3DO7 | pdb_00003do7

X-ray structure of a NF-kB p52/RelB/DNA complex

PDB DOI: https://doi.org/10.2210/pdb3DO7/pdb
NAKB: 3DO7

Classification: TRANSCRIPTION/DNA
Organism(s): Mus musculus, Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2008-07-03 Released: 2009-07-21
Deposition Author(s): Fusco, A., Huang, D.B., Miller, D., Vu, D., Ghosh, G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.05 Å
R-Value Free:
0.273 (Depositor)
R-Value Work:
0.230 (Depositor), 0.242 (DCC)
R-Value Observed:
0.230 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 3DO7

This is version 1.2 of the entry. See complete history.

Literature

NF-kapppaB p52:RelB heterodimer uses different binding modes to recognize different kappaB DNA

Fusco, A., Huang, D.B., Miller, D., Vu, D., Ghosh, G.

To be published.

Macromolecule Content

Total Structure Weight: 76.54 kDa
Atom Count: 5,288
Modeled Residue Count: 621
Deposited Residue Count: 622
Unique protein chains: 2
Unique nucleic acid chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Avian reticuloendotheliosis viral (V-rel) oncogene related B	D [auth A]	296	Mus musculus	Mutation(s): 0 Gene Names: Relb
UniProt
Find proteins for Q04863 (Mus musculus) Explore Q04863 Go to UniProtKB: Q04863
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q04863
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear factor NF-kappa-B p100 subunit	E [auth B]	293	Homo sapiens	Mutation(s): 0 Gene Names: NFKB2, LYT10
UniProt & NIH Common Fund Data Resources
Find proteins for Q00653 (Homo sapiens) Explore Q00653 Go to UniProtKB: Q00653
PHAROS: Q00653 GTEx: ENSG00000077150
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q00653
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by: Sequence

Molecule	Chains	Length	Organism	Image
Entity ID: 1
5'-D(DCPDGPDGPDGPDAPDAPDTPDTPDCPDCP*DC)-3'	A [auth C], B [auth D], C [auth E]	11	N/A
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.05 Å
R-Value Free: 0.273 (Depositor)
R-Value Work: 0.230 (Depositor), 0.242 (DCC)
R-Value Observed: 0.230 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.64	α = 90
b = 124.13	β = 90
c = 189.59	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
AMoRE	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2009-07-21

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2009-07-21
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2024-10-30
Changes: Data collection, Database references, Structure summary

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.