4NN0 | pdb_00004nn0

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.42 Å
R-Value Free:
0.142 (Depositor), 0.148 (DCC)
R-Value Work:
0.104 (Depositor), 0.114 (DCC)
R-Value Observed:
0.106 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

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 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1016/j.jsb.2014.02.001
Primary Citation 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.

Organizational Affiliation

Department of Pharmacology, School of Medicine, Case Western Reserve University, USA.

Macromolecule Content

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

Macromolecules

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| 3D Structure

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 GTEx: ENSG00000223953
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9BXJ0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain X [auth B] SDF format, chain W [auth B] SDF format, chain P [auth A] MOL2 format, chain X [auth B] MOL2 format, chain W [auth B] MOL2 format, chain P [auth A] mmCIF format, chain X [auth B] mmCIF format, chain W [auth B] mmCIF format, chain P [auth A]	P [auth A], W [auth B], X [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain P [auth A] Focus chain W [auth B] Focus chain X [auth B] Interactions & Density Focus chain P [auth A] Focus chain W [auth B] Focus chain X [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain Z [auth C] SDF format, chain V [auth B] SDF format, chain U [auth B] SDF format, chain T [auth B] SDF format, chain S [auth B] SDF format, chain R [auth B] SDF format, chain O [auth A] SDF format, chain N [auth A] SDF format, chain M [auth A] SDF format, chain L [auth A] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain Z [auth C] MOL2 format, chain V [auth B] MOL2 format, chain U [auth B] MOL2 format, chain T [auth B] MOL2 format, chain S [auth B] MOL2 format, chain R [auth B] MOL2 format, chain O [auth A] MOL2 format, chain N [auth A] MOL2 format, chain M [auth A] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain Z [auth C] mmCIF format, chain V [auth B] mmCIF format, chain U [auth B] mmCIF format, chain T [auth B] mmCIF format, chain S [auth B] mmCIF format, chain R [auth B] mmCIF format, chain O [auth A] mmCIF format, chain N [auth A] mmCIF format, chain M [auth A] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A] E [auth A] F [auth A] G [auth A] H [auth A] 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		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain Z [auth C] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain Z [auth C]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain Y [auth B] SDF format, chain Q [auth A] MOL2 format, chain Y [auth B] MOL2 format, chain Q [auth A] mmCIF format, chain Y [auth B] mmCIF format, chain Q [auth A]	Q [auth A], Y [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain Q [auth A] Focus chain Y [auth B] Interactions & Density Focus chain Q [auth A] Focus chain Y [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.42 Å
R-Value Free: 0.142 (Depositor), 0.148 (DCC)
R-Value Work: 0.104 (Depositor), 0.114 (DCC)
R-Value Observed: 0.106 (Depositor)

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

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2014-03-26

Deposition Author(s):

Tu, X.

Palczewski, K.

Revision History (Full details and data files)

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

4NN0 | pdb_00004nn0

Crystal structure of the C1QTNF5 globular domain in space group P63

Literature

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

Biological Assembly 1

Biological Assembly 2

Biological Assembly 3

Macromolecules

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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