2CHD | pdb_00002chd

Crystal structure of the C2A domain of Rabphilin-3A

• PDB DOI: https://doi.org/10.2210/pdb2CHD/pdb

• Classification: PROTEIN TRANSPORT
• Organism(s): Rattus norvegicus
• Expression System: Escherichia coli BL21
• Mutation(s): No 
• Membrane Protein: Yes  OPM


• Deposited: 2006-03-14 Released: 2006-06-28 
• Deposition Author(s): Biadene, M., Montaville, P., Sheldrick, G.M., Becker, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.92 Å
• R-Value Free: 
  0.269 (Depositor), 0.167 (DCC) 
• R-Value Work: 
  0.198 (Depositor), 0.189 (DCC) 
• R-Value Observed: 
  0.201 (Depositor) 

Starting Model: experimental

Literature

Structure of the C2A Domain of Rabphilin-3A.

Biadene, M., Montaville, P., Sheldrick, G.M., Becker, S.

(2006) Acta Crystallogr D Biol Crystallogr 62: 793

• PubMed: 16790935 
• DOI: https://doi.org/10.1107/S0907444906017537
• Primary Citation Related Structures: 
  2CHD


• PubMed Abstract: 
  

  Rabphilin-3A is a neuronal protein containing a C2-domain tandem. To date, only the structure of the C2B domain has been solved. The crystal structure of the Ca2+-free C2A domain has been solved by molecular replacement and refined to 1.92 A resolution. It adopts the classical C2-domain fold consisting of an eight-stranded antiparallel beta-sandwich with type I topology. In agreement with its Ca2+-dependent negatively charged membrane-binding properties, this C2 domain contains all the conserved acidic residues responsible for calcium binding. However, the replacement of a conserved aspartic acid residue by glutamic acid allows formation of an additional strong hydrogen bond, resulting in increased rigidity of calcium-binding loop 1. The electrostatic surface of the C2A domain consists of a large positively charged belt surrounded by two negatively charged patches located at both tips of the domain. In comparison, the structurally very similar C2A domain of synaptotagmin I has a highly acidic electrostatic surface, suggesting completely unrelated functions for these two C2A domains.

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Organizational Affiliation: 
• Department of Structural Chemistry, University of Göttingen, Tammanstrasse 4, 37077 Göttingen, Germany.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PQS (software)

Macromolecule Content 

• Total Structure Weight: 16.31 kDa 
• Atom Count: 1,124 
• Modeled Residue Count: 129 
• Deposited Residue Count: 142 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RABPHILIN-3A	A	142	Rattus norvegicus	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for P47709 (Rattus norvegicus) Explore P47709  Go to UniProtKB:  P47709

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	B [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.92 Å
• R-Value Free:  0.269 (Depositor), 0.167 (DCC) 
• R-Value Work:  0.198 (Depositor), 0.189 (DCC) 
• R-Value Observed: 0.201 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.87	α = 90
b = 39.16	β = 90
c = 88.85	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SAINT	data reduction
SADABS	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-06-28 
Deposition Author(s): Biadene, M., Montaville, P., Sheldrick, G.M., Becker, S.

Revision History  

• Version 1.0: 2006-06-28
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2018-05-30
  Changes: Data collection
• Version 1.3: 2023-12-13
  Changes: Data collection, Database references, Other, Refinement description