Pediatrics, Harvard Medical School, Boston, MA, USA. bchen@crystal.harvard.edu.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Envelope glycoprotein gp160
G
461Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: env
Find proteins for Q70145 (Human immunodeficiency virus 1)
Go to UniProtKB:  Q70145
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
T-cell surface glycoprotein CD4
A
176Homo sapiensMutation(s): 0 
Gene Names: CD4
Find proteins for P01730 (Homo sapiens)
Go to Gene View: CD4
Go to UniProtKB:  P01730
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
C-C chemokine receptor type 5
B
313Homo sapiensMutation(s): 0 
Gene Names: CCR5 (CMKBR5)
Find proteins for P51681 (Homo sapiens)
Go to Gene View: CCR5
Go to UniProtKB:  P51681
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MAN
Query on MAN

Download SDF File 
Download CCD File 
G
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
BMA
Query on BMA

Download SDF File 
Download CCD File 
G
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
A2G
Query on A2G

Download SDF File 
Download CCD File 
B
N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE
C8 H15 N O6
OVRNDRQMDRJTHS-CBQIKETKSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
G
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
TYS
Query on TYS
B
L-PEPTIDE LINKINGC9 H11 N O6 STYR
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.9 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2018-09-06 
  • Released Date: 2018-12-12 
  • Deposition Author(s): Shaik, M.M., Chen, B.

Funding OrganizationLocationGrant Number
National Institutes of Health/National Human Genome Research InstituteUnited StatesAI141002

Revision History 

  • Version 1.0: 2018-12-12
    Type: Initial release
  • Version 1.1: 2018-12-26
    Type: Data collection, Database references
  • Version 1.2: 2019-01-16
    Type: Data collection, Database references