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⇱ RCSB PDB - 1SVC: NFKB P50 HOMODIMER BOUND TO DNA

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251,806
Structures from the PDB archive		1,068,577
Computed Structure Models (CSM)

 1SVC | pdb_00001svc

NFKB P50 HOMODIMER BOUND TO DNA

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 
    0.286 (Depositor) 
  • R-Value Work: 
    0.225 (Depositor) 
  • R-Value Observed: 
    0.225 (Depositor) 

wwPDB Validation  3D Report Full Report


This is version 1.4 of the entry. See complete history. 


Literature

Structure of the NF-kappa B p50 homodimer bound to DNA.

Muller, C.W., Rey, F.A., Sodeoka, M., Verdine, G.L., Harrison, S.C.

(1995) Nature 373: 311-317

  • PubMed: 7830764 Search on PubMed
  • DOI: https://doi.org/10.1038/373311a0
  • Primary Citation Related Structures: 
    1SVC

  • PubMed Abstract: 

    The structure of a large fragment of the p50 subunit of the human transcription factor NF-kappa B, bound as a homodimer to DNA, reveals that the Rel-homology region has two beta-barrel domains that grip DNA in the major groove. Both domains contact the DNA backbone. The amino-terminal specificity domain contains a recognition loop that interacts with DNA bases; the carboxy-terminal dimerization domain bears the site of I-kappa B interaction. The folds of these domains are related to immunoglobulin-like modules. The amino-terminal domain also resembles the core domain of p53.

    • Organizational Affiliation: 
    • Howard Hughes Medical Institute, Cambridge, Massachusetts 02138.

Macromolecule Content 

  • Total Structure Weight: 47.01 kDa 
  • Atom Count: 2,903 
  • Modeled Residue Count: 330 
  • Deposited Residue Count: 384 
  • Unique protein chains: 1
  • Unique nucleic acid chains: 1

Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
PROTEIN (NUCLEAR FACTOR KAPPA-B (NF-KB))B [auth P]365Homo sapiensMutation(s): 1 
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UniProt & NIH Common Fund Data Resources
Find proteins for P19838 (Homo sapiens)
Explore P19838 
Go to UniProtKB:  P19838
PHAROS:  P19838
GTEx:  ENSG00000109320 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP19838
Sequence Annotations
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  • Reference Sequence

Find similar nucleic acids by:  Sequence  

Entity ID: 1
MoleculeChains LengthOrganismImage
DNA (5'-D(*AP*GP*AP*TP*GP*GP*GP*GP*AP*AP*TP*CP*CP*CP*CP*TP*A P*GP*A)-3')A [auth D]19N/A👁 Image
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free:  0.286 (Depositor) 
  • R-Value Work:  0.225 (Depositor) 
  • R-Value Observed: 0.225 (Depositor) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 137α = 90
b = 137β = 90
c = 57γ = 90
Software Package:
Software NamePurpose
X-PLORrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1996-06-10
    Type: Initial release
  • Version 1.1: 2008-05-22
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2021-11-03
    Changes: Database references
  • Version 1.4: 2024-02-14
    Changes: Data collection

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.