[English] 日本語
Yorodumi
- PDB-1o9d: Structural view of a fungal toxin acting on a 14-3-3 regulatory c... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1o9d
TitleStructural view of a fungal toxin acting on a 14-3-3 regulatory complex
Components
  • 14-3-3-LIKE PROTEIN C
  • PLASMA MEMBRANE H+ ATPASE
KeywordsPROTEIN BINDING / PROTEIN-BINDING / FUSICOCCIN / 14-3-3 FAMILY / ACTIVATING DRUG / PLANT PLASMA MEMBRANE (H+)ATPASE
Function / homology
Function and homology information


protein localization / signal transduction / ATP hydrolysis activity / ATP binding / membrane / cytoplasm
Similarity search - Function
14-3-3 domain / Delta-Endotoxin; domain 1 / 14-3-3 proteins signature 2. / 14-3-3 protein, conserved site / 14-3-3 proteins signature 1. / 14-3-3 protein / 14-3-3 homologues / 14-3-3 domain / 14-3-3 domain superfamily / 14-3-3 protein ...14-3-3 domain / Delta-Endotoxin; domain 1 / 14-3-3 proteins signature 2. / 14-3-3 protein, conserved site / 14-3-3 proteins signature 1. / 14-3-3 protein / 14-3-3 homologues / 14-3-3 domain / 14-3-3 domain superfamily / 14-3-3 protein / P-type ATPase / P-type ATPase, transmembrane domain superfamily / haloacid dehalogenase-like hydrolase / HAD superfamily / HAD-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
14-3-3-like protein C / Plasma membrane H+ ATPase
Similarity search - Component
Biological speciesNICOTIANA TABACUM (common tobacco)
NICOTIANA PLUMBAGINIFOLIA (curled-leaved tobacco)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsWurtele, M. / Jelich-Ottmann, C. / Wittinghofer, A. / Oecking, C.
CitationJournal: Embo J. / Year: 2003
Title: Structural View of a Fungal Toxin Acting on a 14-3-3 Regulatory Complex
Authors: Wurtele, M. / Jelich-Ottmann, C. / Wittinghofer, A. / Oecking, C.
History
DepositionDec 12, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 6, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 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
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.pdbx_leaving_atom_flag
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 14-3-3-LIKE PROTEIN C
P: PLASMA MEMBRANE H+ ATPASE


Theoretical massNumber of molelcules
Total (without water)30,0772
Polymers30,0772
Non-polymers00
Water3,153175
1
A: 14-3-3-LIKE PROTEIN C
P: PLASMA MEMBRANE H+ ATPASE

A: 14-3-3-LIKE PROTEIN C
P: PLASMA MEMBRANE H+ ATPASE


Theoretical massNumber of molelcules
Total (without water)60,1534
Polymers60,1534
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_655-x+y+1,y,-z+1/21
Buried area4250 Å2
ΔGint-24.83 kcal/mol
Surface area22770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.126, 110.126, 136.464
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
DetailsTHE ENTRY IS A DIMER OF CHAIN A, WHICH IN COMPLEX WITH PEPTIDE CHAIN P MAKES IT APPEAR AS A TETRAMERIC COMPLEX OF CHAINS A AND P.

-
Components

#1: Protein 14-3-3-LIKE PROTEIN C


Mass: 29399.977 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: GENE BANK AAC49892 / Source: (gene. exp.) NICOTIANA TABACUM (common tobacco) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P93343
#2: Protein/peptide PLASMA MEMBRANE H+ ATPASE


Mass: 676.610 Da / Num. of mol.: 1 / Fragment: RESIDUES 436-440 / Source method: obtained synthetically
Source: (synth.) NICOTIANA PLUMBAGINIFOLIA (curled-leaved tobacco)
References: UniProt: Q40409
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.97 Å3/Da / Density % sol: 69.03 %
Crystal growpH: 6.4 / Details: PEG400, CITRATE PH 4.7, 0.2 MM AMMONIUM ACETATE
Crystal grow
*PLUS
pH: 4.7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
121 %PEG4001reservoir
20.1 mMcitrate1reservoirpH4.7
30.2 mMammonium acetate1reservoirpH7.0
410 mMdithiothreitol1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.979
DetectorDate: Dec 15, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.3→10 Å / Num. obs: 21328 / % possible obs: 95.5 % / Observed criterion σ(I): 2 / Redundancy: 6.2 % / Biso Wilson estimate: 59 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 18.1
Reflection shellResolution: 2.3→2.4 Å / Rmerge(I) obs: 0.351 / Mean I/σ(I) obs: 4 / % possible all: 98.1
Reflection
*PLUS
Lowest resolution: 10 Å / Num. measured all: 131256
Reflection shell
*PLUS
% possible obs: 98.1 %

-
Processing

Software
NameVersionClassification
CNS1.1refinement
XDSdata reduction
XDSdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1A4O

1a4o


Resolution: 2.3→19.38 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 3077461.25 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.244 1041 5 %RANDOM
Rwork0.21 ---
obs0.21 21283 95.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 57.9462 Å2 / ksol: 0.340913 e/Å3
Displacement parametersBiso mean: 60.7 Å2
Baniso -1Baniso -2Baniso -3
1-8.16 Å25.52 Å20 Å2
2--8.16 Å20 Å2
3----16.32 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.3 Å0.29 Å
Refinement stepCycle: LAST / Resolution: 2.3→19.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1875 0 0 175 2050
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.023
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_deg2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d19.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.28
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: 2.3→2.44 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.309 153 4.3 %
Rwork0.284 3396 -
obs--97.8 %
Refinement
*PLUS
Lowest resolution: 10 Å / % reflection Rfree: 5 % / Rfactor Rwork: 0.21
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.02
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg19.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.28

+
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