6Q2V

Crystal structure of SPOC domain of human PHD-finger protein 3 (PHF3)

PDB DOI: https://doi.org/10.2210/pdb6Q2V/pdb

Classification: TRANSCRIPTION
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2018-12-03 Released: 2020-07-15
Deposition Author(s): Grishkovskaya, I., Slade, D., Djinovic-Carugo, K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.59 Å
R-Value Free: 0.259
R-Value Work: 0.206
R-Value Observed: 0.208

wwPDB Validation 3D Report Full Report

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

Literature

PHF3 regulates neuronal gene expression through the Pol II CTD reader domain SPOC

Appel, L.M., Franke, V., Bruno, M., Grishkovskaya, I., Kasiliauskaite, A., Kaufmann, T., Schoeberl, U.E., Puchinger, M.G., Kostrhon, S., Ebenwaldner, C., Sebesta, M., Beltzung, E., Mechtler, K., Lin, G., Vlasova, A., Leeb, M., Pavri, R., Stark, A., Akalin, A., Stefl, R., Bernecky, C., Djinovic-Carugo, K., Slade, D.

(2021) Nat Commun 12: 6078

DOI: https://doi.org/10.1038/s41467-021-26360-2

Macromolecule Content

Total Structure Weight: 147.37 kDa
Atom Count: 9,414
Modelled Residue Count: 1,174
Deposited Residue Count: 1,296
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PHD finger protein 3	A, B, C, D, E A, B, C, D, E, F, G, H	162	Homo sapiens	Mutation(s): 0 Gene Names: PHF3, KIAA0244
UniProt & NIH Common Fund Data Resources
Find proteins for Q92576 (Homo sapiens) Explore Q92576 Go to UniProtKB: Q92576
PHAROS: Q92576 GTEx: ENSG00000118482
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q92576
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 I [auth E] SDF format, chain J [auth F] MOL2 format, chain I [auth E] MOL2 format, chain J [auth F]	I [auth E], J [auth F]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain I [auth E] Focus chain J [auth F] Interactions & Density Focus chain I [auth E] Focus chain J [auth F]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D, E A, B, C, D, E, F, G, H	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.59 Å
R-Value Free: 0.259
R-Value Work: 0.206
R-Value Observed: 0.208
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.745	α = 90
b = 69.306	β = 100.09
c = 127.215	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
Aimless	data scaling
CRANK2	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2020-07-15

Deposition Author(s):

Grishkovskaya, I.

Djinovic-Carugo, K.

Revision History (Full details and data files)

Version 1.0: 2020-07-15
Type: Initial release
Version 1.1: 2021-10-27
Changes: Data collection, Database references

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.