3Q13

The Structure of the Ca2+-binding, Glycosylated F-spondin Domain of F-spondin, A C2-domain Variant from Extracellular Matrix


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.167 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

The structure of the Ca2+-binding, glycosylated F-spondin domain of F-spondin - A C2-domain variant in an extracellular matrix protein.

Tan, K.Lawler, J.

(2011) Bmc Struct.Biol. 11: 22-22

  • DOI: 10.1186/1472-6807-11-22

  • PubMed Abstract: 
  • F-spondin is a multi-domain extracellular matrix (ECM) protein and a contact-repellent molecule that directs axon outgrowth and cell migration during development. The reelin_N domain and the F-spondin domain (FS domain) comprise a proteolytic fragmen ...

    F-spondin is a multi-domain extracellular matrix (ECM) protein and a contact-repellent molecule that directs axon outgrowth and cell migration during development. The reelin_N domain and the F-spondin domain (FS domain) comprise a proteolytic fragment that interacts with the cell membrane and guides the projection of commissural axons to floor plate. The FS domain is found in F-spondins, mindins, M-spondin and amphiF-spondin.


    Organizational Affiliation

    Midwest Center for Structural Genomics and Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, IL 60439, USA. ktan@anl.gov




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Spondin-1
A
258Homo sapiensMutation(s): 0 
Gene Names: SPON1 (KIAA0762, VSGP)
Find proteins for Q9HCB6 (Homo sapiens)
Go to Gene View: SPON1
Go to UniProtKB:  Q9HCB6
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
ACT
Query on ACT

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Download CCD File 
A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
CA
Query on CA

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Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
BMA
Query on BMA

Download SDF File 
Download CCD File 
A
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.167 
  • Space Group: P 6 2 2
Unit Cell:
Length (Å)Angle (°)
a = 120.244α = 90.00
b = 120.244β = 90.00
c = 86.362γ = 120.00
Software Package:
Software NamePurpose
MOLREPphasing
REFMACrefinement
SBC-Collectdata collection
HKL-3000data scaling
HKL-3000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2010-12-16 
  • Released Date: 2011-06-29 
  • Deposition Author(s): Tan, K., Lawler, J.

Revision History 

  • Version 1.0: 2011-06-29
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance