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- PDB-2v52: Structure of MAL-RPEL2 complexed to G-actin -

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Basic information

Entry
Database: PDB / ID: 2v52
TitleStructure of MAL-RPEL2 complexed to G-actin
Components
  • ACTIN, ALPHA SKELETAL MUSCLE
  • MKL/MYOCARDIN-LIKE PROTEIN 1
KeywordsSTRUCTURAL PROTEIN/CONTRACTILE PROTEIN / STRUCTURAL PROTEIN / CONTRACTILE PROTEIN / NUCLEOTIDE-BINDING / ALTERNATIVE SPLICING / TRANSCRIPTION REGULATION / TRANSCRIPTION / PHOSPHOPROTEIN / MUSCLE PROTEIN / METHYLATION / ATP-BINDING / COILED COIL / CYTOSKELETON / MAL / RPEL / ACTIN / NUCLEUS / CYTOPLASM / ACETYLATION / STRUCTURAL PROTEIN-CONTRACTILE PROTEIN complex
Function / homology
Function and homology information


positive regulation of hepatic stellate cell migration / positive regulation of hepatic stellate cell contraction / smooth muscle cell differentiation / SUMOylation of transcription cofactors / positive regulation of hepatic stellate cell proliferation / leucine zipper domain binding / positive regulation of hepatic stellate cell activation / positive regulation of endothelial cell differentiation / RHO GTPases Activate Formins / regulation of modification of postsynaptic structure ...positive regulation of hepatic stellate cell migration / positive regulation of hepatic stellate cell contraction / smooth muscle cell differentiation / SUMOylation of transcription cofactors / positive regulation of hepatic stellate cell proliferation / leucine zipper domain binding / positive regulation of hepatic stellate cell activation / positive regulation of endothelial cell differentiation / RHO GTPases Activate Formins / regulation of modification of postsynaptic structure / forebrain development / positive regulation of actin filament polymerization / wound healing, spreading of cells / cytoskeletal motor activator activity / positive regulation of cardiac muscle hypertrophy / myosin heavy chain binding / tropomyosin binding / actin filament bundle / negative regulation of apoptotic signaling pathway / troponin I binding / filamentous actin / mesenchyme migration / positive regulation of collagen biosynthetic process / negative regulation of cardiac muscle cell apoptotic process / skeletal muscle myofibril / striated muscle thin filament / actin filament bundle assembly / skeletal muscle thin filament assembly / actin monomer binding / positive regulation of neuron differentiation / skeletal muscle fiber development / stress fiber / actin filament polymerization / titin binding / filopodium / actin filament / neuron migration / positive regulation of miRNA transcription / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / neuron projection development / calcium-dependent protein binding / actin cytoskeleton organization / lamellipodium / negative regulation of neuron apoptotic process / presynapse / nuclear membrane / actin binding / cell body / molecular adaptor activity / transcription coactivator activity / postsynapse / transcription cis-regulatory region binding / DNA-binding transcription factor activity / protein domain specific binding / hydrolase activity / positive regulation of gene expression / calcium ion binding / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / glutamatergic synapse / magnesium ion binding / positive regulation of transcription by RNA polymerase II / DNA-templated transcription / nucleoplasm / ATP binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Myocardin-like / RPEL repeat / RPEL repeat / RPEL repeat profile. / Repeat in Drosophila CG10860, human KIAA0680 and C. elegans F26H9.2 / SAP domain superfamily / SAP motif profile. / SAP domain / Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation / SAP domain ...Myocardin-like / RPEL repeat / RPEL repeat / RPEL repeat profile. / Repeat in Drosophila CG10860, human KIAA0680 and C. elegans F26H9.2 / SAP domain superfamily / SAP motif profile. / SAP domain / Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation / SAP domain / ATPase, substrate binding domain, subdomain 4 / Actin; Chain A, domain 4 / ATPase, nucleotide binding domain / Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Actin / Actin family / Actin / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / LATRUNCULIN B / Actin, alpha skeletal muscle / Myocardin-related transcription factor A
Similarity search - Component
Biological speciesORYCTOLAGUS CUNICULUS (rabbit)
MUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsMouilleron, S. / Guettler, S. / Langer, C.A. / Treisman, R. / McDonald, N.Q.
CitationJournal: EMBO J. / Year: 2008
Title: Molecular basis for G-actin binding to RPEL motifs from the serum response factor coactivator MAL.
Authors: Mouilleron, S. / Guettler, S. / Langer, C.A. / Treisman, R. / McDonald, N.Q.
History
DepositionOct 1, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 25, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 12, 2017Group: Advisory / Derived calculations
Category: database_PDB_caveat / pdbx_struct_conn_angle / struct_conn
Item: _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id ..._pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Revision 2.0Feb 28, 2018Group: Atomic model / Database references / Category: atom_site / citation / citation_author
Item: _atom_site.occupancy / _citation.journal_abbrev ..._atom_site.occupancy / _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name
Revision 2.1May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: ACTIN, ALPHA SKELETAL MUSCLE
M: MKL/MYOCARDIN-LIKE PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1307
Polymers46,0182
Non-polymers1,1115
Water6,467359
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2460 Å2
ΔGint-11.8 kcal/mol
Surface area20010 Å2
MethodPQS
Unit cell
Length a, b, c (Å)54.750, 55.440, 138.390
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Protein/peptide , 2 types, 2 molecules BM

#1: Protein ACTIN, ALPHA SKELETAL MUSCLE / ACTIN / ALPHA SKELETAL MUSCLE / ALPHA-ACTIN-1


Mass: 42096.953 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit) / References: UniProt: P68135
#2: Protein/peptide MKL/MYOCARDIN-LIKE PROTEIN 1 / MRTF-A / MAL / MEGAKARYOBLASTIC LEUKEMIA 1 PROTEIN HOMOLOG / BASIC SAP COILED-COIL TRANSCRIPTION ACTIVATOR


Mass: 3921.536 Da / Num. of mol.: 1 / Fragment: RPEL2 / Source method: obtained synthetically / Source: (synth.) MUS MUSCULUS (house mouse) / References: UniProt: Q8K4J6

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Non-polymers , 5 types, 364 molecules

#3: Chemical ChemComp-LAB / LATRUNCULIN B


Mass: 395.513 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H29NO5S
#4: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 359 / 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: 2.01 Å3/Da / Density % sol: 38.22 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Oct 11, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.45→30 Å / Num. obs: 74958 / % possible obs: 99.3 % / Observed criterion σ(I): 1.2 / Redundancy: 5.2 % / Biso Wilson estimate: 17.81 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 6
Reflection shellResolution: 1.45→1.53 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 1.2 / % possible all: 96

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.45→29.352 Å / SU ML: 0.17 / σ(F): 1.35 / Phase error: 15.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1878 3769 5 %
Rwork0.1469 --
obs0.149 74958 99.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 63.742 Å2 / ksol: 0.386 e/Å3
Displacement parametersBiso mean: 24.78 Å2
Baniso -1Baniso -2Baniso -3
1-3.7511 Å20 Å2-0 Å2
2--2.6427 Å20 Å2
3----6.3937 Å2
Refinement stepCycle: LAST / Resolution: 1.45→29.352 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3053 0 71 359 3483
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.063483
X-RAY DIFFRACTIONf_angle_d2.844772
X-RAY DIFFRACTIONf_dihedral_angle_d18.781362
X-RAY DIFFRACTIONf_chiral_restr0.2529
X-RAY DIFFRACTIONf_plane_restr0.02609
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.46840.25121340.22592407X-RAY DIFFRACTION92
1.4684-1.48770.26871210.22442483X-RAY DIFFRACTION95
1.4877-1.50810.24281410.20592528X-RAY DIFFRACTION97
1.5081-1.52960.23851410.19222623X-RAY DIFFRACTION100
1.5296-1.55240.23581350.17992612X-RAY DIFFRACTION100
1.5524-1.57670.21661370.16842614X-RAY DIFFRACTION100
1.5767-1.60250.21861410.1532642X-RAY DIFFRACTION100
1.6025-1.63020.21341330.14832643X-RAY DIFFRACTION100
1.6302-1.65980.20061350.14222638X-RAY DIFFRACTION100
1.6598-1.69170.17621410.13092621X-RAY DIFFRACTION100
1.6917-1.72630.18921410.11992614X-RAY DIFFRACTION100
1.7263-1.76380.16271620.11842618X-RAY DIFFRACTION100
1.7638-1.80480.16761620.11422604X-RAY DIFFRACTION100
1.8048-1.84990.17111260.11022671X-RAY DIFFRACTION100
1.8499-1.90.15221310.10932630X-RAY DIFFRACTION100
1.9-1.95580.14781200.10632671X-RAY DIFFRACTION100
1.9558-2.0190.15491390.11042638X-RAY DIFFRACTION100
2.019-2.09110.14951400.11082652X-RAY DIFFRACTION100
2.0911-2.17480.15311400.11582656X-RAY DIFFRACTION100
2.1748-2.27370.17841300.11942652X-RAY DIFFRACTION100
2.2737-2.39360.17951420.12332649X-RAY DIFFRACTION100
2.3936-2.54350.13431100.13292709X-RAY DIFFRACTION100
2.5435-2.73970.17031570.13582663X-RAY DIFFRACTION100
2.7397-3.01520.16381450.14452673X-RAY DIFFRACTION100
3.0152-3.45090.15981560.14092681X-RAY DIFFRACTION99
3.4509-4.34550.18451390.13312749X-RAY DIFFRACTION100
4.3455-29.35790.22911700.18582848X-RAY DIFFRACTION99

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