1MDM | pdb_00001mdm

INHIBITED FRAGMENT OF ETS-1 AND PAIRED DOMAIN OF PAX5 BOUND TO DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 
    0.310 (Depositor), 0.307 (DCC) 
  • R-Value Work: 
    0.259 (Depositor), 0.260 (DCC) 
  • R-Value Observed: 
    0.259 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history

Literature

STRUCTURAL ANALYSIS OF THE AUTOINHIBITION OF ETS-1 AND ITS ROLE IN PROTEIN PARTNERSHIPS

Garvie, C.W.Pufall, M.A.Graves, B.J.Wolberger, C.

(2002) J Biological Chem 277: 45529-45536

  • DOI: https://doi.org/10.1074/jbc.M206327200
  • Primary Citation Related Structures: 
    1MD0, 1MDM

  • PubMed Abstract: 

    The DNA-binding activity of the eukaryotic transcription factor Ets-1 (E26 avian erythroblastosis virus oncogene-E twenty-six) is negatively regulated by inhibitory regions that flank the ETS domain. Based on the results of solution studies, these N- and C-terminal inhibitory regions have been proposed to pack against the ETS domain and form an autoinhibitory module whose N terminus partially unfolds upon binding of Ets-1 to DNA. Mutations that disrupt autoinhibition of DNA binding also cause a structural change in the inhibitory region. We report here a crystallographic study of fragments of Ets-1 that provide structural details of the inhibitory module and the structural transition that accompanies DNA binding. The structures of free and DNA-bound Ets-1 fragments containing the ETS domain and the inhibitory regions confirm that the N-terminal inhibitory region contains two alpha-helices one of which unfolds upon Ets-1 binding to DNA. The observations from the crystal structure, coupled with mutagenesis experiments, allow us to propose a model for the inhibited form of Ets-1 and lend insight into the flexible interaction between Ets-1 and the acute myeloid leukemia 1 protein, AML1 (RUNX1).


  • Organizational Affiliation
    • Department of Biophysics and Biophysical Chemistry and the Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205-2185, USA.

Macromolecule Content 

  • Total Structure Weight: 51.31 kDa 
  • Atom Count: 3,054 
  • Modeled Residue Count: 305 
  • Deposited Residue Count: 362 
  • Unique protein chains: 2
  • Unique nucleic acid chains: 2

Macromolecules


Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
PAIRED BOX PROTEIN PAX-5C [auth A]149Homo sapiensMutation(s): 0 
Gene Names: Pax5
UniProt & NIH Common Fund Data Resources
Find proteins for Q02548 (Homo sapiens)
Explore Q02548 
Go to UniProtKB:  Q02548
PHAROS:  Q02548
GTEx:  ENSG00000196092 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ02548
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
C-ETS-1 PROTEIND [auth B]161Mus musculusMutation(s): 0 
Gene Names: Ets-1
UniProt
Find proteins for P27577 (Mus musculus)
Explore P27577 
Go to UniProtKB:  P27577
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP27577
Sequence Annotations
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Reference Sequence
Find similar nucleic acids by:  (by identity cutoff) 
Entity ID: 1
MoleculeChains LengthOrganismImage
PAX5/ETS BINDING SITE ON THE MB-1 PROMOTERA [auth C]26N/A
Sequence Annotations
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Reference Sequence
Find similar nucleic acids by:  (by identity cutoff) 
Entity ID: 2
MoleculeChains LengthOrganismImage
PAX5/ETS BINDING SITE ON THE MB-1 PROMOTERB [auth D]26N/A
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free:  0.310 (Depositor), 0.307 (DCC) 
  • R-Value Work:  0.259 (Depositor), 0.260 (DCC) 
  • R-Value Observed: 0.259 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.27α = 90
b = 171.23β = 90
c = 44.71γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
CNSrefinement
CCP4data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-12-11
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-02-14
    Changes: Data collection, Database references, Refinement description