1HHV | pdb_00001hhv

SOLUTION STRUCTURE OF VIRUS CHEMOKINE VMIP-II


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 80 
  • Conformers Submitted: 25 
  • Selection Criteria: LEAST RESTRAINT VIOLATION AND LOWEST ENERGY 

wwPDB Validation 3D Report Full Report

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This is version 1.5 of the entry. See complete history

Literature

CCR2 and CCR5 receptor-binding properties of herpesvirus-8 vMIP-II based on sequence analysis and its solution structure

Shao, W.Fernandez, E.Sachpatzidis, A.Wilken, J.Thompson, D.A.Schweitzer, B.I.Lolis, E.

(2001) Eur J Biochem 268: 2948-2959

  • DOI: https://doi.org/10.1046/j.1432-1327.2001.02184.x
  • Primary Citation Related Structures: 
    1HHV

  • PubMed Abstract: 

    Human herpesvirus-8 (HHV-8) is the infectious agent responsible for Kaposi's sarcoma and encodes a protein, macrophage inflammatory protein-II (vMIP-II), which shows sequence similarity to the human CC chemokines. vMIP-II has broad receptor specificity that crosses chemokine receptor subfamilies, and inhibits HIV-1 viral entry mediated by numerous chemokine receptors. In this study, the solution structure of chemically synthesized vMIP-II was determined by nuclear magnetic resonance. The protein is a monomer and possesses the chemokine fold consisting of a flexible N-terminus, three antiparallel beta strands, and a C-terminal alpha helix. Except for the N-terminal residues (residues 1-13) and the last two C-terminal residues (residues 73-74), the structure of vMIP-II is well-defined, exhibiting average rmsd of 0.35 and 0.90 A for the backbone heavy atoms and all heavy atoms of residues 14-72, respectively. Taking into account the sequence differences between the various CC chemokines and comparing their three-dimensional structures allows us to implicate residues that influence the quaternary structure and receptor binding and activation of these proteins in solution. The analysis of the sequence and three-dimensional structure of vMIP-II indicates the presence of epitopes involved in binding two receptors CCR2 and CCR5. We propose that vMIP-II was initially specific for CCR5 and acquired receptor-binding properties to CCR2 and other chemokine receptors.


  • Organizational Affiliation
    • Walt Disney Memorial Cancer Institute at Florida Hospital, Orlando, FL, USA.

Macromolecule Content 

  • Total Structure Weight: 8.46 kDa 
  • Atom Count: 587 
  • Modeled Residue Count: 74 
  • Deposited Residue Count: 74 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
VIRUS CHEMOKINE VMIP-II74N/AMutation(s): 0 
UniProt
Find proteins for Q98157 (Human herpesvirus 8 type P (isolate GK18))
Explore Q98157 
Go to UniProtKB:  Q98157
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ98157
Sequence Annotations
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Reference Sequence

Small Molecules

Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET

Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 80 
  • Conformers Submitted: 25 
  • Selection Criteria: LEAST RESTRAINT VIOLATION AND LOWEST ENERGY 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-09-16
    Type: Initial release
  • Version 1.1: 2008-04-26
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-01-24
    Changes: Database references, Derived calculations
  • Version 1.4: 2023-12-27
    Changes: Data collection, Database references, Derived calculations
  • Version 1.5: 2024-10-30
    Changes: Structure summary