8JFX | pdb_00008jfx

TruB domain of TruB1

PDB DOI: https://doi.org/10.2210/pdb8JFX/pdb

Classification: RNA BINDING PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2023-05-19 Released: 2024-05-22
Deposition Author(s): Xuan, Y.M., Gong, Q.G.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.242 (Depositor), 0.241 (DCC)
R-Value Work:
0.205 (Depositor), 0.206 (DCC)
R-Value Observed:
0.207 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 8JFX

This is version 1.0 of the entry. See complete history.

Literature

Structural basis of pri-let-7 recognition by human pseudouridine synthase TruB1

Xuan, Y.M., Gong, Q.G.

To be published.

Macromolecule Content

Total Structure Weight: 28.77 kDa
Atom Count: 1,766
Modeled Residue Count: 232
Deposited Residue Count: 263
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pseudouridylate synthase TRUB1	A	263	Homo sapiens	Mutation(s): 1 Gene Names: TRUB1, PUS4 EC: 5.4.99 (PDB Primary Data), 5.4.99.25 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q8WWH5 (Homo sapiens) Explore Q8WWH5 Go to UniProtKB: Q8WWH5
PHAROS: Q8WWH5 GTEx: ENSG00000165832
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8WWH5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BR Query on BR Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain B [auth A]	B [auth A], C [auth A]	BROMIDE ION Br CPELXLSAUQHCOX-UHFFFAOYSA-M		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.242 (Depositor), 0.241 (DCC)
R-Value Work: 0.205 (Depositor), 0.206 (DCC)
R-Value Observed: 0.207 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.315	α = 90
b = 53.487	β = 90
c = 90.134	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
XDS	data reduction
MOLREP	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2024-05-22

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32071221

Revision History (Full details and data files)

Version 1.0: 2024-05-22
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.