3FRY | pdb_00003fry

Crystal structure of the CopA C-terminal metal binding domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.238 (Depositor) 
  • R-Value Work: 
    0.222 (Depositor), 0.234 (DCC) 
  • R-Value Observed: 
    0.222 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.4 of the entry. See complete history

Literature

Structure and interactions of the C-terminal metal binding domain of Archaeoglobus fulgidus CopA.

Agarwal, S.Hong, D.Desai, N.K.Sazinsky, M.H.Arguello, J.M.Rosenzweig, A.C.

(2010) Proteins 78: 2450-2458

  • DOI: https://doi.org/10.1002/prot.22753
  • Primary Citation Related Structures: 
    3FRY

  • PubMed Abstract: 

    The Cu(+)-ATPase CopA from Archaeoglobus fulgidus belongs to the P(1B) family of the P-type ATPases. These integral membrane proteins couple the energy of ATP hydrolysis to heavy metal ion translocation across membranes. A defining feature of P(1B-1)-type ATPases is the presence of soluble metal binding domains at the N-terminus (N-MBDs). The N-MBDs exhibit a conserved ferredoxin-like fold, similar to that of soluble copper chaperones, and bind metal ions via a conserved CXXC motif. The N-MBDs enable Cu(+) regulation of turnover rates apparently through Cu-sensitive interactions with catalytic domains. A. fulgidus CopA is unusual in that it contains both an N-terminal MBD and a C-terminal MBD (C-MBD). The functional role of the unique C-MBD has not been established. Here, we report the crystal structure of the apo, oxidized C-MBD to 2.0 A resolution. In the structure, two C-MBD monomers form a domain-swapped dimer, which has not been observed previously for similar domains. In addition, the interaction of the C-MBD with the other cytoplasmic domains of CopA, the ATP binding domain (ATPBD) and actuator domain (A-domain), has been investigated. Interestingly, the C-MBD interacts specifically with both of these domains, independent of the presence of Cu(+) or nucleotides. These data reinforce the uniqueness of the C-MBD and suggest a distinct structural role for the C-MBD in CopA transport.


  • Organizational Affiliation
    • Department of Biochemistry, Molecular Biology, and Cell Biology, Northwestern University, Evanston, Illinois 60208, USA.

Macromolecule Content 

  • Total Structure Weight: 15.84 kDa 
  • Atom Count: 1,149 
  • Modeled Residue Count: 145 
  • Deposited Residue Count: 146 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Probable copper-exporting P-type ATPase A
A, B
73Archaeoglobus fulgidusMutation(s): 0 
Gene Names: AF_0473copApacS
EC: 3.6.3 (PDB Primary Data), 7.2.2.8 (UniProt)
UniProt
Find proteins for O29777 (Archaeoglobus fulgidus (strain ATCC 49558 / DSM 4304 / JCM 9628 / NBRC 100126 / VC-16))
Explore O29777 
Go to UniProtKB:  O29777
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO29777
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CIT

Query on CIT



Download:Ideal Coordinates CCD File
C [auth A]CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.238 (Depositor) 
  • R-Value Work:  0.222 (Depositor), 0.234 (DCC) 
  • R-Value Observed: 0.222 (Depositor) 
Space Group: P 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.131α = 90
b = 35.989β = 104.89
c = 51.262γ = 90
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-01-12
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2011-11-16
    Changes: Atomic model
  • Version 1.3: 2023-09-06
    Changes: Data collection, Database references, Refinement description
  • Version 1.4: 2024-10-16
    Changes: Structure summary