5H3S | pdb_00005h3s

apo form of GEMIN5-WD

PDB DOI: https://doi.org/10.2210/pdb5H3S/pdb

Classification: RNA BINDING PROTEIN
Organism(s): Homo sapiens
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2016-10-27 Released: 2016-12-28
Deposition Author(s): Bharath, S.R., Tang, X., Song, H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free:
0.261 (Depositor), 0.263 (DCC)
R-Value Work:
0.201 (Depositor), 0.204 (DCC)
R-Value Observed:
0.204 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 5H3S

This is version 1.3 of the entry. See complete history.

Literature

Structural basis for specific recognition of pre-snRNA by Gemin5

Tang, X., Bharath, S.R., Piao, S., Tan, V.Q., Bowler, M.W., Song, H.

(2016) Cell Res 26: 1353-1356

PubMed: 27834343 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/cr.2016.133
Primary Citation Related Structures:
5H3S, 5H3T, 5H3U

Organizational Affiliation

Institute of Molecular and Cell Biology, 61 Biopolis Drive, Proteos, Singapore 138673, Singapore.

Macromolecule Content

Total Structure Weight: 164.68 kDa
Atom Count: 9,755
Modeled Residue Count: 1,300
Deposited Residue Count: 1,480
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Gem-associated protein 5	A, B	740	Homo sapiens	Mutation(s): 0 Gene Names: GEMIN5
UniProt & NIH Common Fund Data Resources
Find proteins for Q8TEQ6 (Homo sapiens) Explore Q8TEQ6 Go to UniProtKB: Q8TEQ6
PHAROS: Q8TEQ6 GTEx: ENSG00000082516
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8TEQ6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain C [auth B] MOL2 format, chain C [auth B] mmCIF format, chain C [auth B]	C [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth B] Interactions & Density Focus chain C [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free: 0.261 (Depositor), 0.263 (DCC)
R-Value Work: 0.201 (Depositor), 0.204 (DCC)
R-Value Observed: 0.204 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.503	α = 90
b = 91.373	β = 100.55
c = 112.571	γ = 90

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2016-12-28

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2016-12-28
Type: Initial release
Version 1.1: 2017-09-27
Changes: Data collection
Version 1.2: 2023-11-08
Changes: Data collection, Database references, Refinement description
Version 1.3: 2025-09-17
Changes: Advisory, Derived calculations, Structure summary

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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.