[English] 日本語
Yorodumi
- PDB-2aso: Structure of Rabbit Actin In Complex With Sphinxolide B -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2aso
TitleStructure of Rabbit Actin In Complex With Sphinxolide B
ComponentsActin, alpha skeletal muscle
KeywordsSTRUCTURAL PROTEIN / actin / sphinxolide B / marine macrolide / toxin / filament capping / filament severing
Function / homology
Function and homology information


cytoskeletal motor activator activity / tropomyosin binding / myosin heavy chain binding / mesenchyme migration / troponin I binding / filamentous actin / actin filament bundle / skeletal muscle thin filament assembly / actin filament bundle assembly / striated muscle thin filament ...cytoskeletal motor activator activity / tropomyosin binding / myosin heavy chain binding / mesenchyme migration / troponin I binding / filamentous actin / actin filament bundle / skeletal muscle thin filament assembly / actin filament bundle assembly / striated muscle thin filament / skeletal muscle myofibril / actin monomer binding / stress fiber / skeletal muscle fiber development / titin binding / actin filament polymerization / filopodium / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / calcium-dependent protein binding / lamellipodium / cell body / hydrolase activity / protein domain specific binding / calcium ion binding / positive regulation of gene expression / magnesium ion binding / ATP binding / identical protein binding / cytoplasm
Similarity search - Function
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 ...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 / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / SPHINXOLIDE B / Actin, alpha skeletal muscle
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsAllingham, J.S. / Zampella, A. / D'Auria, M.V. / Rayment, I.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2005
Title: Structures of microfilament destabilizing toxins bound to actin provide insight into toxin design and activity
Authors: Allingham, J.S. / Zampella, A. / D'Auria, M.V. / Rayment, I.
History
DepositionAug 23, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 11, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 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.pdbx_leaving_atom_flag / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Actin, alpha skeletal muscle
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,3834
Polymers41,8761
Non-polymers1,5073
Water5,657314
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.182, 54.989, 103.520
Angle α, β, γ (deg.)90.00, 92.41, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-651-

HOH

21A-756-

HOH

-
Components

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


Mass: 41875.633 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: P68135
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: 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
#4: Chemical ChemComp-SPX / SPHINXOLIDE B / N-((4R,5R,9S,10S,11S,E)-11-((3R,5Z,7Z,11S,12S,13Z,15R,17S,18S,19Z,21S,23S,24R,25S,29S)-17,29-DIHYDROXY-3,15,21,23-TETRAMETHOXY-5,12,18,24-TETRAMETHYL-9,27-DIOXO-10,26-DIOXABICYCLO[23.3.1]NONACOSA-1(28),5,7,13,19-PENTAEN-11-YL)-4,10-DIMETHOXY-5,9-DIMETHYL-6-OXODODEC-1-ENYL)-N-METHYLFORMAMIDE


Mass: 960.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C53H85NO14
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 314 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 1.87 Å3/Da / Density % sol: 37.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 100mM Na/MES/Acetate, pH 5.5, 12% methyl ether poly(ethylene glycol) 5000, 100mM CaCl2, 1mM TCEP, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9641 Å
DetectorType: SBC-2 / Detector: CCD / Date: Mar 28, 2004 / Details: Rosenbaum-Rock monochromators and mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9641 Å / Relative weight: 1
ReflectionResolution: 1.7→35 Å / Num. obs: 36176 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Biso Wilson estimate: 25.9 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 29.1
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.299 / Mean I/σ(I) obs: 3.8 / % possible all: 95.1

-
Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1QZ5

1qz5


Resolution: 1.7→35 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.941 / SU B: 2.381 / SU ML: 0.078 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.115 / ESU R Free: 0.113 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21347 1792 5 %RANDOM
Rwork0.17298 ---
all0.193 35870 --
obs0.17511 34079 99.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 18.5 Å2
Baniso -1Baniso -2Baniso -3
1-2.4 Å20 Å2-0.15 Å2
2---0.63 Å20 Å2
3----1.78 Å2
Refinement stepCycle: LAST / Resolution: 1.7→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2748 0 100 314 3162
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0212912
X-RAY DIFFRACTIONr_bond_other_d0.0020.022668
X-RAY DIFFRACTIONr_angle_refined_deg1.5321.9973960
X-RAY DIFFRACTIONr_angle_other_deg1.59436202
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6275358
X-RAY DIFFRACTIONr_chiral_restr0.1230.2457
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023156
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02558
X-RAY DIFFRACTIONr_nbd_refined0.2230.2773
X-RAY DIFFRACTIONr_nbd_other0.2430.23301
X-RAY DIFFRACTIONr_nbtor_other0.1180.21940
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.180.2181
X-RAY DIFFRACTIONr_metal_ion_refined0.0910.25
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2920.224
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2310.240
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3380.229
X-RAY DIFFRACTIONr_mcbond_it0.7611.51792
X-RAY DIFFRACTIONr_mcangle_it1.43222904
X-RAY DIFFRACTIONr_scbond_it2.29131120
X-RAY DIFFRACTIONr_scangle_it3.7074.51055
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.265 119
Rwork0.224 2379

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more