2C62

Crystal Structure of the Human Transcription Cofactor PC4 in Complex with Single-Stranded DNA

PDB DOI: https://doi.org/10.2210/pdb2C62/pdb
NAKB: 2C62

Classification: TRANSCRIPTION
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2005-11-07 Released: 2006-01-11
Deposition Author(s): Werten, S., Moras, D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.74 Å
R-Value Free: 0.240
R-Value Work: 0.229
R-Value Observed: 0.229

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

A Global Transcription Cofactor Bound to Juxtaposed Strands of Unwound DNA

Werten, S., Moras, D.

(2006) Nat Struct Mol Biol 13: 181

PubMed: 16415882 Search on PubMed
DOI: https://doi.org/10.1038/nsmb1044
Primary Citation of Related Structures:
2C62

PubMed Abstract:
The 1.74-A crystal structure of the human transcription cofactor PC4 in complex with a single-stranded 20-mer oligonucleotide reveals how symmetry-related beta-surfaces of the protein homodimer interact with juxtaposed 5-nucleotide DNA regions running in opposite directions. The structure explains high-affinity binding of PC4 to the complementary strands of unwinding duplex DNA, and it suggests the cofactor may have a role in relaxing negative supercoils or exposing unpaired bases for sequence-specific recognition by other biomolecules.

Organizational Affiliation

Département de Biologie et Génomique Structurales, Institut de Génétique et de Biologie Moléculaire et Cellulaire, B.P. 10142, 67404 Illkirch Cedex, France.

Macromolecule Content

Total Structure Weight: 21.82 kDa
Atom Count: 1,599
Modelled Residue Count: 148
Deposited Residue Count: 152
Unique protein chains: 1
Unique nucleic acid chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ACTIVATED RNA POLYMERASE II TRANSCRIPTIONAL COACTIVATOR P15	A, B	66	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P53999 (Homo sapiens) Explore P53999 Go to UniProtKB: P53999
PHAROS: P53999 GTEx: ENSG00000113387
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P53999
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-D(TPTPTPTPTPTPTPTPTPTP TPTPTPTPTPTPTPTPTPG)-3'	C	20	N/A
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 D [auth A] SDF format, chain E [auth C] MOL2 format, chain D [auth A] MOL2 format, chain E [auth C]	D [auth A], E [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth A] Focus chain E [auth C] Interactions & Density Focus chain D [auth A] Focus chain E [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.74 Å
R-Value Free: 0.240
R-Value Work: 0.229
R-Value Observed: 0.229
Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.242	α = 90
b = 67.242	β = 90
c = 131.899	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
EPMR	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2006-01-11

Deposition Author(s):

Werten, S.

Moras, D.

Revision History (Full details and data files)

Version 1.0: 2006-01-11
Type: Initial release
Version 1.1: 2011-05-08
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2023-12-13
Changes: Data collection, Database references, Other, Refinement description, Source and taxonomy