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URL: https://www.rcsb.org/structure/1DOM

⇱ RCSB PDB - 1DOM: SOLUTION STRUCTURE OF THE MONOCYTE CHEMOATTRACTANT PROTEIN-1 DIMER USING HETERONUCLEAR, NMR, MINIMIZED AVERAGE STRUCTURE

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Computed Structure Models (CSM)

 1DOM | pdb_00001dom

SOLUTION STRUCTURE OF THE MONOCYTE CHEMOATTRACTANT PROTEIN-1 DIMER USING HETERONUCLEAR, NMR, MINIMIZED AVERAGE STRUCTURE

Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Submitted: 1 

This is version 1.4 of the entry. See complete history. 

Literature

Heteronuclear (1H, 13C, 15N) NMR assignments and solution structure of the monocyte chemoattractant protein-1 (MCP-1) dimer.

Handel, T.M., Domaille, P.J.

(1996) Biochemistry 35: 6569-6584

  • DOI: https://doi.org/10.1021/bi9602270
  • Primary Citation Related Structures: 
    1DOM, 1DON

  • PubMed Abstract: 

    A full high-resolution three-dimensional solution structure of the monocyte chemoattractant protein-1 (MCP-1 or MCAF) homodimer has been determined by heteronuclear multidimensional NMR. MCP-1 is a member of a family of small proteins which play a crucial role in immune surveillance by orchestrating the recruitment of specific leukocytes to areas of immune challenge. The protein was uniformly isotopically enriched with 13C and 15N by expression in Escherichia coli, and complete sequence-specific resonance assignments were obtained by a combination of heteronuclear double- and triple-resonance experiments. The secondary structure was deduced from characteristic patterns of NOEs, 13 C alpha/beta chemical shifts, measurements of 3JHNH alpha scalar couplings, and patterns of slowly exchanging amide protons. Because MCP-1 forms symmetrical homodimers, additional experiments were carried out to unambiguously establish the quaternary contacts. NOEs from these novel experiments were merged with more traditional heteronuclear separated NOE measurements in an iterative strategy to partition the restraints between explicit inter/intrasubunit contacts and a class wherein both were retained as ambiguous. With more than 30 restraints per residue, the three-dimensional structure is well-defined with a backbone rmsd of 0.37 A to the mean over residues 5-69 of the dimer. We compare the structure with those recently reported for the related chemokines MIP-1 beta and RANTES and highlight the differences in terms of receptor specificity and function as well as interpret the known biological activity data of MCP-1 mutants.

    • Organizational Affiliation: 
    • Department of Molecular and Cell Biology, University of California at Berkeley 94720, USA.

Macromolecule Content 

  • Total Structure Weight: 17.4 kDa 
  • Atom Count: 1,214 
  • Modeled Residue Count: 152 
  • Deposited Residue Count: 152 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
MCP-1
A, B
76Homo sapiensMutation(s): 0 
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UniProt & NIH Common Fund Data Resources
Find proteins for P13500 (Homo sapiens)
Explore P13500 
Go to UniProtKB:  P13500
PHAROS:  P13500
GTEx:  ENSG00000108691 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP13500
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Submitted: 1 

Structure Validation

View Full Validation Report

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1996-10-14
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2022-02-16
    Changes: Database references, Derived calculations, Other
  • Version 1.4: 2024-10-23
    Changes: Data collection, Structure summary

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.