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- PDB-1srs: SERUM RESPONSE FACTOR (SRF) CORE COMPLEXED WITH SPECIFIC SRE DNA -

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Basic information

Entry
Database: PDB / ID: 1srs
TitleSERUM RESPONSE FACTOR (SRF) CORE COMPLEXED WITH SPECIFIC SRE DNA
Components
  • DNA (5'-D(*CP*CP*(5IU)P*TP*CP*CP*TP*AP*AP*TP*TP*AP*GP*GP*CP*CP*AP*TP*G)-3')
  • DNA (5'-D(*CP*CP*AP*TP*GP*GP*CP*CP*TP*AP*AP*TP*TP*AP*GP*GP*A P*AP*G)-3')
  • PROTEIN (SERUM RESPONSE FACTOR (SRF))
KeywordsTRANSCRIPTION/DNA / TRANSCRIPTION REGULATION / MADS-DOMAIN / COMPLEX (DNA BINDING PROTEIN-DNA) / TRANSCRIPTION-DNA COMPLEX
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 / morphogenesis of an epithelial sheet / dorsal aorta morphogenesis / regulation of smooth muscle cell differentiation / epithelial structure maintenance ...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 / morphogenesis of an epithelial sheet / dorsal aorta morphogenesis / regulation of smooth muscle cell differentiation / epithelial structure maintenance / primitive streak formation / tangential migration from the subventricular zone to the olfactory bulb / Regulation of NPAS4 gene transcription / primary miRNA binding / negative regulation of amyloid-beta clearance / epithelial cell-cell adhesion / cardiac myofibril assembly / skin morphogenesis / cardiac muscle cell myoblast differentiation / trophectodermal cell differentiation / positive regulation of smooth muscle contraction / bicellular tight junction assembly / filopodium assembly / angiogenesis involved in wound healing / heart trabecula formation / NGF-stimulated transcription / positive thymic T cell selection / axon extension / cell migration involved in sprouting angiogenesis / Cardiogenesis / long-term synaptic depression / positive regulation of filopodium assembly / platelet formation / megakaryocyte development / branching involved in blood vessel morphogenesis / sarcomere organization / muscle cell cellular homeostasis / lung morphogenesis / stress fiber assembly / heart looping / eyelid development in camera-type eye / face development / erythrocyte development / associative learning / thyroid gland development / mesoderm formation / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / positive regulation of transcription initiation by RNA polymerase II / hematopoietic stem cell differentiation / neuron development / establishment of skin barrier / positive regulation of axon extension / regulation of cell adhesion / long-term memory / negative regulation of cell migration / cell-matrix adhesion / negative regulation of miRNA transcription / thymus development / response to hormone / response to cytokine / RHO GTPases Activate Formins / hippocampus development / positive regulation of cell differentiation / cellular response to glucose stimulus / neuron migration / chromatin DNA binding / response to toxic substance / platelet activation / positive regulation of DNA-binding transcription factor activity / histone deacetylase binding / positive regulation of miRNA transcription / cellular senescence / sequence-specific double-stranded DNA binding / 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 / response to hypoxia / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of cell population proliferation / chromatin / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / 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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Serum response factor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 3.2 Å
AuthorsPellegrini, L. / Tan, S. / Richmond, T.J.
CitationJournal: Nature / Year: 1995
Title: Structure of serum response factor core bound to DNA.
Authors: Pellegrini, L. / Tan, S. / Richmond, T.J.
History
DepositionJul 28, 1995Processing site: NDB
Revision 1.0Jul 28, 1995Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
W: DNA (5'-D(*CP*CP*(5IU)P*TP*CP*CP*TP*AP*AP*TP*TP*AP*GP*GP*CP*CP*AP*TP*G)-3')
C: DNA (5'-D(*CP*CP*AP*TP*GP*GP*CP*CP*TP*AP*AP*TP*TP*AP*GP*GP*A P*AP*G)-3')
A: PROTEIN (SERUM RESPONSE FACTOR (SRF))
B: PROTEIN (SERUM RESPONSE FACTOR (SRF))


Theoretical massNumber of molelcules
Total (without water)32,3224
Polymers32,3224
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)106.840, 106.840, 76.880
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
DetailsTHERE IS ONE COMPLEX PER ASYMMETRIC UNIT CONSISTING OF TWO IDENTICAL POLYPEPTIDE CHAINS LABELLED *A* AND *B* AND TWO DNA CHAINS LABELLED *W* AND *C*.

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Components

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


Mass: 5867.605 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(*CP*CP*AP*TP*GP*GP*CP*CP*TP*AP*AP*TP*TP*AP*GP*GP*A P*AP*G)-3')


Mass: 5853.812 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein PROTEIN (SERUM RESPONSE FACTOR (SRF))


Mass: 10300.120 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SRF CORE (RESIDUES 132-223) / Plasmid: PET3A / Species (production host): Escherichia coli / Gene (production host): SRF CORE (RESIDUES 132-223) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P11831

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.36 Å3/Da / Density % sol: 63.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: pH 6.50, VAPOR DIFFUSION, HANGING DROP, temperature 293.00K
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2PEG 600011
3NH4 CITRATE11
4BIS-TRIS-PROPANE11
5MGCL211
Crystal grow
*PLUS
Temperature: 20 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.2 mMprotein DNA complex1drop
250-150 mM1drop(NH)4H citrate
350 mMbis-Tris1drop
430 mM1dropMgCl2
56 %PEG60001drop
650-150 mM1reservoir(NH)4H citrate
750 mMbis-Tris1reservoir
830 mM1reservoirMgCl2
96 %PEG60001reservoir

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Data collection

DiffractionMean temperature: 277 K
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 3.2→25 Å / Num. obs: 7629 / % possible obs: 98 % / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Rmerge(I) obs: 0.106
Reflection
*PLUS
Highest resolution: 3.2 Å / Lowest resolution: 25 Å / % possible obs: 98 %

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Processing

SoftwareName: X-PLOR / Version: 3.1 / Classification: refinement
RefinementResolution: 3.2→10 Å / σ(F): 2
RfactorNum. reflection% reflection
Rwork0.228 --
obs0.228 7162 96 %
Refinement stepCycle: LAST / Resolution: 3.2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1304 769 1 0 2074
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.006
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_deg0.9
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d35.7
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.87
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1
X-RAY DIFFRACTIONx_mcangle_it1.5
X-RAY DIFFRACTIONx_scbond_it1.5
X-RAY DIFFRACTIONx_scangle_it2
Refinement
*PLUS
Highest resolution: 3.2 Å / Lowest resolution: 10 Å / σ(F): 2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 40.4 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_angle_deg0.9
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg35.7
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.87
X-RAY DIFFRACTIONx_mcbond_it1
X-RAY DIFFRACTIONx_scbond_it1.5
X-RAY DIFFRACTIONx_mcangle_it1.5
X-RAY DIFFRACTIONx_scangle_it2

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