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- PDB-2zwh: Model for the F-actin structure -

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Basic information

Entry
Database: PDB / ID: 2zwh
TitleModel for the F-actin structure
ComponentsActin, alpha skeletal muscle
KeywordsCONTRACTILE PROTEIN / F-actin / G-actin / cytoskelton / ATP-binding / Cytoskeleton / Methylation / Muscle protein / Nucleotide-binding / Phosphoprotein
Function / homology
Function and homology information


cytoskeletal motor activator activity / tropomyosin binding / myosin heavy chain binding / mesenchyme migration / troponin I binding / actin filament bundle / filamentous actin / actin filament bundle assembly / skeletal muscle thin filament assembly / striated muscle thin filament ...cytoskeletal motor activator activity / tropomyosin binding / myosin heavy chain binding / mesenchyme migration / troponin I binding / actin filament bundle / filamentous actin / actin filament bundle assembly / skeletal muscle thin filament assembly / striated muscle thin filament / skeletal muscle myofibril / 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 / calcium-dependent protein binding / lamellipodium / cell body / hydrolase activity / protein domain specific binding / calcium ion binding / positive regulation of gene expression / magnesium ion binding / ATP binding / identical protein binding / cytoplasm
Similarity search - Function
Actin; Chain A, domain 2 / Actin; Chain A, domain 2 / 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; Chain A, domain 2 / Actin; Chain A, domain 2 / 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 / Roll / Alpha-Beta Complex / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Actin, alpha skeletal muscle
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodFIBER DIFFRACTION / SYNCHROTRON / Resolution: 3.3 Å
AuthorsOda, T. / Iwasa, M. / Aihara, T. / Maeda, Y. / Narita, A.
CitationJournal: Nature / Year: 2009
Title: The nature of the globular- to fibrous-actin transition.
Authors: Oda, T. / Iwasa, M. / Aihara, T. / Maeda, Y. / Narita, A.
History
DepositionDec 5, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 20, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 11, 2015Group: Other
Revision 1.3Oct 14, 2015Group: Refinement description
Revision 1.4Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Actin, alpha skeletal muscle
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,3433
Polymers41,8761
Non-polymers4672
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)1.000, 1.000, 1.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number1
Space group name H-MP1
DetailsF-ACTIN IS A HELICAL POLYMER OF ACTIN MOLECULES. THE Z-AXIS OF THE ACTIN COORDINATES SHOWN IN THIS PDB-FILE IS A HELIX AXIS. THE NEXT SUBUNIT IN F-ACTIN IS POSITIONED BY 166.4 DEGREE RIGHT ROTATION ABOUT THE HELIX AXIS AND 27.59 ANGSTROM SHIFT ALONG THE HELIX AXIS.

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Components

#1: Protein Actin, alpha skeletal muscle / / Alpha-actin-1


Mass: 41875.633 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Rabbit skeletal muscle / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: P68135
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca

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Experimental details

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Experiment

ExperimentMethod: FIBER DIFFRACTION

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Data collection

Diffraction
IDCrystal-ID
11
21
31
41
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSPring-8 BL41XU11
SYNCHROTRONSPring-8 BL40B221
SYNCHROTRONSPring-8 BL40B231
SYNCHROTRONSPring-8 BL45XU40.9
Detector
TypeIDDetectorDate
RIGAKU RAXIS IV1IMAGE PLATEOct 13, 1998
RIGAKU RAXIS IV2IMAGE PLATESep 17, 2001
RIGAKU RAXIS IV3IMAGE PLATEMay 28, 2004
RIGAKU RAXIS IV4IMAGE PLATENov 18, 2006
Radiation
IDMonochromatic (M) / Laue (L)Wavelength-ID
1M1
2M1
3M1
4M1
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.91

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Processing

SoftwareName: X-PLOR / Version: 3.1 / Classification: refinement
RefinementResolution: 3.3→56 Å / Rfactor all: 0.143
Details: THE DIFFRACTION DATA WERE EXTRACTED USING THE PROPER HELICAL SYMMETRY SUCH AS A SELECTION RULE L=-153N+331M AND A REPEAT DISTANCE 9135 ANGSTRUM. THE LAYER-LINE DISTRIBUTION BY THE SELECTOIN ...Details: THE DIFFRACTION DATA WERE EXTRACTED USING THE PROPER HELICAL SYMMETRY SUCH AS A SELECTION RULE L=-153N+331M AND A REPEAT DISTANCE 9135 ANGSTRUM. THE LAYER-LINE DISTRIBUTION BY THE SELECTOIN RULE IS CLOSE TO THAT BY L=-6N+13M IN PRINCILE ONE LAYER-LINE BY L=-6N+13M SEPARATES SEVERAL LAYER-LINES BY L=-153N+331M. BUT THE SEPARATIONS WERE NOT CLEAR AND THE LAYER-LINE INTENSITYIES WERE EXTRACTED AS "GROUPING LAYER-LINE INTENSITIES" FROM EXPERIMANTAL PATTERNS. THEN THE LAYER-LINE INTENSTITIES WERE HANDLED AS "GROUPING LAYER-LINE INTENSITIES" RE-INDEXED BY L=-6N+13M. THE INITIAL MODELS OF F-ACTIN WERE MADE FROM THE THREE CRYSTAL STRUCTURE OF 1J6Z, 2BTF AND 1HLU. FIRST THE RADIUS AND THREE ORIENTAIONS OF THE SUBUNIT IN F-ACTIN WERE DETERMINED BY THE RIGID BODY SEARCH USING THE DIFFRACTION DATA OF 56-7.2 ANGSTROM. NEXT THE SUBUNIT COMFORMATIONS WERE SEARCHED ALONG THE ADDITIONAL 12 LOWEST ELASTIC NORMAL MODES OF ACTIN MONOMER VIBRATIONS BY COMPARISON BETWEEN THE EXPERIMETAL DIFFRACTION DATA AND THE CALCULATION AT 56-7.2 ANGSTROM. THE DIFFRACTION WAS CALCULATED USING A REPEAT DISTANCE OF 9135A AND A SELECTION RULE L=-153N+331M. THE CALCULATED LAYER-LINE INTENSTITIES ALSO WERE HANDLED A "GROUPING LAYER-LINE INTENSITIES" RE-INDEXED BY L=- 6N+13M. WE CAN NOT FIND THE GOOD SOLVENT MODEL AROUND F-ACTIN. THEN WE USED TWO KINDS OF ATOMIC SCATTERING FACTORS AT THE HIGH RESOLUTION AND THE LOW RESOLUTION DATA.THE MOLECULAR DYNAMICS REFINEMENT AND ENERGY-MINIMIZATION WERE REPEATED IN TRUN USING THE LOW RESOLUTION DATA (RADIALLY 6.5-56 A FROM ORIGIN) AND THE HIGH RESOLUTION DATA (RADIALLY 3.3-5.5 A AND LATERALLY FROM THE MERIDIAN TO 5.5 A) BY FX-PLOR. TO JUDGE THE MODELS, TWO KINDS OF R-FACTORS WERE CALUCLATED AGAINT THE DIFFRACTION PATTERN TO AVOID THE DECOMVOLUTION ERROR. R-FACTOR-FIT IS AN R-FACTOR AGAINST FITTING AREA (THE AREA RADIAL 6.5-56 and 3.6-5.5A AND LATERALLY FROM THE MERIDIAN TO 5.8 A). THE R-FACTOR-NON-FIT IS AN R-FACTOR AGAINST NON-FITTING AREA (THE AREA RADIALLY 5.5 - 6.5 A AND LATERALLY TO 15 A). R-FACTOR-FIT : 0.143 R-FACTOR-NON-FIT : 0.207
Refinement stepCycle: LAST / Resolution: 3.3→56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2933 0 28 0 2961

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