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- PDB-1ijj: THE X-RAY CRYSTAL STRUCTURE OF THE COMPLEX BETWEEN RABBIT SKELETA... -

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Basic information

Entry
Database: PDB / ID: 1ijj
TitleTHE X-RAY CRYSTAL STRUCTURE OF THE COMPLEX BETWEEN RABBIT SKELETAL MUSCLE ACTIN AND LATRUNCULIN A AT 2.85 A RESOLUTION
ComponentsACTIN, ALPHA SKELETAL MUSCLE
KeywordsCONTRACTILE PROTEIN / actin / latrunculin / cytoskeleton
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'-TRIPHOSPHATE / LATRUNCULIN A / Actin, alpha skeletal muscle
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsVorobiev, S.M. / Bubb, M.R. / Almo, S.C.
Citation
Journal: J.Biol.Chem. / Year: 2002
Title: Polylysine induces an antiparallel actin dimer that nucleates filament assembly: crystal structure at 3.5-A resolution
Authors: Bubb, M.R. / Govindasamy, L. / Yarmola, E.G. / Vorobiev, S.M. / Almo, S.C. / Somasundaram, T. / Chapman, M.S. / Agbandje-McKenna, M. / McKenna, R.
#1: Journal: J.Biol.Chem. / Year: 2000
Title: Actin-latrunculin A structure and function. Differential modulation of actin-binding protein function by latrunculin A
Authors: Yarmola, E.G. / Somasundaram, T. / Boring, T.A. / Spector, I. / Bubb, M.R.
#2: Journal: Nat.Cell Biol. / Year: 2000
Title: Latrunculin alters the actin-monomer subunit interface to prevent polymerization
Authors: Morton, W.M. / Ayscough, K.R. / McLaughlin, P.J.
History
DepositionApr 26, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 15, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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

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Assembly

Deposited unit
A: ACTIN, ALPHA SKELETAL MUSCLE
B: ACTIN, ALPHA SKELETAL MUSCLE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,1008
Polymers84,1942
Non-polymers1,9066
Water1,00956
1
A: ACTIN, ALPHA SKELETAL MUSCLE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,0504
Polymers42,0971
Non-polymers9533
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ACTIN, ALPHA SKELETAL MUSCLE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,0504
Polymers42,0971
Non-polymers9533
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)100.304, 102.183, 124.218
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121

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Components

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


Mass: 42096.953 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Tissue: MUSCLESkeletal muscle / References: UniProt: P68135
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: Chemical ChemComp-LAR / LATRUNCULIN A / 4-(17-HYDROXY-5,12-DIMETHYL-3-OXO-2,16-DIOXABICYCLO[13.3.1]NONADECA-4,8,10-TRIEN-17-YL)-2-THIAZOLIDINONE / Latrunculin


Mass: 421.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H31NO5S / Comment: toxin*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 3.78 Å3/Da / Density % sol: 67.46 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: ammonium sulfate, magnesium chloride, pH 6.8, VAPOR DIFFUSION, HANGING DROP at 298 K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.984 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.984 Å / Relative weight: 1
ReflectionResolution: 2.85→30 Å / Num. obs: 29997 / % possible obs: 98.7 % / Redundancy: 4 % / Rmerge(I) obs: 0.049
Reflection shellResolution: 2.85→2.95 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.527 / Num. unique all: 2969 / % possible all: 99.3

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1YAG

1yag


Resolution: 2.85→15 Å / Isotropic thermal model: RESTRAINED / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.309 1166 4 %RANDOM
Rwork0.233 ---
all-30205 --
obs-29269 96.9 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.61 Å20 Å20 Å2
2--1.21 Å20 Å2
3---0.4 Å2
Refine analyzeLuzzati coordinate error obs: 0.48 Å
Refinement stepCycle: LAST / Resolution: 2.85→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5498 0 122 56 5676
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.017
X-RAY DIFFRACTIONc_angle_d2.1
X-RAY DIFFRACTIONc_dihedral_angle_d25.4
X-RAY DIFFRACTIONc_improper_angle_d1.22

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