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- PDB-1bc7: SERUM RESPONSE FACTOR ACCESSORY PROTEIN 1A (SAP-1)/DNA COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1bc7
TitleSERUM RESPONSE FACTOR ACCESSORY PROTEIN 1A (SAP-1)/DNA COMPLEX
Components
  • DNA (5'-D(*CP*AP*CP*AP*TP*CP*CP*TP*GP*TP*C)-3')
  • DNA (5'-D(*GP*AP*CP*AP*GP*GP*AP*TP*GP*TP*G)-3')
  • PROTEIN (ETS-DOMAIN PROTEIN)
KeywordsTRANSCRIPTION/DNA / ETS DOMAIN / DNA-BINDING DOMAIN / WINGED HELIX-TURN-HELIX / DNA-BINDING SPECIFICITY / COMPLEX (DNA-BINDING PROTEIN-DNA) / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information


sequence-specific double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor activity, RNA polymerase II-specific / cell differentiation / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / chromatin binding / regulation of transcription by RNA polymerase II / chromatin / negative regulation of transcription by RNA polymerase II ...sequence-specific double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor activity, RNA polymerase II-specific / cell differentiation / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / chromatin binding / regulation of transcription by RNA polymerase II / chromatin / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
Ets-domain signature 1. / Ets-domain signature 2. / Ets domain / ETS family / Ets-domain / Ets-domain profile. / erythroblast transformation specific domain / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily ...Ets-domain signature 1. / Ets-domain signature 2. / Ets domain / ETS family / Ets-domain / Ets-domain profile. / erythroblast transformation specific domain / 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) / ETS domain-containing protein Elk-4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.01 Å
AuthorsMo, Y. / Vaessen, B. / Johnston, K. / Marmorstein, R.
CitationJournal: Mol.Cell / Year: 1998
Title: Structures of SAP-1 bound to DNA targets from the E74 and c-fos promoters: insights into DNA sequence discrimination by Ets proteins.
Authors: Mo, Y. / Vaessen, B. / Johnston, K. / Marmorstein, R.
History
DepositionMay 5, 1998Deposition site: BNL / Processing site: NDB
Revision 1.0Jan 21, 1999Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA (5'-D(*GP*AP*CP*AP*GP*GP*AP*TP*GP*TP*G)-3')
B: DNA (5'-D(*CP*AP*CP*AP*TP*CP*CP*TP*GP*TP*C)-3')
C: PROTEIN (ETS-DOMAIN PROTEIN)


Theoretical massNumber of molelcules
Total (without water)17,9273
Polymers17,9273
Non-polymers00
Water2,468137
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.503, 62.306, 38.865
Angle α, β, γ (deg.)90.00, 107.17, 90.00
Int Tables number4
Cell settingmonoclinic
Space group name H-MP1211

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Components

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


Mass: 3438.259 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(*CP*AP*CP*AP*TP*CP*CP*TP*GP*TP*C)-3')


Mass: 3269.149 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein PROTEIN (ETS-DOMAIN PROTEIN) / SAP-1 / SERUM RESPONSE FACTOR ACCESSORY PROTEIN 1A / ELK4 / SRF ACCESSORY PROTEIN 1


Mass: 11219.207 Da / Num. of mol.: 1 / Fragment: ETS DOMAIN, RESIDUES 1-93
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cellular location: NUCLEUS / Gene: SAP-1 RESIDUES 1-93 / Gene (production host): SAP-1 RESIDUES 1-93 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / Variant (production host): LYSS / References: UniProt: P28324
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 137 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.22 Å3/Da / Density % sol: 44.6 %
Description: WITH ALTERED DNA BASE PAIRS APPROPRIATELY MODIFIED
Crystal growpH: 5.8 / Details: pH 5.8
Components of the solutions
IDNameCrystal-IDSol-ID
1SODIUM CACODYLATE11
2PEG 800011
3(NH4)2SO411
4NACL11
5MGCL211
6PEG 800012
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
125 mMsodium cacodylate1drop
275 mMammonium sulfate1drop
310 mM1dropNaCl
410 mM1dropMgCl2
57.0 %PEG80001drop
61

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 15, 1997 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.01→21.4 Å / Num. all: 10425 / Num. obs: 10425 / % possible obs: 98.9 % / Redundancy: 2.8 % / Biso Wilson estimate: 15.7 Å2 / Rmerge(I) obs: 0.041 / Net I/σ(I): 21.8
Reflection shellResolution: 2.01→2.1 Å / Rmerge(I) obs: 0.142 / % possible all: 94
Reflection
*PLUS
Reflection shell
*PLUS
% possible obs: 94 %

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SAP-1/E74(DNA) COMPLEX

Resolution: 2.01→21.4 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.286 -10.4 %RANDOM
Rwork0.222 ---
obs-10370 98.4 %-
Displacement parametersBiso mean: 21.6 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.31 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 2.01→21.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms790 445 0 137 1372
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.17
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d22.6
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.05
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.01→2.1 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.368 -9.2 %
Rwork0.3387 1103 -
obs--93.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPHCSDX.PRO
X-RAY DIFFRACTION2DNA-RNA.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3TOPH11.WAT
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Num. reflection all: 10425 / Rfactor obs: 0.222
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg22.6
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.05
LS refinement shell
*PLUS
Rfactor Rfree: 0.368

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