4NN0

Crystal structure of the C1QTNF5 globular domain in space group P63

• PDB DOI:  https://doi.org/10.2210/pdb4NN0/pdb

• Classification: CELL ADHESION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-11-15 Released: 2014-03-26 
• Deposition Author(s): Tu, X., Palczewski, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.42 Å
• R-Value Free: 0.142 
• R-Value Work: 0.104 
• R-Value Observed: 0.106 

Literature

The macular degeneration-linked C1QTNF5 (S163) mutation causes higher-order structural rearrangements.

Tu, X., Palczewski, K.

(2014) J Struct Biol 186: 86-94

• PubMed: 24531000 
• DOI: https://doi.org/10.1016/j.jsb.2014.02.001
• Primary Citation of Related Structures:  
  4NN0


• PubMed Abstract: 
  

The C1q-tumor necrosis factor 5 (C1QTNF5) protein plays a significant role in retinal pigmented epithelium (RPE) cellular adhesion. The C1QTNF5 gene is co-transcribed with the frizzled-related protein (MFRP) gene. A Ser-to-Arg mutation at site 163 (S163R) in C1QTNF5 is known to cause late-onset retinal macular degeneration (L-ORMD). Here we also found that C1QTNF5 monomers can multimerize into a bouquet-like octadecamer. We found that a novel intermolecular hydrogen-bond network of S163 that glues adjacent globular heads of C1QTNF5 together was weakened or abolished by the R163 pathogenic mutation. These findings could underlie the structural basis of this protein's adhesive function and relate to the pathogenesis of its S163R mutation. Additionally, the fact that C1QTNF5 immobilized to a resin selectively enriched detergent extracted membrane-bound MFRP, further confirmed their interaction, implying functions other than cellular adhesion for C1QTNF5.

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Organizational Affiliation: 

Department of Pharmacology, School of Medicine, Case Western Reserve University, USA. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (3D View)
Global Stoichiometry: Homo 3-mer - A3 

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

Biological Assembly 2  

Global Symmetry: Cyclic - C3  (3D View)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Cyclic - C3  (3D View)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 50.8 kDa 
• Atom Count: 3,681 
• Modelled Residue Count: 416 
• Deposited Residue Count: 444 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Complement C1q tumor necrosis factor-related protein 5	A, B, C	148	Homo sapiens	Mutation(s): 0  Gene Names: C1QTNF5, CTRP5, UNQ303/PRO344
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BXJ0 (Homo sapiens) Explore Q9BXJ0  Go to UniProtKB:  Q9BXJ0
PHAROS:  Q9BXJ0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	P [auth A], W [auth B], X [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], R [auth B], S [auth B], T [auth B], U [auth B], V [auth B], Z [auth C]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACT	Q [auth A], Y [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.42 Å
• R-Value Free: 0.142 
• R-Value Work: 0.104 
• R-Value Observed: 0.106 
• Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.603	α = 90
b = 50.603	β = 90
c = 268.531	γ = 120

Software Package:

Software Name	Purpose
ADSC	data collection
PHASER	phasing
REFMAC	refinement
DPS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-03-26 
Deposition Author(s): Tu, X., Palczewski, K.

Revision History  

• Version 1.0: 2014-03-26
  Type: Initial release
  
• Version 1.1: 2014-04-23
  Changes: Database references
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description