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- PDB-2vcp: Crystal structure of N-Wasp VC domain in complex with skeletal actin -

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Basic information

Entry
Database: PDB / ID: 2vcp
TitleCrystal structure of N-Wasp VC domain in complex with skeletal actin
Components
  • ACTIN, ALPHA SKELETAL MUSCLE
  • NEURAL WISKOTT-ALDRICH SYNDROME PROTEIN
KeywordsSTRUCTURAL PROTEIN / ACTIN-BINDING / TRANSCRIPTION / MUSCLE PROTEIN / NUCLEOTIDE-BINDING / TRANSCRIPTION REGULATION / METHYLATION / ATP-BINDING / CYTOSKELETON / PHOSPHORYLATION / WH2 / WASP / ACTIN / NUCLEUS / TWINNING
Function / homology
Function and homology information


negative regulation of membrane tubulation / spindle localization / positive regulation of clathrin-dependent endocytosis / negative regulation of lymphocyte migration / NOSTRIN mediated eNOS trafficking / GTPase regulator activity / actin cap / vesicle organization / vesicle budding from membrane / vesicle transport along actin filament ...negative regulation of membrane tubulation / spindle localization / positive regulation of clathrin-dependent endocytosis / negative regulation of lymphocyte migration / NOSTRIN mediated eNOS trafficking / GTPase regulator activity / actin cap / vesicle organization / vesicle budding from membrane / vesicle transport along actin filament / actin polymerization or depolymerization / dendritic spine morphogenesis / protein-containing complex localization / DCC mediated attractive signaling / Nephrin family interactions / regulation of postsynapse organization / positive regulation of filopodium assembly / cytoskeletal motor activator activity / RHOV GTPase cycle / tropomyosin binding / myosin heavy chain binding / mesenchyme migration / troponin I binding / RHOJ GTPase cycle / RHOQ GTPase cycle / actin filament bundle / filamentous actin / actin filament bundle assembly / skeletal muscle thin filament assembly / striated muscle thin filament / CDC42 GTPase cycle / skeletal muscle myofibril / actin monomer binding / RHO GTPases Activate WASPs and WAVEs / skeletal muscle fiber development / stress fiber / titin binding / RAC1 GTPase cycle / EPHB-mediated forward signaling / actin filament polymerization / filopodium / actin filament / response to bacterium / FCGR3A-mediated phagocytosis / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / Regulation of actin dynamics for phagocytic cup formation / calcium-dependent protein binding / endocytic vesicle membrane / regulation of protein localization / actin cytoskeleton / lamellipodium / Clathrin-mediated endocytosis / cell body / actin binding / cytoplasmic vesicle / microtubule binding / protein-containing complex assembly / hydrolase activity / cell division / protein domain specific binding / glutamatergic synapse / calcium ion binding / endoplasmic reticulum membrane / positive regulation of gene expression / magnesium ion binding / positive regulation of transcription by RNA polymerase II / extracellular exosome / ATP binding / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Actin nucleation-promoting factor WAS, C-terminal / WASP family, EVH1 domain / WH2 motif / Wiskott Aldrich syndrome homology region 2 / WH2 domain / WH2 domain profile. / WH1/EVH1 domain / WH1 domain / WH1 domain profile. / WASP homology region 1 ...Actin nucleation-promoting factor WAS, C-terminal / WASP family, EVH1 domain / WH2 motif / Wiskott Aldrich syndrome homology region 2 / WH2 domain / WH2 domain profile. / WH1/EVH1 domain / WH1 domain / WH1 domain profile. / WASP homology region 1 / Actin; Chain A, domain 2 / Actin; Chain A, domain 2 / CRIB domain superfamily / P21-Rho-binding domain / CRIB domain profile. / P21-Rho-binding domain / CRIB 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 / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / PH-like domain superfamily / Roll / Alpha-Beta Complex / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Actin nucleation-promoting factor WASL / Actin, alpha skeletal muscle
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
ORYCTOLAGUS CUNICULUS (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsGaucher, J.F. / Didry, D. / Carlier, M.F.
CitationJournal: J. Biol. Chem. / Year: 2012
Title: Interactions of isolated C-terminal fragments of neural Wiskott-Aldrich syndrome protein (N-WASP) with actin and Arp2/3 complex.
Authors: Gaucher, J.F. / Mauge, C. / Didry, D. / Guichard, B. / Renault, L. / Carlier, M.F.
History
DepositionSep 26, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 4, 2008Provider: repository / Type: Initial release
Revision 1.1Aug 8, 2012Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary / Version format compliance
Revision 1.2Jan 30, 2013Group: Database references
Revision 1.3Feb 28, 2018Group: Database references / Source and taxonomy / Category: citation / entity_src_gen
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_scientific_name
Revision 1.4Feb 27, 2019Group: Data collection / Derived calculations / Experimental preparation
Category: exptl_crystal_grow / struct_conn
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp / _struct_conn.pdbx_leaving_atom_flag
Revision 1.5Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _pdbx_database_status.status_code_sf / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.ptnr1_label_seq_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_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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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
D: NEURAL WISKOTT-ALDRICH SYNDROME PROTEIN
E: NEURAL WISKOTT-ALDRICH SYNDROME PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,5008
Polymers103,4054
Non-polymers1,0954
Water0
1
A: ACTIN, ALPHA SKELETAL MUSCLE
D: NEURAL WISKOTT-ALDRICH SYNDROME PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,2504
Polymers51,7032
Non-polymers5472
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2730 Å2
ΔGint-27.9 kcal/mol
Surface area17460 Å2
MethodPISA
2
B: ACTIN, ALPHA SKELETAL MUSCLE
E: NEURAL WISKOTT-ALDRICH SYNDROME PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,2504
Polymers51,7032
Non-polymers5472
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2760 Å2
ΔGint-29.3 kcal/mol
Surface area17550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.240, 136.240, 205.410
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.6585, -0.75257, -0.00279), (-0.75257, -0.65851, 0.0022), (-0.00349, 0.00065, -0.99999)0.1224, -0.01228, 58.81274
2given(0.66473, -0.74702, 0.00998), (-0.74691, -0.6648, -0.01318), (0.01648, 0.0013, -0.99986)-0.63953, 1.5029, 59.61977

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Components

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


Mass: 41875.633 Da / Num. of mol.: 2 / Fragment: RESIDUES 3-377 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit) / Tissue: SKELETAL MUSCLE / References: UniProt: P68135
#2: Protein NEURAL WISKOTT-ALDRICH SYNDROME PROTEIN / N-WASP


Mass: 9827.051 Da / Num. of mol.: 2 / Fragment: WH2 1,2 AND C DOMAIN, RESIDUES 392-484
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PBAD33 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: O00401
#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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca

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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: 5.2 Å3/Da / Density % sol: 76.2 %
Description: MOLECULAR REPLACEMENT WAS PERFORMED IN THE SUPER GROUP P6122
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 7
Details: VAPOR DIFFUSION METHOD (4 C) PROTEIN SOLUTION: 0.18MM ACTIN, 0.36MM N-WASP PEPTIDE, 5MM TRIS.HCL PH7.0, ATP 0.2MM, CACL2 0.02MM, TCEP 20MM, NAN3 0.01%. RESERVOIR: 10.2% (V/V) TACSIMATE, 13. ...Details: VAPOR DIFFUSION METHOD (4 C) PROTEIN SOLUTION: 0.18MM ACTIN, 0.36MM N-WASP PEPTIDE, 5MM TRIS.HCL PH7.0, ATP 0.2MM, CACL2 0.02MM, TCEP 20MM, NAN3 0.01%. RESERVOIR: 10.2% (V/V) TACSIMATE, 13.2%(W/V)PEG 8000, 100MM HEPES PH7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.97551
DetectorType: ADSC CCD / Detector: CCD / Date: Dec 10, 2006 / Details: DOUBLE CRYSTAL, SI(111)
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97551 Å / Relative weight: 1
ReflectionResolution: 3.2→48.3 Å / Num. obs: 35056 / % possible obs: 98.5 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 35.9 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 8.8
Reflection shellResolution: 3.2→3.37 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2.3 / % possible all: 95

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2A3Z

2a3z


Resolution: 3.2→20 Å / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 3 / Stereochemistry target values: TWIN_LSQ
Details: 1. BULK SOLVENT MODEL USED. 2. THE DATA WERE MEROHEDRALLY TWINNED IN THE SPACE GROUP P61 WITH THE TWIN LAW H,-H-K,-L. THE TWINNING FRACTION WAS 0.432. 3. THE REFINEMENT WAS AGAINST THE NON- ...Details: 1. BULK SOLVENT MODEL USED. 2. THE DATA WERE MEROHEDRALLY TWINNED IN THE SPACE GROUP P61 WITH THE TWIN LAW H,-H-K,-L. THE TWINNING FRACTION WAS 0.432. 3. THE REFINEMENT WAS AGAINST THE NON-DETWINNED DATA USING CNS IN THE TWIN MODE. 4. ALL R FACTORS, ARE SO CALLED TWINNED R FACTORS, AND ARE CALCULATED FROM THE DIFFERENCE BETWEEN THE TWINNED FOBS AND THE TWINNED FCALC. 5. STRICT NCS BETWEEN MOLECULES A, D,F AND B,E,G WERE FIRST USED. RESTRAINT NCS WERE USED FOR THE LATEST STAGES OF REFINEMENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.331 1453 4.1 %RANDOM
Rwork0.275 ---
obs0.275 32407 91.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 45.584 Å2 / ksol: 0.25991 e/Å3
Displacement parametersBiso mean: 28.6 Å2
Baniso -1Baniso -2Baniso -3
1--2.07 Å2-6.5 Å20 Å2
2---2.07 Å20 Å2
3---5.42 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.52 Å0.44 Å
Luzzati d res low-6 Å
Luzzati sigma a0.39 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 3.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6092 0 64 0 6156
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.01
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 3.2→3.31 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.325 107 4.1 %
Rwork0.296 2338 -
obs--70 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ATP.PARATP.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP

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