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- PDB-5wfn: Revised model of leiomodin 2-mediated actin regulation (alternate... -

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Basic information

Entry
Database: PDB / ID: 5wfn
TitleRevised model of leiomodin 2-mediated actin regulation (alternate refinement of PDB 4RWT)
Components
  • Actin-5C
  • Leiomodin-2
KeywordsMOTOR PROTEIN / actin regulation / leiomodin / filament nucleation
Function / homology
Function and homology information


Gap junction degradation / Formation of annular gap junctions / EPHB-mediated forward signaling / EPH-ephrin mediated repulsion of cells / Recycling pathway of L1 / VEGFA-VEGFR2 Pathway / : / Cell-extracellular matrix interactions / RHOBTB2 GTPase cycle / RHOF GTPase cycle ...Gap junction degradation / Formation of annular gap junctions / EPHB-mediated forward signaling / EPH-ephrin mediated repulsion of cells / Recycling pathway of L1 / VEGFA-VEGFR2 Pathway / : / Cell-extracellular matrix interactions / RHOBTB2 GTPase cycle / RHOF GTPase cycle / pointed-end actin filament capping / MAP2K and MAPK activation / Platelet degranulation / RHO GTPases Activate WASPs and WAVEs / Regulation of actin dynamics for phagocytic cup formation / DNA Damage Recognition in GG-NER / UCH proteinases / Clathrin-mediated endocytosis / myofibril assembly / sperm individualization / actin nucleation / brahma complex / maintenance of protein location in cell / tube formation / Ino80 complex / M band / sarcomere organization / myofibril / tropomyosin binding / positive regulation of actin filament polymerization / striated muscle thin filament / mitotic cytokinesis / actin monomer binding / actin filament polymerization / sarcomere / muscle contraction / actin filament organization / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / actin binding / cytoskeleton / hydrolase activity / chromatin remodeling / ATP binding / cytoplasm
Similarity search - Function
Tropomodulin / Tropomodulin / WH2 domain / WH2 domain profile. / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / ATPase, substrate binding domain, subdomain 4 / Actin; Chain A, domain 4 / Alpha-Beta Horseshoe / ATPase, nucleotide binding domain ...Tropomodulin / Tropomodulin / WH2 domain / WH2 domain profile. / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / ATPase, substrate binding domain, subdomain 4 / Actin; Chain A, domain 4 / Alpha-Beta Horseshoe / 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 / Leucine-rich repeat domain superfamily / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Actin-5C / Leiomodin-2
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3 Å
AuthorsYurtsever, Z. / Eck, M.J. / Dominguez, R.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM073791 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM110352 United States
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2015
Title: Mechanisms of leiomodin 2-mediated regulation of actin filament in muscle cells.
Authors: Chen, X. / Ni, F. / Kondrashkina, E. / Ma, J. / Wang, Q.
History
DepositionJul 12, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 30, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 31, 2018Group: Database references / Category: pdbx_related_exp_data_set / Item: _pdbx_related_exp_data_set.data_reference
Revision 1.3Aug 22, 2018Group: Data collection / Database references / Category: pdbx_related_exp_data_set / Item: _pdbx_related_exp_data_set.data_reference
Revision 1.4Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 23, 2020Group: Database references / Derived calculations / Category: pdbx_related_exp_data_set / struct_conn
Item: _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id ..._struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id
Revision 1.6Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 0This entry reflects an alternative modeling of the original data in 4RWT, determined by X.Chen, F. ...This entry reflects an alternative modeling of the original data in 4RWT, determined by X.Chen, F.Ni, E.Kondrashkina, J.Ma, Q.Wang.
Remark 200SEE THE ORIGINAL DATA, ENTRY 4RWT
Remark 280SEE THE ORIGINAL DATA, ENTRY 4RWT

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Actin-5C
C: Leiomodin-2
B: Actin-5C
D: Leiomodin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)200,3428
Polymers199,2814
Non-polymers1,0614
Water0
1
A: Actin-5C
C: Leiomodin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,1714
Polymers99,6402
Non-polymers5312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5540 Å2
ΔGint-33 kcal/mol
Surface area24100 Å2
MethodPISA
2
B: Actin-5C
D: Leiomodin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,1714
Polymers99,6402
Non-polymers5312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5480 Å2
ΔGint-32 kcal/mol
Surface area24120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.350, 65.650, 81.920
Angle α, β, γ (deg.)101.29, 90.94, 107.97
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Actin-5C


Mass: 42886.793 Da / Num. of mol.: 2 / Mutation: K291E, P322K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Act5C, CG4027 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P10987
#2: Protein Leiomodin-2 / Cardiac leiomodin / C-LMOD / Leiomodin


Mass: 56753.699 Da / Num. of mol.: 2
Mutation: del(97-128), del(421-440), K426G, K427S, K428G, K429S, K431G, K432S, K434G, K435S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LMOD2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6P5Q4
#3: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / 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: 1.64 Å3/Da / Density % sol: 24.98 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 20% PEG3350, 0.2 M magnesium acetate

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 24, 2014
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.98→51.07 Å / Num. obs: 25186 / % possible obs: 97.5 %
Reflection shellHighest resolution: 2.98 Å

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Processing

SoftwareName: PHENIX / Version: (1.11.1_2575: ???) / Classification: refinement
RefinementResolution: 3→44.245 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 2.12 / Phase error: 25.8
RfactorNum. reflection% reflection
Rfree0.2463 1261 5.11 %
Rwork0.2081 --
obs0.2101 24687 97.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3→44.245 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8842 0 64 0 8906
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0099064
X-RAY DIFFRACTIONf_angle_d0.88812262
X-RAY DIFFRACTIONf_dihedral_angle_d15.655532
X-RAY DIFFRACTIONf_chiral_restr0.0481400
X-RAY DIFFRACTIONf_plane_restr0.0061570
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.12010.31691180.26642654X-RAY DIFFRACTION97
3.1201-3.26210.30831380.25612581X-RAY DIFFRACTION97
3.2621-3.4340.31031670.24522560X-RAY DIFFRACTION97
3.434-3.64910.28631300.22792625X-RAY DIFFRACTION97
3.6491-3.93070.2571360.21042594X-RAY DIFFRACTION98
3.9307-4.32590.22651400.18712597X-RAY DIFFRACTION98
4.3259-4.95120.19371480.17112607X-RAY DIFFRACTION98
4.9512-6.23520.24041400.20722608X-RAY DIFFRACTION98
6.2352-44.24970.21271440.19182600X-RAY DIFFRACTION97

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