1.6 Angstrom crystal structure of the human neuroreceptor anchoring and molybdenum cofactor biosynthesis protein gephyrin

Experimental Data Snapshot

  • Resolution: 1.60 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.147 
  • R-Value Observed: 0.148 

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Crystal structures of human gephyrin and plant Cnx1 G domains: comparative analysis and functional implications.

Schwarz, G.Schrader, N.Mendel, R.R.Hecht, H.J.Schindelin, H.

(2001) J Mol Biol 312: 405-418

  • DOI: https://doi.org/10.1006/jmbi.2001.4952
  • Primary Citation of Related Structures:  
    1EAV, 1JLJ

  • PubMed Abstract: 

    The molybdenum cofactor (Moco) consists of a unique and conserved pterin derivative, usually referred to as molybdopterin (MPT), which coordinates the essential transition metal molybdenum (Mo). Moco is required for the enzymatic activities of all Mo-enzymes, with the exception of nitrogenase and is synthesized by an evolutionary old multi-step pathway that is dependent on the activities of at least six gene products. In eukaryotes, the final step of Moco biosynthesis, i.e. transfer and insertion of Mo into MPT, is catalyzed by the two-domain proteins Cnx1 in plants and gephyrin in mammals. Gephyrin is ubiquitously expressed, and was initially found in the central nervous system, where it is essential for clustering of inhibitory neuroreceptors in the postsynaptic membrane. Gephyrin and Cnx1 contain at least two functional domains (E and G) that are homologous to the Escherichia coli proteins MoeA and MogA, the atomic structures of which have been solved recently. Here, we present the crystal structures of the N-terminal human gephyrin G domain (Geph-G) and the C-terminal Arabidopsis thaliana Cnx1 G domain (Cnx1-G) at 1.7 and 2.6 A resolution, respectively. These structures are highly similar and compared to MogA reveal four major differences in their three-dimensional structures: (1) In Geph-G and Cnx1-G an additional alpha-helix is present between the first beta-strand and alpha-helix of MogA. (2) The loop between alpha 2 and beta 2 undergoes conformational changes in all three structures. (3) A beta-hairpin loop found in MogA is absent from Geph-G and Cnx1-G. (4) The C terminus of Geph-G follows a different path from that in MogA. Based on the structures of the eukaryotic proteins and their comparisons with E. coli MogA, the predicted binding site for MPT has been further refined. In addition, the characterized alternative splice variants of gephyrin are analyzed in the context of the three-dimensional structure of Geph-G.

  • Organizational Affiliation

    Department of Biochemistry and Center for Structural Biology, State University of New York at Stony Brook, Stony Brook, NY 11794-5115, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B, C
189Homo sapiensMutation(s): 0 
Gene Names: GEPHYRIN
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NQX3 (Homo sapiens)
Explore Q9NQX3 
Go to UniProtKB:  Q9NQX3
GTEx:  ENSG00000171723 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NQX3
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on FMT

Download Ideal Coordinates CCD File 
C H2 O2
Query on NA

Download Ideal Coordinates CCD File 
Experimental Data & Validation

Experimental Data

  • Resolution: 1.60 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.147 
  • R-Value Observed: 0.148 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 114.269α = 90
b = 66.008β = 93.27
c = 73.122γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-09-21
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-08-16
    Changes: Data collection, Database references, Derived calculations, Refinement description