6IC9

Crystal structure of the SPOC domain of human PHF3 in complex with RNA polymerase II CTD diheptapeptide phosphorylated on Ser2Ser7

PDB DOI: https://doi.org/10.2210/pdb6IC9/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., Djinovic-Carugo, K., Slade, D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free: 0.232
R-Value Work: 0.195
R-Value Observed: 0.197

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: 39.98 kDa
Atom Count: 2,710
Modelled Residue Count: 315
Deposited Residue Count: 352
Unique protein chains: 2

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	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

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
TYR-SEP-PRO-THR-SER-PRO-SEP-TYR-SEP-PRO-THR-SER-PRO	C, D	14	Homo sapiens	Mutation(s): 0 EC: 3.1.13 (UniProt), 2.7.7.48 (UniProt), 2.7.7.6 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P24928 (Homo sapiens) Explore P24928 Go to UniProtKB: P24928
PHAROS: P24928
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P24928
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEP Query on SEP	C, D	L-PEPTIDE LINKING	C₃ H₈ N O₆ P		SER

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free: 0.232
R-Value Work: 0.195
R-Value Observed: 0.197
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.215	α = 90
b = 68.106	β = 90
c = 100.874	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
Aimless	data scaling
PHASER	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 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.