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- PDB-1hbx: Ternary Complex of SAP-1 and SRF with specific SRE DNA -

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Basic information

Entry
Database: PDB / ID: 1hbx
TitleTernary Complex of SAP-1 and SRF with specific SRE DNA
Components
  • 5'-D(*CP*AP*CP*AP*CP*CP*GP*GP*AP*AP*GP*TP*CP* CP*TP*AP*AP*TP*TP*AP*GP*GP*CP*CP*AP*T)-3'
  • 5'-D(*GP*AP*TP*GP*GP*CP*CP*TP*AP*AP*TP*TP*AP* GP*GP*AP*CP*TP*TP*CP*CP*GP*GP*TP*G)-3'
  • ETS-DOMAIN PROTEIN ELK-4
  • SERUM RESPONSE FACTOR
KeywordsGENE REGULATION / TRANSCRIPTION COMPLEX / SERUM RESPONSE FACTOR / TERNARY COMPLEX FACTOR
Function / homology
Function and homology information


serum response element binding / positive regulation of transcription by glucose / bronchus cartilage development / lung smooth muscle development / cardiac vascular smooth muscle cell differentiation / trachea cartilage development / dorsal aorta morphogenesis / morphogenesis of an epithelial sheet / regulation of smooth muscle cell differentiation / primitive streak formation ...serum response element binding / positive regulation of transcription by glucose / bronchus cartilage development / lung smooth muscle development / cardiac vascular smooth muscle cell differentiation / trachea cartilage development / dorsal aorta morphogenesis / morphogenesis of an epithelial sheet / regulation of smooth muscle cell differentiation / primitive streak formation / Regulation of NPAS4 gene transcription / tangential migration from the subventricular zone to the olfactory bulb / primary miRNA binding / epithelial cell-cell adhesion / epithelial structure maintenance / negative regulation of amyloid-beta clearance / skin morphogenesis / cardiac muscle cell myoblast differentiation / trophectodermal cell differentiation / bicellular tight junction assembly / cardiac myofibril assembly / positive regulation of smooth muscle contraction / filopodium assembly / NGF-stimulated transcription / heart trabecula formation / positive thymic T cell selection / axon extension / angiogenesis involved in wound healing / cell migration involved in sprouting angiogenesis / Cardiogenesis / long-term synaptic depression / positive regulation of filopodium assembly / platelet formation / sarcomere organization / megakaryocyte development / muscle cell cellular homeostasis / branching involved in blood vessel morphogenesis / stress fiber assembly / eyelid development in camera-type eye / heart looping / face development / lung morphogenesis / associative learning / thyroid gland development / mesoderm formation / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / long-term memory / hematopoietic stem cell differentiation / positive regulation of transcription initiation by RNA polymerase II / establishment of skin barrier / positive regulation of axon extension / neuron development / erythrocyte development / regulation of cell adhesion / response to hormone / response to cytokine / negative regulation of miRNA transcription / positive regulation of DNA-binding transcription factor activity / negative regulation of cell migration / thymus development / hippocampus development / cell-matrix adhesion / positive regulation of cell differentiation / RHO GTPases Activate Formins / cellular response to glucose stimulus / chromatin DNA binding / positive regulation of miRNA transcription / platelet activation / histone deacetylase binding / response to toxic substance / neuron migration / sequence-specific double-stranded DNA binding / cellular senescence / heart development / actin cytoskeleton organization / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor binding / RNA polymerase II-specific DNA-binding transcription factor binding / transcription by RNA polymerase II / cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / response to hypoxia / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of cell population proliferation / chromatin binding / regulation of transcription by RNA polymerase II / chromatin / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
MADS SRF-like / : / SRF-like / Transcription factor, MADS-box / Transcription factor, MADS-box / Transcription factor, MADS-box superfamily / SRF-type transcription factor (DNA-binding and dimerisation domain) / MADS-box domain signature. / MADS-box domain profile. / MADS ...MADS SRF-like / : / SRF-like / Transcription factor, MADS-box / Transcription factor, MADS-box / Transcription factor, MADS-box superfamily / SRF-type transcription factor (DNA-binding and dimerisation domain) / MADS-box domain signature. / MADS-box domain profile. / MADS / 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 / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Serum response factor / ETS domain-containing protein Elk-4
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.15 Å
AuthorsHassler, M. / Richmond, T.J.
CitationJournal: Embo J. / Year: 2001
Title: The B-Box Dominates Sap-1/Srf Interactions in the Structure of the Ternary Complex
Authors: Hassler, M. / Richmond, T.J.
History
DepositionApr 20, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 27, 2001Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SERUM RESPONSE FACTOR
B: SERUM RESPONSE FACTOR
C: 5'-D(*GP*AP*TP*GP*GP*CP*CP*TP*AP*AP*TP*TP*AP* GP*GP*AP*CP*TP*TP*CP*CP*GP*GP*TP*G)-3'
D: SERUM RESPONSE FACTOR
E: SERUM RESPONSE FACTOR
F: 5'-D(*GP*AP*TP*GP*GP*CP*CP*TP*AP*AP*TP*TP*AP* GP*GP*AP*CP*TP*TP*CP*CP*GP*GP*TP*G)-3'
G: ETS-DOMAIN PROTEIN ELK-4
H: ETS-DOMAIN PROTEIN ELK-4
W: 5'-D(*CP*AP*CP*AP*CP*CP*GP*GP*AP*AP*GP*TP*CP* CP*TP*AP*AP*TP*TP*AP*GP*GP*CP*CP*AP*T)-3'
X: 5'-D(*CP*AP*CP*AP*CP*CP*GP*GP*AP*AP*GP*TP*CP* CP*TP*AP*AP*TP*TP*AP*GP*GP*CP*CP*AP*T)-3'


Theoretical massNumber of molelcules
Total (without water)109,09810
Polymers109,09810
Non-polymers00
Water00
1
A: SERUM RESPONSE FACTOR
B: SERUM RESPONSE FACTOR
C: 5'-D(*GP*AP*TP*GP*GP*CP*CP*TP*AP*AP*TP*TP*AP* GP*GP*AP*CP*TP*TP*CP*CP*GP*GP*TP*G)-3'
G: ETS-DOMAIN PROTEIN ELK-4
W: 5'-D(*CP*AP*CP*AP*CP*CP*GP*GP*AP*AP*GP*TP*CP* CP*TP*AP*AP*TP*TP*AP*GP*GP*CP*CP*AP*T)-3'


Theoretical massNumber of molelcules
Total (without water)54,5495
Polymers54,5495
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
D: SERUM RESPONSE FACTOR
E: SERUM RESPONSE FACTOR
F: 5'-D(*GP*AP*TP*GP*GP*CP*CP*TP*AP*AP*TP*TP*AP* GP*GP*AP*CP*TP*TP*CP*CP*GP*GP*TP*G)-3'
H: ETS-DOMAIN PROTEIN ELK-4
X: 5'-D(*CP*AP*CP*AP*CP*CP*GP*GP*AP*AP*GP*TP*CP* CP*TP*AP*AP*TP*TP*AP*GP*GP*CP*CP*AP*T)-3'


Theoretical massNumber of molelcules
Total (without water)54,5495
Polymers54,5495
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)142.680, 144.390, 75.930
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsCOMPLEX OF HOMODIMERIC SERUM RESPONSE FACTOR , THEETS-DOMAIN PROTEIN ELK-4 AND THE DOUBLE STRANDED DNA.

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Components

#1: Protein
SERUM RESPONSE FACTOR / SRF


Mass: 10300.120 Da / Num. of mol.: 4 / Fragment: CORE RESIDUES 132-223
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Gene: SRF (132-223) / Plasmid: PET3A / Gene (production host): SRF CORE (132-223) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: P11831
#2: DNA chain 5'-D(*GP*AP*TP*GP*GP*CP*CP*TP*AP*AP*TP*TP*AP* GP*GP*AP*CP*TP*TP*CP*CP*GP*GP*TP*G)-3'


Mass: 8034.175 Da / Num. of mol.: 2 / Fragment: SRE SPECIFIC DNA / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human)
#3: Protein ETS-DOMAIN PROTEIN ELK-4 / SERUM RESPONSE FACTOR ACCESSORY PROTEIN 1 / SAP-1


Mass: 17973.408 Da / Num. of mol.: 2 / Fragment: RESIDUES 2-156
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Gene: SAP-1 (1-156) / Plasmid: PET3A / Gene (production host): SAP-1 (1-156) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: P28324
#4: DNA chain 5'-D(*CP*AP*CP*AP*CP*CP*GP*GP*AP*AP*GP*TP*CP* CP*TP*AP*AP*TP*TP*AP*GP*GP*CP*CP*AP*T)-3'


Mass: 7941.145 Da / Num. of mol.: 2 / Fragment: SRE SPECIFIC DNA / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human)

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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: 3.6 Å3/Da / Density % sol: 63.8 %
Crystal growpH: 6.5 / Details: PEG 1500, NH4NO3, BIS-TRIS BUFFER, DTT, pH 6.50
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop / PH range low: 6.8 / PH range high: 6.3
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
12.5 mg/mlprotein1dropternary complex
28-10 %PEG15001drop
325 mMBis-Tris1drop
450 mM1dropNH4NO3
50.5 mMdithiothreitol1drop
616-20 %PEG15001reservoir
750 mMBis-Tris1reservoir
8100 mM1reservoirNH4NO3
91.0 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.9326
DetectorType: ADSC Q4 / Detector: CCD / Date: Apr 15, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9326 Å / Relative weight: 1
ReflectionResolution: 3→51 Å / Num. obs: 31747 / % possible obs: 98.5 % / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Biso Wilson estimate: 84.1 Å2 / Rmerge(I) obs: 0.042 / Net I/σ(I): 30.4
Reflection shellResolution: 3→3.05 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.583 / Mean I/σ(I) obs: 1.98 / % possible all: 96.7
Reflection shell
*PLUS
% possible obs: 96.7 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSphasing
CNS0.9refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1SRS, 1BC7

1srs

1bc7


Resolution: 3.15→51 Å / Rfactor Rfree error: 0.005 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
Details: REFINED ALSO WITH REFMAC BY MURSHUDOV, VAGIN, DODSON
RfactorNum. reflection% reflectionSelection details
Rfree0.285 2735 10 %RANDOM
Rwork0.252 ---
obs0.252 27520 98.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 44.37 Å2 / ksol: 0.25 e/Å3
Displacement parametersBiso mean: 83.6 Å2
Baniso -1Baniso -2Baniso -3
1-7.86 Å20 Å20 Å2
2---3.85 Å20 Å2
3----4.01 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.53 Å0.43 Å
Luzzati d res low-6 Å
Luzzati sigma a0.52 Å0.43 Å
Refinement stepCycle: LAST / Resolution: 3.15→51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4562 2120 0 0 6682
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.3
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 3.15→3.35 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.426 450 10 %
Rwork0.369 4020 -
obs--98.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.3

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