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- PDB-2yje: Oligomeric assembly of actin bound to MRTF-A -

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Basic information

Entry
Database: PDB / ID: 2yje
TitleOligomeric assembly of actin bound to MRTF-A
Components
  • ACTIN, ALPHA SKELETAL MUSCLE
  • MKL/MYOCARDIN-LIKE PROTEIN 1
KeywordsMOTOR PROTEIN
Function / homology
Function and homology information


SUMOylation of transcription cofactors / RHO GTPases Activate Formins / regulation of modification of postsynaptic structure / cytoskeletal motor activator activity / myosin heavy chain binding / tropomyosin binding / actin filament bundle / troponin I binding / filamentous actin / forebrain development ...SUMOylation of transcription cofactors / RHO GTPases Activate Formins / regulation of modification of postsynaptic structure / cytoskeletal motor activator activity / myosin heavy chain binding / tropomyosin binding / actin filament bundle / troponin I binding / filamentous actin / forebrain development / mesenchyme migration / skeletal muscle myofibril / actin filament bundle assembly / negative regulation of apoptotic signaling pathway / striated muscle thin filament / skeletal muscle thin filament assembly / actin monomer binding / skeletal muscle fiber development / stress fiber / 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 / presynapse / lamellipodium / cell body / actin binding / actin cytoskeleton organization / molecular adaptor activity / transcription coactivator activity / transcription cis-regulatory region binding / postsynapse / hydrolase activity / DNA-binding transcription factor activity / protein domain specific binding / calcium ion binding / positive regulation of gene expression / positive regulation of DNA-templated transcription / glutamatergic synapse / magnesium ion binding / positive regulation of transcription by RNA polymerase II / nucleoplasm / ATP binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Helix Hairpins - #2040 / 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 ...Helix Hairpins - #2040 / 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 / Helix Hairpins / 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 / Helix non-globular / Special / 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: 3.1 Å
AuthorsMouilleron, S. / Langer, C.A. / Guettler, S. / McDonald, N.Q. / Treisman, R.
CitationJournal: Sci Signal / Year: 2011
Title: Structure of a pentavalent G-actin*MRTF-A complex reveals how G-actin controls nucleocytoplasmic shuttling of a transcriptional coactivator.
Authors: Mouilleron, S. / Langer, C.A. / Guettler, S. / McDonald, N.Q. / Treisman, R.
History
DepositionMay 19, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 6, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2011Group: Database references / Other / Version format compliance
Revision 1.2Apr 11, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.page_first ..._citation.journal_abbrev / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site
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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)144,85413
Polymers142,0734
Non-polymers2,7819
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)90.935, 90.935, 321.613
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
12
22
32

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 6:21 OR RESSEQ 27:40 OR RESSEQ...
211CHAIN C AND (RESSEQ 6:21 OR RESSEQ 27:40 OR RESSEQ...
311CHAIN B AND (RESSEQ 6:21 OR RESSEQ 27:40 OR RESSEQ...
112CHAIN A AND (RESSEQ 6:21 OR RESSEQ 27:40 OR RESSEQ...
212CHAIN C AND (RESSEQ 6:21 OR RESSEQ 27:40 OR RESSEQ...
312CHAIN B AND (RESSEQ 6:21 OR RESSEQ 27:40 OR RESSEQ...

NCS ensembles :
ID
1
2

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Components

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


Mass: 42096.953 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ORYCTOLAGUS CUNICULUS (rabbit) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): ROSETTA PLYSS / References: UniProt: P68135
#2: Protein MKL/MYOCARDIN-LIKE PROTEIN 1 / BASIC SAP COILED-COIL TRANSCRIPTION ACTIVATOR / MEGAKARYOBLASTIC LEUKEMIA 1 PROTEIN HOMOLOG / ...BASIC SAP COILED-COIL TRANSCRIPTION ACTIVATOR / MEGAKARYOBLASTIC LEUKEMIA 1 PROTEIN HOMOLOG / MYOCARDIN-RELATED TRANSCRIPTION FACTOR A / MRTF-A


Mass: 15782.284 Da / Num. of mol.: 1 / Fragment: RPEL DOMAIN, RESIDUES 16-142
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): ROSETTA PLYSS / References: UniProt: Q8K4J6
#3: Chemical ChemComp-LAB / LATRUNCULIN B


Mass: 395.513 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C20H29NO5S
#4: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 3 / 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.: 3 / Source method: obtained synthetically / Formula: Mg

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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: 2.34 Å3/Da / Density % sol: 47.42 % / Description: NONE
Crystal growpH: 8.25
Details: 0.1 M BTP PH 8.25, 20.5% PEG 3350, 0.2 M SODIUM NITRATE.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 10, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 3.1→45 Å / Num. obs: 24795 / % possible obs: 97.5 % / Observed criterion σ(I): 2 / Redundancy: 6 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 12.4
Reflection shellResolution: 3.1→3.27 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 2.3 / % possible all: 97.5

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2V52

2v52


Resolution: 3.1→19.883 Å / SU ML: 0.39 / σ(F): 0 / Phase error: 25.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2798 1229 5.1 %
Rwork0.2348 --
obs0.2371 24183 95.17 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 81.24 Å2 / ksol: 0.382 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-4.3258 Å20 Å20 Å2
2--4.3258 Å20 Å2
3----8.6515 Å2
Refinement stepCycle: LAST / Resolution: 3.1→19.883 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8022 0 177 0 8199
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0128754
X-RAY DIFFRACTIONf_angle_d1.11511473
X-RAY DIFFRACTIONf_dihedral_angle_d19.983023
X-RAY DIFFRACTIONf_chiral_restr0.0691329
X-RAY DIFFRACTIONf_plane_restr0.0051458
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1228X-RAY DIFFRACTIONPOSITIONAL
12C1228X-RAY DIFFRACTIONPOSITIONAL0.048
13B1284X-RAY DIFFRACTIONPOSITIONAL0.038
21A1032X-RAY DIFFRACTIONPOSITIONAL
22C1032X-RAY DIFFRACTIONPOSITIONAL0.051
23B992X-RAY DIFFRACTIONPOSITIONAL0.042
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.22370.37841350.322377X-RAY DIFFRACTION91
3.2237-3.36970.28361280.25892448X-RAY DIFFRACTION93
3.3697-3.54640.30411190.24132511X-RAY DIFFRACTION95
3.5464-3.76720.29851270.24052597X-RAY DIFFRACTION97
3.7672-4.05580.27741370.2442567X-RAY DIFFRACTION98
4.0558-4.45980.25831410.21582594X-RAY DIFFRACTION98
4.4598-5.09560.25441680.21242587X-RAY DIFFRACTION97
5.0956-6.38440.2891430.24592652X-RAY DIFFRACTION97
6.3844-19.88320.28061310.22682621X-RAY DIFFRACTION91
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)
11.80560.28270.24151.57340.74861.7580.3425-0.06820.30590.3146-0.3136-0.01320.34640.0796-0.03370.4772-0.2106-0.00220.4173-0.00860.410418.202-14.2883-9.9859
21.33430.46220.93361.68241.08141.01950.24960.3789-0.1922-0.2781-0.207-0.0687-0.07750.1466-0.13390.55430.0312-0.02180.8177-0.0920.460320.9331-31.6718-27.4452
32.13720.2879-0.4510.33440.35430.7050.00320.1358-0.08740.19380.3984-0.99430.11911.076-0.32320.53140.1691-0.18971.125-0.07671.105143.2593-35.6002-18.5015
40.5627-0.2909-0.06241.20990.81841.27220.21180.3653-0.3643-0.2275-0.33650.38910.2969-0.0739-0.02350.92870.4812-0.49740.9182-0.87910.777-0.674-54.0702-41.2233
52.7877-0.9181-2.17810.62640.61631.73360.15030.63740.1185-0.156-0.1352-0.012-0.04420.2555-0.0610.87820.3584-0.45271.3173-0.27620.91048.5619-39.4889-53.7722
60.444-0.60340.43180.8189-0.62390.85860.14560.2909-0.4458-0.08180.00080.29510.0938-0.50370.04620.4720.1299-0.17450.9975-0.30780.8196-17.5486-38.8001-32.2854
70.12490.0028-0.11510.10590.02021.220.13650.23010.03730.02430.0125-0.0426-0.356-0.03370.22050.75860.5395-0.31121.2983-0.42860.0493-5.8296-20.5754-42.6731
80.5226-0.13590.0380.6565-0.43740.944-0.07810.031-0.03630.57220.21560.924-0.43640.0395-0.15080.4357-0.02470.22680.34140.10690.8328-4.8067-37.25673.046
92.135-1.242-0.98281.93892.27762.851-0.3518-0.11230.0170.66240.0460.2663-0.39440.00450.22151.02280.05140.19690.33110.05160.51086.5142-29.512717.136
101.31460.26070.45690.6764-0.07021.58620.06330.0161-0.46650.21170.00410.4620.37230.09840.00710.6021-0.1650.10310.3522-0.01620.622611.1753-55.5094-2.3895
111.04930.23340.74941.8261-0.25181.0504-0.0444-0.1052-0.02390.7691-0.2126-0.608-0.02620.21790.07660.6501-0.1605-0.09560.38180.120.433527.6851-44.539311.5832
123.3640.20571.09773.6381-0.17290.4078-0.0743-0.02530.16320.337-0.1096-0.0103-0.7539-0.62340.08850.80870.1813-0.08020.98280.26750.543413.3601-11.2275-30.8639
131.1772-0.86080.7450.6961-0.32312.66260.3510.4031-0.1166-0.5881-0.1294-0.0237-0.41790.3947-0.12620.57960.1417-0.02720.6487-0.1390.41750.5008-22.5577-27.6141
140.6452-0.05620.96670.5116-1.13853.804-0.38740.0077-0.284-0.0287-0.0169-0.1615-0.8327-0.6150.34950.7015-0.0750.0190.5239-0.09730.54352.257-32.3335-20.0308
150.6895-0.8053-0.86721.39150.49263.6954-0.38140.324-0.13030.04080.35130.6810.42660.078-0.15030.7411-0.0865-0.00880.2021-0.02020.5374-1.7979-47.6083-18.8826
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 5:34 OR RESID 69:144 OR RESID 338:375)
2X-RAY DIFFRACTION2CHAIN A AND (RESID 145:180 OR RESID 270:337)
3X-RAY DIFFRACTION3CHAIN A AND (RESID 181:269)
4X-RAY DIFFRACTION4CHAIN B AND (RESID 5:32 OR RESID 70:144 OR RESID 338:375)
5X-RAY DIFFRACTION5CHAIN B AND (RESID 33:69)
6X-RAY DIFFRACTION6CHAIN B AND (RESID 145:180 OR RESID 270:337)
7X-RAY DIFFRACTION7CHAIN B AND (RESID 181:269)
8X-RAY DIFFRACTION8CHAIN C AND (RESID 5:32 OR RESID 70:144 OR RESID 338:375)
9X-RAY DIFFRACTION9CHAIN C AND (RESID 33:69)
10X-RAY DIFFRACTION10CHAIN C AND (RESID 145:180 OR RESID 270:337)
11X-RAY DIFFRACTION11CHAIN C AND (RESID 181:269)
12X-RAY DIFFRACTION12CHAIN M AND (RESID 64:79)
13X-RAY DIFFRACTION13CHAIN M AND (RESID 80:89)
14X-RAY DIFFRACTION14CHAIN M AND (RESID 90:102)
15X-RAY DIFFRACTION15CHAIN M AND (RESID 103:122)

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