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- PDB-3mn5: Structures of actin-bound WH2 domains of Spire and the implicatio... -

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Basic information

Entry
Database: PDB / ID: 3mn5
TitleStructures of actin-bound WH2 domains of Spire and the implication for filament nucleation
Components
  • Actin, alpha skeletal muscle
  • Protein spire
KeywordsContractile Protein/Protein binding / WH2 domain / Spire / Actin complex / Contractile Protein-Protein binding complex
Function / homology
Function and homology information


chorion-containing eggshell formation / pole plasm RNA localization / oocyte karyosome formation / establishment of meiotic spindle localization / actin filament-based process / pole plasm oskar mRNA localization / pole plasm assembly / polar body extrusion after meiotic divisions / actin filament network formation / actin nucleation ...chorion-containing eggshell formation / pole plasm RNA localization / oocyte karyosome formation / establishment of meiotic spindle localization / actin filament-based process / pole plasm oskar mRNA localization / pole plasm assembly / polar body extrusion after meiotic divisions / actin filament network formation / actin nucleation / Golgi vesicle transport / cleavage furrow formation / cytoskeletal motor activator activity / oogenesis / positive regulation of mitochondrial fission / myosin heavy chain binding / tropomyosin binding / regulation of cytoskeleton organization / actin filament bundle / troponin I binding / filamentous actin / mesenchyme migration / actin filament bundle assembly / skeletal muscle myofibril / striated muscle thin filament / skeletal muscle thin filament assembly / actin monomer binding / intracellular transport / skeletal muscle fiber development / stress fiber / vesicle-mediated transport / titin binding / actin filament polymerization / cytoplasmic vesicle membrane / actin filament organization / filopodium / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / calcium-dependent protein binding / protein transport / lamellipodium / actin binding / cell body / actin cytoskeleton organization / cell cortex / microtubule binding / mitochondrial outer membrane / cytoskeleton / hydrolase activity / protein domain specific binding / calcium ion binding / positive regulation of gene expression / perinuclear region of cytoplasm / magnesium ion binding / ATP binding / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
Protein Spire / Kinase non-catalytic C-lobe domain / KIND domain / KIND domain profile. / kinase non-catalytic C-lobe domain / Wiskott Aldrich syndrome homology region 2 / WH2 domain profile. / WH2 domain / ATPase, substrate binding domain, subdomain 4 / Actin; Chain A, domain 4 ...Protein Spire / Kinase non-catalytic C-lobe domain / KIND domain / KIND domain profile. / kinase non-catalytic C-lobe domain / Wiskott Aldrich syndrome homology region 2 / WH2 domain profile. / WH2 domain / 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 / Zinc finger, FYVE/PHD-type / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / Zinc finger, RING/FYVE/PHD-type / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / LATRUNCULIN B / Actin, alpha skeletal muscle / Protein spire
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
Oryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsDucka, A.M. / Sitar, T. / Popowicz, G.M. / Huber, R. / Holak, T.A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Structures of actin-bound Wiskott-Aldrich syndrome protein homology 2 (WH2) domains of Spire and the implication for filament nucleation.
Authors: Ducka, A.M. / Joel, P. / Popowicz, G.M. / Trybus, K.M. / Schleicher, M. / Noegel, A.A. / Huber, R. / Holak, T.A. / Sitar, T.
History
DepositionApr 21, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 6, 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 / 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_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.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.value / _struct_conn.pdbx_dist_value / _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.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_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, alpha skeletal muscle
S: Protein spire
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3425
Polymers44,4002
Non-polymers9433
Water8,809489
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3580 Å2
ΔGint-31 kcal/mol
Surface area15400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.960, 71.810, 100.720
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Detailscomplex of Actin and Spire

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AS

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


Mass: 40087.578 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: P68135
#2: Protein/peptide Protein spire


Mass: 4311.981 Da / Num. of mol.: 1 / Fragment: UNP residues 448-485, WH2 2 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: spir, p150-Spir, CG10076 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9U1K1

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Non-polymers , 4 types, 492 molecules

#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#5: Chemical ChemComp-LAB / LATRUNCULIN B


Mass: 395.513 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H29NO5S
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 489 / 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: 2.16 Å3/Da / Density % sol: 43.06 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.9
Details: 0.2 Magnesium formate pH 5.9 20% PEG 3350 , VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9801 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Sep 20, 2009 / Details: LN2 cooled fixed-exit Si(111) monochromator
RadiationMonochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. all: 62290 / Num. obs: 49209 / % possible obs: 79 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.049
Reflection shellResolution: 1.5→1.6 Å / Rmerge(I) obs: 0.203 / Mean I/σ(I) obs: 4.4 / % possible all: 38.1

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Processing

Software
NameVersionClassification
MAR345data collection
MOLREPphasing
REFMAC5.5.0072refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1NWK

1nwk


Resolution: 1.5→39.25 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.937 / SU B: 1.334 / SU ML: 0.051 / Cross valid method: THROUGHOUT / ESU R: 0.091 / ESU R Free: 0.096 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.216 2511 5.1 %RANDOM
Rwork0.17164 ---
obs0.17386 46688 79.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.832 Å2
Baniso -1Baniso -2Baniso -3
1--0.34 Å20 Å20 Å2
2---0.06 Å20 Å2
3---0.4 Å2
Refinement stepCycle: LAST / Resolution: 1.5→39.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2870 0 59 489 3418
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0222990
X-RAY DIFFRACTIONr_angle_refined_deg2.4031.9924054
X-RAY DIFFRACTIONr_dihedral_angle_1_deg11.9425363
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.95223.92125
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.7615515
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.6691519
X-RAY DIFFRACTIONr_chiral_restr0.3820.2454
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.0212207
X-RAY DIFFRACTIONr_mcbond_it1.4591.51826
X-RAY DIFFRACTIONr_mcangle_it2.38922953
X-RAY DIFFRACTIONr_scbond_it3.62831164
X-RAY DIFFRACTIONr_scangle_it5.6064.51101
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.23 64 -
Rwork0.188 1245 -
obs--28.78 %

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