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- PDB-3el2: Crystal Structure of Monomeric Actin Bound to Ca-ATP -

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Basic information

Entry
Database: PDB / ID: 3el2
TitleCrystal Structure of Monomeric Actin Bound to Ca-ATP
ComponentsActin-5C
KeywordsCONTRACTILE PROTEIN / Motor protein / ATP-state / Acetylation / ATP-binding / Cytoplasm / Cytoskeleton / Nucleotide-binding
Function / homology
Function and homology information


Gap junction degradation / Formation of annular gap junctions / EPHB-mediated forward signaling / EPH-ephrin mediated repulsion of cells / VEGFA-VEGFR2 Pathway / Cell-extracellular matrix interactions / RHOBTB2 GTPase cycle / RHOF GTPase cycle / MAP2K and MAPK activation / Platelet degranulation ...Gap junction degradation / Formation of annular gap junctions / EPHB-mediated forward signaling / EPH-ephrin mediated repulsion of cells / VEGFA-VEGFR2 Pathway / Cell-extracellular matrix interactions / RHOBTB2 GTPase cycle / RHOF GTPase cycle / 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 / sperm individualization / brahma complex / maintenance of protein location in cell / Ino80 complex / tube formation / RSC-type complex / SWI/SNF complex / mitotic cytokinesis / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / cytoskeleton / hydrolase activity / chromatin remodeling / regulation of transcription by RNA polymerase II / ATP binding / cytoplasm
Similarity search - Function
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 ...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 / Actin-5C
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsNair, U.B. / Joel, P.B. / Wan, Q. / Lowey, S. / Rould, M.A. / Trybus, K.M.
Citation
Journal: J.Mol.Biol. / Year: 2008
Title: Crystal structures of monomeric actin bound to cytochalasin D.
Authors: Nair, U.B. / Joel, P.B. / Wan, Q. / Lowey, S. / Rould, M.A. / Trybus, K.M.
#1: Journal: J.Biol.Chem. / Year: 2006
Title: Crystal Structures of Expressed Non-polymerizable Monomeric Actin in the ADP and ATP states
Authors: Rould, M.A. / Wan, Q. / Joel, P.B. / Lowey, S. / Trybus, K.M.
History
DepositionSep 19, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...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_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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Actin-5C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,4144
Polymers41,8271
Non-polymers5873
Water3,531196
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)206.634, 54.023, 36.972
Angle α, β, γ (deg.)90.000, 98.160, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Actin-5C


Mass: 41826.668 Da / Num. of mol.: 1 / Mutation: A204E, P243K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Act5C, CG4027 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9 / References: UniProt: P10987
#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


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


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 196 / 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: 2.44 Å3/Da / Density % sol: 49.63 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.2
Details: 20% MPD, 0.1M sodium acetate, 0.1M NaCl, 0.02M CaCl2, pH 5.2, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Sep 21, 2004
RadiationMonochromator: XENOCS MULTILAYER OPTICS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→15 Å / Num. all: 13523 / Num. obs: 13523 / % possible obs: 95.8 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.093 / Χ2: 1.033 / Net I/σ(I): 12.8
Reflection shellResolution: 2.5→2.59 Å / Rmerge(I) obs: 0.268 / Mean I/σ(I) obs: 3.2 / Num. unique all: 1088 / Χ2: 0.904 / % possible all: 77.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT3.006data extraction
MAR345dtbdata collection
EPMRphasing
RefinementStarting model: Protein only from 3EKU

3eku


Resolution: 2.5→15 Å / Occupancy max: 1 / Occupancy min: 1 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.262 1249 8.9 %same cross-validated reflections as used for refinement of 3EKU
Rwork0.203 ---
all0.231 12698 --
obs0.231 12698 90.1 %-
Solvent computationBsol: 31.069 Å2
Displacement parametersBiso max: 83.5 Å2 / Biso mean: 31.53 Å2 / Biso min: 1 Å2
Baniso -1Baniso -2Baniso -3
1--15.616 Å20 Å2-10.563 Å2
2--15.432 Å20 Å2
3---0.184 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.42 Å0.35 Å
Refinement stepCycle: LAST / Resolution: 2.5→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2822 0 33 196 3051
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.1721.5
X-RAY DIFFRACTIONc_scbond_it1.7982
X-RAY DIFFRACTIONc_mcangle_it1.9242
X-RAY DIFFRACTIONc_scangle_it2.6962.5
X-RAY DIFFRACTIONc_bond_d0.0064
X-RAY DIFFRACTIONc_angle_deg1.28
LS refinement shellResolution: 2.5→2.54 Å /
RfactorNum. reflection
Rfree0.381 37
Rwork0.273 -
obs-383
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2cns_atp_param
X-RAY DIFFRACTION3ion.param
X-RAY DIFFRACTION4water_rep.param

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