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- PDB-1d4x: Crystal Structure of Caenorhabditis Elegans Mg-ATP Actin Complexe... -

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Basic information

Entry
Database: PDB / ID: 1d4x
TitleCrystal Structure of Caenorhabditis Elegans Mg-ATP Actin Complexed with Human Gelsolin Segment 1 at 1.75 A resolution.
Components
  • C. ELEGANS ACTIN 1/3
  • GELSOLIN
KeywordsCONTRACTILE PROTEIN / ACTIN / GELSOLIN S1 / C.ELEGANS / MG-ATP
Function / homology
Function and homology information


Gap junction degradation / Formation of annular gap junctions / EPHB-mediated forward signaling / EPH-ephrin mediated repulsion of cells / Recycling pathway of L1 / Cell-extracellular matrix interactions / RHO GTPases activate IQGAPs / RHO GTPases Activate Formins / MAP2K and MAPK activation / RHOF GTPase cycle ...Gap junction degradation / Formation of annular gap junctions / EPHB-mediated forward signaling / EPH-ephrin mediated repulsion of cells / Recycling pathway of L1 / Cell-extracellular matrix interactions / RHO GTPases activate IQGAPs / RHO GTPases Activate Formins / MAP2K and MAPK activation / RHOF GTPase cycle / VEGFA-VEGFR2 Pathway / Regulation of actin dynamics for phagocytic cup formation / RHO GTPases Activate WASPs and WAVEs / Platelet degranulation / Clathrin-mediated endocytosis / 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 / phosphatidylinositol 3-kinase catalytic subunit binding / actin cap / regulation of podosome assembly / sequestering of actin monomers / myosin II binding / negative regulation of viral entry into host cell / actin filament severing / actin filament capping / actin filament depolymerization / actin polymerization or depolymerization / barbed-end actin filament capping / cell projection assembly / cardiac muscle cell contraction / Sensory processing of sound by outer hair cells of the cochlea / embryo development ending in birth or egg hatching / relaxation of cardiac muscle / podosome / cortical actin cytoskeleton organization / phagocytosis, engulfment / cortical actin cytoskeleton / hepatocyte apoptotic process / mitotic cytokinesis / sarcoplasm / cilium assembly / Caspase-mediated cleavage of cytoskeletal proteins / phagocytic vesicle / phosphatidylinositol-4,5-bisphosphate binding / response to muscle stretch / actin filament polymerization / actin filament organization / central nervous system development / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / protein destabilization / structural constituent of cytoskeleton / cellular response to type II interferon / actin filament binding / actin cytoskeleton / lamellipodium / actin binding / secretory granule lumen / blood microparticle / ficolin-1-rich granule lumen / amyloid fibril formation / cytoskeleton / hydrolase activity / Amyloid fiber formation / focal adhesion / calcium ion binding / Neutrophil degranulation / positive regulation of gene expression / extracellular space / extracellular exosome / extracellular region / ATP binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
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 ...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 / Alpha-Beta Complex / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / SULFUR DIOXIDE / Gelsolin / Actin-1 / Actin-1
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.75 Å
AuthorsVorobiev, S. / Ono, S. / Almo, S.C.
Citation
Journal: Proc.Natl.Acad.Sci.Usa / Year: 2003
Title: The structure of nonvertebrate actin: implications for the ATP hydrolytic mechanism.
Authors: Vorobiev, S. / Strokopytov, B. / Drubin, D.G. / Frieden, C. / Ono, S. / Condeelis, J. / Rubenstein, P.A. / Almo, S.C.
#1: Journal: Nature / Year: 1993
Title: Structure of gelsolin segment 1-actin complex and mechanosm of filament severing
Authors: McLaughlin, P.J. / Gooch, J.T. / Mannherz, H.-G. / Weeds, A.G.
#2: Journal: Nature / Year: 1990
Title: Atomic structure of the actin:DNase I complex
Authors: Kabsch, W. / Mannherz, H.-G. / Suck, D. / Pai, E.F. / Holmes, K.C.
History
DepositionOct 6, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 2, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 7, 2021Group: Derived calculations / Refinement description
Category: pdbx_struct_conn_angle / refine ...pdbx_struct_conn_angle / refine / struct_conn / struct_sheet / struct_site
Item: _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr1_label_seq_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 / _refine.ls_percent_reflns_R_free / _refine.ls_percent_reflns_obs / _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.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_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: C. ELEGANS ACTIN 1/3
G: GELSOLIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,6437
Polymers55,9122
Non-polymers7325
Water9,044502
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3520 Å2
ΔGint-49 kcal/mol
Surface area20500 Å2
MethodPISA
2
A: C. ELEGANS ACTIN 1/3
G: GELSOLIN
hetero molecules

A: C. ELEGANS ACTIN 1/3
G: GELSOLIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,28614
Polymers111,8234
Non-polymers1,46310
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area9440 Å2
ΔGint-111 kcal/mol
Surface area38920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)177.820, 68.989, 56.593
Angle α, β, γ (deg.)90.00, 104.15, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-684-

SO2

21A-1124-

HOH

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Components

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Protein , 2 types, 2 molecules AG

#1: Protein C. ELEGANS ACTIN 1/3


Mass: 41710.492 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Production host: Escherichia coli (E. coli) / References: UniProt: P10983, UniProt: P0DM41*PLUS
#2: Protein GELSOLIN


Mass: 14201.010 Da / Num. of mol.: 1 / Fragment: SEGMENT 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P06396

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Non-polymers , 6 types, 507 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#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: Chemical ChemComp-SO2 / SULFUR DIOXIDE


Mass: 64.064 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O2S
#7: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 502 / 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: 3.01 Å3/Da / Density % sol: 59.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 100 MM TRIS-HCL, PH 8.0, 2 MM MG-ATP, 1.60 M LI2SO4,, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
22 mMTris-HCl1drop
32 mMATP1drop
44 mM1dropMgCl2
50.5 mMEGTA1drop
61 mM1dropNaN3
71.55 M1reservoirLiSO4
82 mMMg2+-ATP1reservoir
90.5 mMEGTA1reservoir
1gelsolin1drop1:1.25 stoichiometry
100.1 MHEPES1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 1.072
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 1, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.072 Å / Relative weight: 1
ReflectionResolution: 1.75→25 Å / Num. all: 64713 / Num. obs: 64713 / % possible obs: 96.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.91 % / Biso Wilson estimate: 17.041 Å2 / Rmerge(I) obs: 0.041 / Net I/σ(I): 24.2
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 2.57 % / Rmerge(I) obs: 0.102 / % possible all: 88.3
Reflection shell
*PLUS
% possible obs: 88.3 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLOR3.851refinement
X-PLORphasing
RefinementResolution: 1.75→23.2 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: R. A. ENGH AND R. HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.233 2533 4 %RANDOM
Rwork0.1986 ---
all0.2307 64712 --
obs0.2307 64711 96.9 %-
Refinement stepCycle: LAST / Resolution: 1.75→23.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3822 0 41 502 4365
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d1.624
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 25 Å / Rfactor Rwork: 0.199
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 24.14 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_deg1.434

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