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- PDB-2ff3: Crystal structure of Gelsolin domain 1:N-wasp V2 motif hybrid in ... -

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Basic information

Entry
Database: PDB / ID: 2ff3
TitleCrystal structure of Gelsolin domain 1:N-wasp V2 motif hybrid in complex with actin
Components
  • Actin, alpha skeletal muscle
  • Gelsolin
  • Neural Wiskott-Aldrich syndrome protein
KeywordsSTRUCTURAL PROTEIN/CONTRACTILE PROTEIN / Protein-Protein complex / STRUCTURAL PROTEIN-CONTRACTILE PROTEIN COMPLEX
Function / homology
Function and homology information


negative regulation of membrane tubulation / spindle localization / positive regulation of clathrin-dependent endocytosis / negative regulation of lymphocyte migration / vesicle transport along actin filament / striated muscle atrophy / regulation of establishment of T cell polarity / regulation of plasma membrane raft polarization / regulation of receptor clustering / renal protein absorption ...negative regulation of membrane tubulation / spindle localization / positive regulation of clathrin-dependent endocytosis / negative regulation of lymphocyte migration / vesicle transport along actin filament / striated muscle atrophy / regulation of establishment of T cell polarity / regulation of plasma membrane raft polarization / regulation of receptor clustering / renal protein absorption / positive regulation of keratinocyte apoptotic process / positive regulation of protein processing in phagocytic vesicle / positive regulation of actin nucleation / GTPase regulator activity / phosphatidylinositol 3-kinase catalytic subunit binding / NOSTRIN mediated eNOS trafficking / actin cap / regulation of podosome assembly / myosin II binding / vesicle organization / host-mediated suppression of symbiont invasion / actin filament severing / vesicle budding from membrane / barbed-end actin filament capping / actin filament depolymerization / actin filament capping / dendritic spine morphogenesis / actin polymerization or depolymerization / cell projection assembly / protein-containing complex localization / cardiac muscle cell contraction / Nephrin family interactions / DCC mediated attractive signaling / Sensory processing of sound by outer hair cells of the cochlea / regulation of postsynapse organization / podosome / positive regulation of filopodium assembly / relaxation of cardiac muscle / cytoskeletal motor activator activity / phagocytosis, engulfment / cortical actin cytoskeleton / RHOV GTPase cycle / myosin heavy chain binding / hepatocyte apoptotic process / tropomyosin binding / RHOJ GTPase cycle / RHOQ GTPase cycle / troponin I binding / filamentous actin / mesenchyme migration / actin filament bundle / actin filament bundle assembly / CDC42 GTPase cycle / skeletal muscle myofibril / striated muscle thin filament / sarcoplasm / skeletal muscle thin filament assembly / actin monomer binding / cilium assembly / RHO GTPases Activate WASPs and WAVEs / Caspase-mediated cleavage of cytoskeletal proteins / stress fiber / skeletal muscle fiber development / phagocytic vesicle / titin binding / response to muscle stretch / phosphatidylinositol-4,5-bisphosphate binding / actin filament polymerization / EPHB-mediated forward signaling / RAC1 GTPase cycle / central nervous system development / actin filament organization / filopodium / actin filament / FCGR3A-mediated phagocytosis / response to bacterium / protein destabilization / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / Regulation of actin dynamics for phagocytic cup formation / cellular response to type II interferon / calcium-dependent protein binding / actin filament binding / endocytic vesicle membrane / lamellipodium / actin cytoskeleton / regulation of protein localization / Clathrin-mediated endocytosis / actin binding / cell body / actin cytoskeleton organization / protein-containing complex assembly / cytoplasmic vesicle / secretory granule lumen / blood microparticle / amyloid fibril formation / ficolin-1-rich granule lumen / hydrolase activity / protein domain specific binding / Amyloid fiber formation / cell division
Similarity search - Function
Actin nucleation-promoting factor WAS, C-terminal / WASP family, EVH1 domain / Wiskott Aldrich syndrome homology region 2 / WH2 motif / WH1/EVH1 domain / WH1 domain / WH1 domain profile. / WASP homology region 1 / WH2 domain / WH2 domain profile. ...Actin nucleation-promoting factor WAS, C-terminal / WASP family, EVH1 domain / Wiskott Aldrich syndrome homology region 2 / WH2 motif / WH1/EVH1 domain / WH1 domain / WH1 domain profile. / WASP homology region 1 / WH2 domain / WH2 domain profile. / CRIB domain superfamily / P21-Rho-binding domain / CRIB domain profile. / P21-Rho-binding domain / CRIB domain / Villin/Gelsolin / Gelsolin homology domain / Severin / Severin / Gelsolin-like domain / Gelsolin repeat / ADF-H/Gelsolin-like domain superfamily / 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 / Alpha-Beta Complex / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Actin nucleation-promoting factor WASL / Gelsolin / Actin, alpha skeletal muscle
Similarity search - Component
Biological speciesHomo sapiens (human)
Oryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsXue, B. / Aguda, A.H. / Robinson, R.C.
CitationJournal: Structure / Year: 2006
Title: The Structural Basis of Actin Interaction with Multiple WH2/beta-Thymosin Motif-Containing Proteins
Authors: Aguda, A.H. / Xue, B. / Irobi, E. / Preat, T. / Robinson, R.C.
History
DepositionDec 19, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 21, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_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: Gelsolin
C: Neural Wiskott-Aldrich syndrome protein
B: Actin, alpha skeletal muscle
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,8147
Polymers60,1863
Non-polymers6274
Water6,107339
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.996, 69.347, 179.868
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Gelsolin / Actin-depolymerizing factor / ADF / Brevin / AGEL


Mass: 16867.998 Da / Num. of mol.: 1 / Fragment: Gelsolin domain 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Tissue: Plasma / Plasmid: pHis8-3 / Production host: Escherichia coli (E. coli) / References: UniProt: P06396
#3: Protein Actin, alpha skeletal muscle / Alpha-actin-1


Mass: 41862.613 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Tissue: Skeletal Muscle / References: UniProt: P68135

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Protein/peptide , 1 types, 1 molecules C

#2: Protein/peptide Neural Wiskott-Aldrich syndrome protein / N-WASP


Mass: 1455.479 Da / Num. of mol.: 1 / Fragment: N-wasp second WH2 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pHis8-3 / Production host: Escherichia coli (E. coli) / References: UniProt: O00401

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Non-polymers , 3 types, 343 molecules

#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#5: 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
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 339 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 3.08 Å3/Da / Density % sol: 60.01 %
Crystal growTemperature: 293.15 K / Method: microbatch / pH: 6.5
Details: 5% PEG 8000, 0.1M sodium acetate, 10mM calcium chloride, pH 6.5, microbatch, temperature 293.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9756 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 18, 2004
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9756 Å / Relative weight: 1
ReflectionResolution: 1.99→89.8 Å / Num. all: 49185 / Num. obs: 45279 / % possible obs: 97.03 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
CCP4(SCALA)data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→54.88 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.91 / SU B: 3.753 / SU ML: 0.106 / Cross valid method: THROUGHOUT / ESU R: 0.166 / ESU R Free: 0.156 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2501 2419 5.1 %RANDOM
Rwork0.2102 ---
obs0.21218 45279 97.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.671 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2---0.78 Å20 Å2
3---0.78 Å2
Refinement stepCycle: LAST / Resolution: 2→54.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3819 0 34 339 4192
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0223940
X-RAY DIFFRACTIONr_angle_refined_deg1.0521.9535345
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8125483
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.25624.157178
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.75215658
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.961521
X-RAY DIFFRACTIONr_chiral_restr0.0720.2582
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022987
X-RAY DIFFRACTIONr_nbd_refined0.180.21829
X-RAY DIFFRACTIONr_nbtor_refined0.30.22641
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.120.2306
X-RAY DIFFRACTIONr_metal_ion_refined0.0680.212
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1960.244
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.160.214
X-RAY DIFFRACTIONr_mcbond_it0.7991.52502
X-RAY DIFFRACTIONr_mcangle_it0.79423885
X-RAY DIFFRACTIONr_scbond_it1.51331679
X-RAY DIFFRACTIONr_scangle_it2.0044.51460
LS refinement shellResolution: 1.999→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 188 -
Rwork0.244 3236 -
obs--95.14 %

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