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- PDB-4rwt: Structure of actin-Lmod complex -

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Basic information

Entry
Database: PDB / ID: 4rwt
TitleStructure of actin-Lmod complex
Components
  • Actin-5C
  • Leiomodin-2
KeywordsSTRUCTURAL PROTEIN / leucine rich region / actin nucleation / actin
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 / tropomyosin binding / myofibril / 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 / MOLECULAR REPLACEMENT / Resolution: 2.98 Å
AuthorsChen, X. / Ni, F. / Wang, Q.
CitationJournal: Proc.Natl.Acad.Sci.USA / 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
DepositionDec 5, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 28, 2015Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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 / _struct_ref_seq_dif.details / _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-5C
C: Leiomodin-2
D: Leiomodin-2
B: Actin-5C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)200,3428
Polymers199,2814
Non-polymers1,0614
Water0
1
A: 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 area5930 Å2
ΔGint-32 kcal/mol
Surface area31930 Å2
MethodPISA
2
C: Leiomodin-2
B: Actin-5C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,1714
Polymers99,6402
Non-polymers5312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3720 Å2
ΔGint-19 kcal/mol
Surface area23330 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
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1112A6 - 371
2112B6 - 371
1125C198 - 360
2125D198 - 360

NCS ensembles :
ID
1
2
Detailsone binds to each of the dimer of Assembly Identifier 1

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Components

#1: Protein Actin-5C


Mass: 42886.793 Da / Num. of mol.: 2 / Fragment: UNP residues 1-376
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


Mass: 56753.699 Da / Num. of mol.: 2 / Fragment: UNP residues 153-547
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% PGE3350, 0.2M Magnesium acetate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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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: C(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: 97.47 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1
Reflection shellResolution: 3→3.078 Å / % possible all: 97.55

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Processing

Software
NameVersionClassification
PHENIXmodel building
REFMAC5.2.0019refinement
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.98→51.07 Å / Cor.coef. Fo:Fc: 0.888 / Cor.coef. Fo:Fc free: 0.869 / SU B: 23.355 / SU ML: 0.426 / Cross valid method: THROUGHOUT / ESU R Free: 0.491 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2572 1288 5.1 %RANDOM
Rwork0.24818 ---
obs0.24865 23898 97.46 %-
all-24052 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 50.34 Å2
Baniso -1Baniso -2Baniso -3
1--2.63 Å2-1.16 Å2-1.18 Å2
2---1.15 Å20.72 Å2
3---3.3 Å2
Refinement stepCycle: LAST / Resolution: 2.98→51.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9253 0 64 0 9317
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0229489
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2891.97312848
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.48151181
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.84424.545418
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.945151709
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5621561
X-RAY DIFFRACTIONr_chiral_restr0.0870.21461
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.027041
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2640.24807
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3170.26463
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2450.2338
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3430.296
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1290.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1456tight positional0.090.05
1A1380medium positional0.710.5
2C652medium positional0.250.5
2C641loose positional0.725
LS refinement shellResolution: 2.98→3.057 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.351 86 -
Rwork0.317 1758 -
obs--97.88 %

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