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- PDB-3mn6: Structures of actin-bound WH2 domains of Spire and the implicatio... -

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Basic information

Entry
Database: PDB / ID: 3mn6
TitleStructures of actin-bound WH2 domains of Spire and the implication for filament nucleation
Components
  • Actin-5C
  • 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 / Gap junction degradation / Formation of annular gap junctions / EPHB-mediated forward signaling / EPH-ephrin mediated repulsion of cells / Cell-extracellular matrix interactions / RHOBTB2 GTPase cycle / RHOF GTPase cycle / VEGFA-VEGFR2 Pathway ...chorion-containing eggshell formation / pole plasm RNA localization / Gap junction degradation / Formation of annular gap junctions / EPHB-mediated forward signaling / EPH-ephrin mediated repulsion of cells / Cell-extracellular matrix interactions / RHOBTB2 GTPase cycle / RHOF GTPase cycle / VEGFA-VEGFR2 Pathway / ovarian fusome organization / oocyte karyosome formation / Platelet degranulation / MAP2K and MAPK activation / establishment of meiotic spindle localization / RHO GTPases Activate WASPs and WAVEs / Regulation of actin dynamics for phagocytic cup formation / actin filament-based process / pole plasm oskar mRNA localization / DNA Damage Recognition in GG-NER / pole plasm assembly / Clathrin-mediated endocytosis / polar body extrusion after meiotic divisions / actin filament network formation / sperm individualization / UCH proteinases / actin nucleation / Golgi vesicle transport / maintenance of protein location in cell / cleavage furrow formation / brahma complex / tube formation / Ino80 complex / oogenesis / positive regulation of mitochondrial fission / regulation of cytoskeleton organization / mitotic cytokinesis / intracellular transport / vesicle-mediated transport / cytoplasmic vesicle membrane / actin filament organization / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / protein transport / actin cytoskeleton / actin binding / actin cytoskeleton organization / cell cortex / microtubule binding / mitochondrial outer membrane / cytoskeleton / hydrolase activity / chromatin remodeling / perinuclear region of cytoplasm / ATP 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 / Actin-5C / Protein spire
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 1.3Oct 6, 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_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.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.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.ptnr2_auth_asym_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
Revision 1.4Sep 6, 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

Downloads & links

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Assembly

Deposited unit
A: Actin-5C
F: Actin-5C
K: Actin-5C
X: Protein spire
Y: Protein spire
Z: Protein spire
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,71712
Polymers130,0766
Non-polymers1,6426
Water14,052780
1
A: Actin-5C
X: Protein spire
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,9064
Polymers43,3592
Non-polymers5472
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2020 Å2
ΔGint-25 kcal/mol
Surface area16870 Å2
MethodPISA
2
F: Actin-5C
Y: Protein spire
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,9064
Polymers43,3592
Non-polymers5472
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1990 Å2
ΔGint-24 kcal/mol
Surface area16890 Å2
MethodPISA
3
K: Actin-5C
Z: Protein spire
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,9064
Polymers43,3592
Non-polymers5472
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2020 Å2
ΔGint-25 kcal/mol
Surface area16920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.300, 55.950, 125.370
Angle α, β, γ (deg.)90.00, 120.04, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Actin-5C


Mass: 41723.527 Da / Num. of mol.: 3 / 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) / References: UniProt: P10987
#2: Protein/peptide Protein spire


Mass: 1635.006 Da / Num. of mol.: 3 / Fragment: Spire
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
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 780 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE OF CHAINs X,Y,Z IS : ELTPY EILMGDIRAK KYQLRKVMVN GDIPPRVKKD AHAMILEFIR SRPPLKKASD ...THE SEQUENCE OF CHAINs X,Y,Z IS : ELTPY EILMGDIRAK KYQLRKVMVN GDIPPRVKKD AHAMILEFIR SRPPLKKASD RQLGPPRMCE PSPREQLMES IRKGKELKQI TPPEA

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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: 2.92 Å3/Da / Density % sol: 57.94 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.6
Details: 0.2 M ammonium formate pH 6.6 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: 1.63→50 Å / Num. all: 102374 / Num. obs: 90708 / % possible obs: 80.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.056
Reflection shellResolution: 2→2.1 Å / Rmerge(I) obs: 0.195 / Mean I/σ(I) obs: 5 / % possible all: 47.6

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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: 2HF4

2hf4


Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.916 / SU B: 4.048 / SU ML: 0.114 / Cross valid method: THROUGHOUT / ESU R: 0.203 / ESU R Free: 0.182 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23865 4107 5 %RANDOM
Rwork0.19057 ---
obs0.19294 78737 81.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.837 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å20 Å2-0.01 Å2
2---0.14 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8736 0 96 780 9612
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0229012
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.221.97612237
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.05651128
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.25223.871372
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.15151497
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3631554
X-RAY DIFFRACTIONr_chiral_restr0.0790.21377
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0216723
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5151.55655
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.00429081
X-RAY DIFFRACTIONr_scbond_it1.5533357
X-RAY DIFFRACTIONr_scangle_it2.6664.53156
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.264 157 -
Rwork0.217 2991 -
obs--42.27 %

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