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- PDB-2v51: Structure of MAL-RPEL1 complexed to actin -

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Basic information

Entry
Database: PDB / ID: 2v51
TitleStructure of MAL-RPEL1 complexed to actin
Components
  • ACTIN, ALPHA SKELETAL MUSCLE
  • MKL/MYOCARDIN-LIKE PROTEIN 1
KeywordsSTRUCTURAL PROTEIN/CONTRACTILE PROTEIN / STRUCTURAL PROTEIN-CONTRACTILE PROTEIN COMPLEX / CONTRACTILE PROTEIN / STRUCTURAL PROTEIN / NUCLEOTIDE-BINDING / TRANSCRIPTION REGULATION / TRANSCRIPTION / PHOSPHOPROTEIN / MUSCLE PROTEIN / METHYLATION / ATP-BINDING / CYTOSKELETON / MAL / RPEL / ACTIN / NUCLEUS
Function / homology
Function and homology information


SUMOylation of transcription cofactors / RHO GTPases Activate Formins / cytoskeletal motor activator activity / myosin heavy chain binding / tropomyosin binding / troponin I binding / filamentous actin / mesenchyme migration / actin filament bundle / negative regulation of apoptotic signaling pathway ...SUMOylation of transcription cofactors / RHO GTPases Activate Formins / cytoskeletal motor activator activity / myosin heavy chain binding / tropomyosin binding / troponin I binding / filamentous actin / mesenchyme migration / actin filament bundle / negative regulation of apoptotic signaling pathway / actin filament bundle assembly / skeletal muscle myofibril / striated muscle thin filament / skeletal muscle thin filament assembly / actin monomer binding / forebrain development / stress fiber / skeletal muscle fiber development / titin binding / actin filament polymerization / filopodium / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / neuron migration / neuron projection development / calcium-dependent protein binding / lamellipodium / actin binding / cell body / actin cytoskeleton organization / molecular adaptor activity / transcription coactivator activity / hydrolase activity / transcription cis-regulatory region binding / protein domain specific binding / DNA-binding transcription factor activity / calcium ion binding / positive regulation of gene expression / positive regulation of DNA-templated transcription / magnesium ion binding / positive regulation of transcription by RNA polymerase II / ATP binding / identical protein binding / nucleus / 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 / DI(HYDROXYETHYL)ETHER / THIOCYANATE ION / 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: 2.35 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 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Feb 28, 2018Group: Database references / Structure summary / Category: audit_author / citation / citation_author
Item: _audit_author.name / _citation.journal_abbrev ..._audit_author.name / _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name
Revision 1.3May 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_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
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
D: ACTIN, ALPHA SKELETAL MUSCLE
E: MKL/MYOCARDIN-LIKE PROTEIN 1
F: MKL/MYOCARDIN-LIKE PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,09116
Polymers91,7614
Non-polymers2,33012
Water3,837213
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5240 Å2
ΔGint-40.2 kcal/mol
Surface area37790 Å2
MethodPQS
Unit cell
Length a, b, c (Å)53.092, 59.071, 166.203
Angle α, β, γ (deg.)90.00, 90.06, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Protein/peptide , 2 types, 4 molecules BDEF

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


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


Mass: 3783.469 Da / Num. of mol.: 2 / Fragment: RPEL1 MOTIF, RESIDUES 16-41 / Source method: obtained synthetically / Source: (synth.) MUS MUSCULUS (house mouse) / References: UniProt: Q8K4J6

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Non-polymers , 6 types, 225 molecules

#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-LAB / LATRUNCULIN B


Mass: 395.513 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H29NO5S / Comment: toxin*YM
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical
ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CNS
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 213 / 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: 2.9 Å3/Da / Density % sol: 58 % / Description: NONE
Crystal growpH: 6.5 / Details: pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Jun 27, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.35→30 Å / Num. obs: 35522 / % possible obs: 86.7 % / Observed criterion σ(I): 1.3 / Redundancy: 2.8 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 9.1
Reflection shellResolution: 2.35→2.48 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 1.3 / % possible all: 72.3

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Processing

Software
NameVersionClassification
REFMAC5.4.0066refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→20 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.903 / SU B: 16.379 / SU ML: 0.188 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.354 / ESU R Free: 0.261 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.248 1890 5.1 %RANDOM
Rwork0.183 ---
obs0.186 35471 86.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.3 Å2
Baniso -1Baniso -2Baniso -3
1-0.2 Å20 Å20.09 Å2
2---0.01 Å20 Å2
3----0.19 Å2
Refinement stepCycle: LAST / Resolution: 2.35→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5878 0 144 213 6235
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0226144
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0371.9918339
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1725751
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.02924.118255
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.382151015
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.8651536
X-RAY DIFFRACTIONr_chiral_restr0.1230.2941
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0214558
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7421.53791
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.39926115
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.56232353
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.9414.52224
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.35→2.41 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.33 99
Rwork0.261 2127
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.705-0.23590.58271.1648-0.09281.54430.0649-0.111-0.0339-0.09480.008-0.0440.12130.0683-0.0729-0.029-0.03140.0579-0.20430.0112-0.15553.91994.958912.691
21.72770.2461-0.66131.2027-0.08381.77840.04520.08680.01850.08510.0118-0.0411-0.12780.1037-0.0569-0.02720.0268-0.0507-0.16460.0102-0.15063.9015.905370.4439
39.5374-6.81586.030810.3596-7.588910.38180.08950.321-0.375-0.0710.3845-0.24530.2870.0606-0.4740.25760.01090.00230.2571-0.00230.012-2.5999-2.880548.5357
47.6213.7706-6.408310.2878-5.51846.35610.0307-0.3050.30420.07750.2585-0.0392-0.12950.0517-0.28920.2671-0.0494-0.07170.23370.0116-0.024-2.762213.71134.6074
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B5 - 371
2X-RAY DIFFRACTION1B1372
3X-RAY DIFFRACTION1B1374
4X-RAY DIFFRACTION2D5 - 371
5X-RAY DIFFRACTION2D1372
6X-RAY DIFFRACTION2D1374
7X-RAY DIFFRACTION3E70 - 97
8X-RAY DIFFRACTION4F70 - 97

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