6JBM

Crystal structure of the TRIM14 PRYSPRY domain

PDB DOI: https://doi.org/10.2210/pdb6JBM/pdb

Classification: PROTEIN BINDING
Organism(s): Homo sapiens
Expression System: Escherichia coli DH5[alpha]
Mutation(s): No

Deposited: 2019-01-26 Released: 2020-03-04
Deposition Author(s): Yin, Y.X., Yu, Y., Liang, L.
Funding Organization(s): National Natural Science Foundation of China

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.242
R-Value Work: 0.213
R-Value Observed: 0.215

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

The TRIM14 PRYSPRY domain mediates protein interaction via its basic interface.

Yu, Y., Liang, L., Jin, Y., Yin, Y.

(2019) FEBS Lett 593: 1122-1129

PubMed: 30973643 Search on PubMed
DOI: https://doi.org/10.1002/1873-3468.13386
Primary Citation of Related Structures:
6JBM

PubMed Abstract:
Tripartite motif (TRIM)14 was recently shown to be an important molecule against pathogens. Its PRYSPRY domain acts as a protein-protein interaction module. TRIM14 exerts distinct functions via its PRYSPRY domain by interacting with different partners. However, the structural basis for its binding specificity remains unknown. Here we solved the crystal structure of the TRIM14 PRYSPRY domain, and found a positively charged surface that may mediate its partner specificity. Isothermal titration calorimetry reveals that the TRIM14 PRYSPRY domain binds to acidic peptides, and the analysis of the reported partners of TRIM14 is consistent with our assumption. Therefore, we demonstrate that the PRYSPRY domain of TRIM14 harbors a putative basic interface that may favorably bind to acidic amino acid residues.

Organizational Affiliation

Institute of Systems Biomedicine, Department of Pathology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China.

Macromolecule Content

Total Structure Weight: 92.73 kDa
Atom Count: 6,296
Modelled Residue Count: 737
Deposited Residue Count: 800
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tripartite motif-containing protein 14	A [auth B], B [auth A], C, D	200	Homo sapiens	Mutation(s): 0 Gene Names: TRIM14, KIAA0129
UniProt & NIH Common Fund Data Resources
Find proteins for Q14142 (Homo sapiens) Explore Q14142 Go to UniProtKB: Q14142
PHAROS: Q14142 GTEx: ENSG00000106785
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q14142
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain F [auth B] SDF format, chain G [auth B] SDF format, chain H [auth B] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth C] SDF format, chain M [auth D] SDF format, chain N [auth D] SDF format, chain O [auth D] SDF format, chain P [auth D] MOL2 format, chain E [auth B] MOL2 format, chain F [auth B] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth C] MOL2 format, chain M [auth D] MOL2 format, chain N [auth D] MOL2 format, chain O [auth D] MOL2 format, chain P [auth D]	E [auth B] F [auth B] G [auth B] H [auth B] I [auth A] E [auth B], F [auth B], G [auth B], H [auth B], I [auth A], J [auth A], K [auth A], L [auth C], M [auth D], N [auth D], O [auth D], P [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth B] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth C] Focus chain M [auth D] Focus chain N [auth D] Focus chain O [auth D] Focus chain P [auth D] Interactions & Density Focus chain E [auth B] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth C] Focus chain M [auth D] Focus chain N [auth D] Focus chain O [auth D] Focus chain P [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.242
R-Value Work: 0.213
R-Value Observed: 0.215
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.326	α = 90
b = 104.02	β = 91.49
c = 93.381	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Coot	model building
HKL-2000	data scaling

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2020-03-04

Deposition Author(s):

Yin, Y.X.

Yu, Y.

Liang, L.

Funding Organization	Location	Grant Number
National Natural Science Foundation of China	China	81430056
National Natural Science Foundation of China	China	31420103905
National Natural Science Foundation of China	China	31800626