5UIW

Crystal Structure of CC Chemokine Receptor 5 (CCR5) in complex with high potency HIV entry inhibitor 5P7-CCL5


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.204 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.216 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of CC Chemokine Receptor 5 with a Potent Chemokine Antagonist Reveals Mechanisms of Chemokine Recognition and Molecular Mimicry by HIV.

Zheng, Y.Han, G.W.Abagyan, R.Wu, B.Stevens, R.C.Cherezov, V.Kufareva, I.Handel, T.M.

(2017) Immunity 46: 1005-1017.e5

  • DOI: 10.1016/j.immuni.2017.05.002

  • PubMed Abstract: 
  • CCR5 is the primary chemokine receptor utilized by HIV to infect leukocytes, whereas CCR5 ligands inhibit infection by blocking CCR5 engagement with┬áHIV gp120. To guide the design of improved therapeutics, we solved the structure of CCR5 in complex w ...

    CCR5 is the primary chemokine receptor utilized by HIV to infect leukocytes, whereas CCR5 ligands inhibit infection by blocking CCR5 engagement with HIV gp120. To guide the design of improved therapeutics, we solved the structure of CCR5 in complex with chemokine antagonist [5P7]CCL5. Several structural features appeared to contribute to the anti-HIV potency of [5P7]CCL5, including the distinct chemokine orientation relative to the receptor, the near-complete occupancy of the receptor binding pocket, the dense network of intermolecular hydrogen bonds, and the similarity of binding determinants with the FDA-approved HIV inhibitor Maraviroc. Molecular modeling indicated that HIV gp120 mimicked the chemokine interaction with CCR5, providing an explanation for the ability of CCR5 to recognize diverse ligands and gp120 variants. Our findings reveal that structural plasticity facilitates receptor-chemokine specificity and enables exploitation by HIV, and provide insight into the design of small molecule and protein inhibitors for HIV and other CCR5-mediated diseases.


    Organizational Affiliation

    University of California, San Diego, Skaggs School of Pharmacy and Pharmaceutical Sciences, La Jolla, CA 92093, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
C-C chemokine receptor type 5,Rubredoxin chimera
A
411Homo sapiensClostridium pasteurianum
This entity is chimeric
Mutation(s): 4 
Gene Names: CCR5 (CMKBR5),
Find proteins for P51681 (Homo sapiens)
Go to Gene View: CCR5
Go to UniProtKB:  P51681
Find proteins for P00268 (Clostridium pasteurianum)
Go to UniProtKB:  P00268
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
C-C motif chemokine 5
B
75Homo sapiensMutation(s): 0 
Gene Names: CCL5 (D17S136E, SCYA5)
Find proteins for P13501 (Homo sapiens)
Go to Gene View: CCL5
Go to UniProtKB:  P13501
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OLC
Query on OLC

Download SDF File 
Download CCD File 
A
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
1-Oleoyl-R-glycerol
C21 H40 O4
RZRNAYUHWVFMIP-GDCKJWNLSA-N
 Ligand Interaction
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
OLA
Query on OLA

Download SDF File 
Download CCD File 
A
OLEIC ACID
C18 H34 O2
ZQPPMHVWECSIRJ-KTKRTIGZSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PCA
Query on PCA
B
L-PEPTIDE LINKINGC5 H7 N O3GLU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.204 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.216 
  • Space Group: P 2 21 21
Unit Cell:
Length (Å)Angle (°)
a = 38.010α = 90.00
b = 52.640β = 90.00
c = 302.670γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
Aimlessdata scaling
XDSdata reduction
PDB_EXTRACTdata extraction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited StatesAI118985

Revision History 

  • Version 1.0: 2017-06-28
    Type: Initial release
  • Version 1.1: 2017-09-13
    Type: Author supporting evidence
  • Version 1.2: 2018-04-18
    Type: Data collection, Database references