[English] 日本語
Yorodumi
- PDB-5l0w: Structure of post-translational translocation Sec71/Sec72 complex -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: PDB / ID: 5l0w
TitleStructure of post-translational translocation Sec71/Sec72 complex
Components
  • Sec71
  • Sec72
KeywordsMEMBRANE PROTEIN / protein translocation / TPR domain
Function / homologyTetratricopeptide-like helical domain superfamily / Tetratricopeptide repeat-containing domain / Translocation protein Sec66 / Tetratricopeptide repeat / Preprotein translocase subunit Sec66 / TPR repeat region circular profile. / Sec62/Sec63 complex / posttranslational protein targeting to membrane, translocation / integral component of membrane / Translocation protein (Sec66)-like protein / Uncharacterized protein
Function and homology information
Specimen sourceChaetomium thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / 3.035 Å resolution
AuthorsTripathi, A. / Rapoport, T.A.
Funding supportUnited States , 1 items
OrganizationGrant numberCountry
National Institutes of HealthUnited States
CitationJournal: J. Biol. Chem. / Year: 2017
Title: Two alternative binding mechanisms connect the protein translocation Sec71-Sec72 complex with heat shock proteins.
Authors: Tripathi, A. / Mandon, E.C. / Gilmore, R. / Rapoport, T.A.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jul 28, 2016 / Release: Mar 22, 2017
RevisionDateData content typeGroupProviderType
1.0Mar 22, 2017Structure modelrepositoryInitial release
1.1Mar 29, 2017Structure modelDatabase references
1.2May 24, 2017Structure modelDatabase references

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Sec72
A: Sec71


Theoretical massNumber of molelcules
Total (without water)45,4452
Polyers45,4452
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)4470
ΔGint (kcal/M)-34
Surface area (Å2)21270
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)108.600, 108.600, 271.170
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP 65 2 2

-
Components

#1: Protein/peptide Sec72


Mass: 24074.787 Da / Num. of mol.: 1 / Source: (gene. exp.) Chaetomium thermophilum (fungus) / Production host: Escherichia coli (E. coli) / References: UniProt: G0SH41
#2: Protein/peptide Sec71 / Translocation protein (Sec66)-like protein


Mass: 21369.971 Da / Num. of mol.: 1 / Fragment: UNP residues 48-202 / Source: (gene. exp.) Chaetomium thermophilum (fungus) / Production host: Escherichia coli (E. coli) / References: UniProt: G0S0B5

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 5.44 / Density percent sol: 77.37 %
Crystal growTemp: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 1.4M ammonium tatrate dibasic, 0.1M Tris/HCl pH 8.5

-
Data collection

DiffractionMean temperature: 100 kelvins
SourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Collection date: Oct 10, 2013
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionD resolution high: 3.035 Å / D resolution low: 20.1 Å / Number obs: 18882 / Rmerge I obs: 0.137 / NetI over sigmaI: 17 / Redundancy: 9.4 % / Percent possible obs: 99.8
Reflection shellRmerge I obs: 1.7 / Highest resolution: 3.035 Å / Lowest resolution: 3.13 Å / Redundancy: 9.1 % / Percent possible all: 99

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PDB_EXTRACT3.20data extraction
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefineMethod to determine structure: SAD / Overall SU ML: 0.34 / Cross valid method: FREE R-VALUE / Sigma F: 1.76 / Overall phase error: 28.01 / Stereochemistry target values: MLHL
Solvent computationSolvent shrinkage radii: 0.9 Å / Solvent vdw probe radii: 1.11 Å / Solvent model details: FLAT BULK SOLVENT MODEL
Displacement parametersB iso max: 243.32 Å2 / B iso mean: 90.0117 Å2 / B iso min: 33.31 Å2
Least-squares processR factor R free: 0.2502 / R factor R work: 0.2228 / R factor obs: 0.2242 / Highest resolution: 3.035 Å / Lowest resolution: 20.1 Å / Number reflection R free: 1703 / Number reflection R work: 32465 / Number reflection obs: 34168 / Percent reflection R free: 4.98 / Percent reflection obs: 99.12
Refine hist #finalHighest resolution: 3.035 Å / Lowest resolution: 20.1 Å / Number residues total: 371
Number of atoms included #finalProtein: 2962 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 2962
Refine LS restraints
Refine IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053017
X-RAY DIFFRACTIONf_angle_d0.9114073
X-RAY DIFFRACTIONf_chiral_restr0.034438
X-RAY DIFFRACTIONf_plane_restr0.004539
X-RAY DIFFRACTIONf_dihedral_angle_d15.2491170
Refine LS shell

Refine ID: X-RAY DIFFRACTION / Total number of bins used: 12

Highest resolutionR factor R freeR factor R workLowest resolutionNumber reflection R freeNumber reflection R workNumber reflection allPercent reflection obs
3.03530.33680.37963.12431272441256890.0000
3.12430.30940.33703.224714427192863100.0000
3.22470.31440.32403.339515027282878100.0000
3.33950.35300.31773.472514627412887100.0000
3.47250.34890.28313.629713327472880100.0000
3.62970.30020.25503.819813927032842100.0000
3.81980.24710.22694.057314627362882100.0000
4.05730.24750.20554.367614127452886100.0000
4.36760.22140.19524.801714627142860100.0000
4.80170.29270.21195.484214327282871100.0000
5.48420.24200.21106.863514327282871100.0000
6.86350.16650.156620.100414527352880100.0000

+
About Yorodumi

-
News

-
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. (see PDBe EMDB page)
  • 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 at PDBe / 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. See below links for details.
  • 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

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

Read more

-
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.

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