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- PDB-2stw: SOLUTION NMR STRUCTURE OF THE HUMAN ETS1/DNA COMPLEX, RESTRAINED ... -

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Basic information

Entry
Database: PDB / ID: 2stw
TitleSOLUTION NMR STRUCTURE OF THE HUMAN ETS1/DNA COMPLEX, RESTRAINED REGULARIZED MEAN STRUCTURE
Components
  • DNA (5'-D(*TP*CP*GP*AP*AP*CP*TP*TP*CP*CP*GP*GP*CP*TP*CP*GP*A)-3')
  • DNA (5'-D(*TP*CP*GP*AP*GP*CP*CP*GP*GP*AP*AP*GP*TP*TP*CP*GP*A)-3')
  • ETS1
KeywordsDNA BINDING PROTEIN/DNA / COMPLEX (DNA-BINDING PROTEIN-DNA) / PROTO-ONCOGENE / DNA-BINDING / NUCLEAR PROTEIN / PHOSPHORYLATION / DNA BINDING PROTEIN-DNA COMPLEX
Function / homology
Function and homology information


PML body organization / positive regulation of leukocyte adhesion to vascular endothelial cell / negative regulation of cell cycle / positive regulation of blood vessel endothelial cell migration / regulation of angiogenesis / positive regulation of endothelial cell migration / transcription corepressor binding / nuclear receptor coactivator activity / positive regulation of erythrocyte differentiation / cell motility ...PML body organization / positive regulation of leukocyte adhesion to vascular endothelial cell / negative regulation of cell cycle / positive regulation of blood vessel endothelial cell migration / regulation of angiogenesis / positive regulation of endothelial cell migration / transcription corepressor binding / nuclear receptor coactivator activity / positive regulation of erythrocyte differentiation / cell motility / Oncogene Induced Senescence / positive regulation of inflammatory response / positive regulation of miRNA transcription / positive regulation of angiogenesis / DNA-binding transcription activator activity, RNA polymerase II-specific / regulation of apoptotic process / RNA polymerase II-specific DNA-binding transcription factor binding / transcription by RNA polymerase II / nucleic acid binding / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / immune response / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of cell population proliferation / response to antibiotic / chromatin / positive regulation of gene expression / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Protein C-ets-1, pointed domain / Transforming protein C-ets / Ets1, N-terminal flanking region of Ets domain / Ets1 N-terminal flanking region of Ets domain / SAM / Pointed domain / Pointed domain / Sterile alpha motif (SAM)/Pointed domain / Pointed (PNT) domain profile. / Ets-domain signature 1. / ETS family ...Protein C-ets-1, pointed domain / Transforming protein C-ets / Ets1, N-terminal flanking region of Ets domain / Ets1 N-terminal flanking region of Ets domain / SAM / Pointed domain / Pointed domain / Sterile alpha motif (SAM)/Pointed domain / Pointed (PNT) domain profile. / Ets-domain signature 1. / ETS family / Ets-domain signature 2. / Ets domain / Ets-domain / Ets-domain profile. / erythroblast transformation specific domain / Sterile alpha motif/pointed domain superfamily / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Protein C-ets-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsClore, G.M. / Werner, M.H. / Gronenborn, A.M.
CitationJournal: J.Biomol.NMR / Year: 1997
Title: Correction of the NMR structure of the ETS1/DNA complex.
Authors: Werner, M.H. / Clore, G.M. / Fisher, C.L. / Fisher, R.J. / Trinh, L. / Shiloach, J. / Gronenborn, A.M.
History
DepositionAug 5, 1996Processing site: BNL
SupersessionMar 12, 1997ID: 1STW
Revision 1.0Mar 12, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 16, 2022Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: DNA (5'-D(*TP*CP*GP*AP*GP*CP*CP*GP*GP*AP*AP*GP*TP*TP*CP*GP*A)-3')
C: DNA (5'-D(*TP*CP*GP*AP*AP*CP*TP*TP*CP*CP*GP*GP*CP*TP*CP*GP*A)-3')
A: ETS1


Theoretical massNumber of molelcules
Total (without water)21,6723
Polymers21,6723
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / -REGULARIZED MEAN STRUCTURE
Representative

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Components

#1: DNA chain DNA (5'-D(*TP*CP*GP*AP*GP*CP*CP*GP*GP*AP*AP*GP*TP*TP*CP*GP*A)-3')


Mass: 5252.410 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(*TP*CP*GP*AP*AP*CP*TP*TP*CP*CP*GP*GP*CP*TP*CP*GP*A)-3')


Mass: 5163.348 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein ETS1 /


Mass: 11255.954 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P14921

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR

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Sample preparation

Sample conditionspH: 6.80 / Temperature: 305.00 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AMX500BrukerAMX5005001
Bruker AMX600BrukerAMX6006002

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
NMR software
NameClassification
XPLORstructure solution
XPLORrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: THE RESTRAINED REGULARIZED MEAN STRUCTURE IS PRESENTED IN ENTRY 2STW AND 25 STRUCTURES ARE PRESENTED IN ENTRY 2STT. IN 2STW THE LAST COLUMN REPRESENTS THE RMS OF THE 25 INDIVIDUAL SIMULATED ...Details: THE RESTRAINED REGULARIZED MEAN STRUCTURE IS PRESENTED IN ENTRY 2STW AND 25 STRUCTURES ARE PRESENTED IN ENTRY 2STT. IN 2STW THE LAST COLUMN REPRESENTS THE RMS OF THE 25 INDIVIDUAL SIMULATED ANNEALING STRUCTURES ABOUT THE MEAN COORDINATE POSITIONS. THE LAST COLUMN IN THE INDIVIDUAL SA STRUCTURES HAS NO MEANING. BEST FITTING TO GENERATE THE AVERAGE STRUCTURE IS WITH RESPECT TO RESIDUES 24 - 105 OF THE PROTEIN AND BASE PAIRS 1 - 17 OF THE DNA (RESIDUES 10 - 24 ARE DISORDERED IN SOLUTION). RESIDUE 10 CORRESPONDS TO RESIDUE 320 OF THE NATURAL SEQUENCE. NOTE THE OCCUPANCY FIELD HAS NO MEANING.
NMR ensembleConformer selection criteria: REGULARIZED MEAN STRUCTURE / Conformers submitted total number: 1

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