[English] 日本語
Yorodumi
- PDB-5ubc: The structure of the Arabidopsis thaliana Toc75 POTRA domains -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ubc
TitleThe structure of the Arabidopsis thaliana Toc75 POTRA domains
ComponentsProtein TOC75-3, chloroplastic
KeywordsMEMBRANE PROTEIN / POTRA / chloroplast
Function / homology
Function and homology information


Toc complex / TOC-TIC supercomplex I / protein import into chloroplast stroma / protein targeting to chloroplast / chloroplast organization / protein-transporting ATPase activity / embryonic morphogenesis / plant-type vacuole / chloroplast envelope / plastid ...Toc complex / TOC-TIC supercomplex I / protein import into chloroplast stroma / protein targeting to chloroplast / chloroplast organization / protein-transporting ATPase activity / embryonic morphogenesis / plant-type vacuole / chloroplast envelope / plastid / chloroplast / intracellular protein transport / cytosol
Similarity search - Function
Chloroplast envelope protein translocase, IAP75 / Surface antigen D15-like / Bacterial surface antigen (D15) / Omp85 superfamily domain
Similarity search - Domain/homology
Protein TOC75-3, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.862 Å
AuthorsO'Neil, P.K. / Noinaj, N.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1K22AI113078-01 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)2RO1-GM061893 United States
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: The POTRA domains of Toc75 exhibit chaperone-like function to facilitate import into chloroplasts.
Authors: O'Neil, P.K. / Richardson, L.G.L. / Paila, Y.D. / Piszczek, G. / Chakravarthy, S. / Noinaj, N. / Schnell, D.
History
DepositionDec 20, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 7, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jun 21, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_id_ASTM ..._citation.country / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.6Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Protein TOC75-3, chloroplastic
B: Protein TOC75-3, chloroplastic


Theoretical massNumber of molelcules
Total (without water)72,2762
Polymers72,2762
Non-polymers00
Water0
1
A: Protein TOC75-3, chloroplastic


Theoretical massNumber of molelcules
Total (without water)36,1381
Polymers36,1381
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Protein TOC75-3, chloroplastic


Theoretical massNumber of molelcules
Total (without water)36,1381
Polymers36,1381
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)92.368, 50.453, 94.802
Angle α, β, γ (deg.)90.00, 115.56, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Protein TOC75-3, chloroplastic / 75 kDa translocon at the outer-envelope-membrane of chloroplasts 3 / AtTOC75-III


Mass: 36137.758 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: TOC75-3, TOC75, At3g46740, T6H20.230 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9STE8

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.79 Å3/Da / Density % sol: 55.91 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / Details: 100 mM HEPES:NaOH, pH7.5, 20% PEG 8000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Dec 6, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.85→50 Å / Num. obs: 16654 / % possible obs: 89.9 % / Redundancy: 2.4 % / CC1/2: 0.48 / Rsym value: 0.15 / Net I/σ(I): 8.8
Reflection shellResolution: 2.85→2.9 Å / Redundancy: 2.4 % / Mean I/σ(I) obs: 1.3 / CC1/2: 0.48 / Rsym value: 1 / % possible all: 93.1

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
DENZOHKL2000data reduction
SCALEPACKHKL2000data scaling
PHASERPHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5UAY

5uay


Resolution: 2.862→47.207 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.57
RfactorNum. reflection% reflection
Rfree0.2804 1673 10.05 %
Rwork0.2244 --
obs0.2301 16654 89.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.862→47.207 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4501 0 0 0 4501
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074575
X-RAY DIFFRACTIONf_angle_d1.2056211
X-RAY DIFFRACTIONf_dihedral_angle_d16.3311647
X-RAY DIFFRACTIONf_chiral_restr0.045714
X-RAY DIFFRACTIONf_plane_restr0.005822
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8618-2.9460.34011440.30421252X-RAY DIFFRACTION91
2.946-3.04110.32741430.26981265X-RAY DIFFRACTION93
3.0411-3.14970.27991370.25021278X-RAY DIFFRACTION92
3.1497-3.27580.3051340.25571254X-RAY DIFFRACTION91
3.2758-3.42490.32021450.24681274X-RAY DIFFRACTION91
3.4249-3.60540.27591400.2411248X-RAY DIFFRACTION90
3.6054-3.83120.35761370.23511238X-RAY DIFFRACTION89
3.8312-4.12680.24991400.22421209X-RAY DIFFRACTION89
4.1268-4.54180.24941430.19691246X-RAY DIFFRACTION89
4.5418-5.19830.22631420.19051243X-RAY DIFFRACTION90
5.1983-6.54660.31681360.22711251X-RAY DIFFRACTION88
6.5466-47.21380.25631320.19911223X-RAY DIFFRACTION83

+
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