[English] 日本語
Yorodumi
- PDB-5eul: Structure of the SecA-SecY complex with a translocating polypepti... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5eul
TitleStructure of the SecA-SecY complex with a translocating polypeptide substrate
Components
  • (Protein translocase subunit ...) x 2
  • AYC08
  • Preprotein translocase SecE subunit
KeywordsPROTEIN TRANSPORT / SecY / SecA / ATPase / channel
Function / homology
Function and homology information


cell envelope Sec protein transport complex / protein-exporting ATPase activity / protein-secreting ATPase / protein transport by the Sec complex / intracellular protein transmembrane transport / protein import / protein transmembrane transporter activity / protein secretion / protein targeting / membrane raft ...cell envelope Sec protein transport complex / protein-exporting ATPase activity / protein-secreting ATPase / protein transport by the Sec complex / intracellular protein transmembrane transport / protein import / protein transmembrane transporter activity / protein secretion / protein targeting / membrane raft / ATP binding / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
SecA P-loop domain / SEC-C motif / SecE subunit of protein translocation complex, bacterial-like / SecE superfamily / SEC-C motif / SecA, C-terminal helicase domain / Protein translocase subunit SecA / SecA DEAD-like, N-terminal / SecA Wing/Scaffold / SecA, preprotein cross-linking domain ...SecA P-loop domain / SEC-C motif / SecE subunit of protein translocation complex, bacterial-like / SecE superfamily / SEC-C motif / SecA, C-terminal helicase domain / Protein translocase subunit SecA / SecA DEAD-like, N-terminal / SecA Wing/Scaffold / SecA, preprotein cross-linking domain / SecA motor DEAD / SecA conserved site / SecA, Wing/Scaffold superfamily / SecA, preprotein cross-linking domain superfamily / SecA preprotein cross-linking domain / SecA Wing and Scaffold domain / SecA DEAD-like domain / SecA family signature. / SecA family profile. / SecA DEAD-like domain / SecA preprotein cross-linking domain / Protein translocase subunit SecY / Protein secE/sec61-gamma signature. / Protein secY signature 1. / Protein secY signature 2. / SecE/Sec61-gamma subunits of protein translocation complex / Protein translocase complex, SecE/Sec61-gamma subunit / SecY/SEC61-alpha family / SecY domain superfamily / SecY conserved site / SecY / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / Immunoglobulins / Immunoglobulin-like / Sandwich / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / BERYLLIUM TRIFLUORIDE ION / HEXATANTALUM DODECABROMIDE / Protein translocase subunit SecE / Protein translocase subunit SecY / Protein translocase subunit SecA
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
synthetic construct (others)
Geobacillus thermodenitrificans (bacteria)
Vicugna pacos (alpaca)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.7 Å
AuthorsLi, L. / Park, E. / Ling, J. / Ingram, J. / Ploegh, H. / Rapoport, T.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM052586 United States
CitationJournal: Nature / Year: 2016
Title: Crystal structure of a substrate-engaged SecY protein-translocation channel.
Authors: Li, L. / Park, E. / Ling, J. / Ingram, J. / Ploegh, H. / Rapoport, T.A.
History
DepositionNov 18, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 23, 2016Group: Database references
Revision 1.2Mar 30, 2016Group: Database references
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Protein translocase subunit SecA, Insertion Peptide Chimera
Y: Protein translocase subunit SecY
E: Preprotein translocase SecE subunit
V: AYC08
hetero molecules


Theoretical massNumber of molelcules
Total (without water)201,17225
Polymers163,8534
Non-polymers37,31921
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22960 Å2
ΔGint-131 kcal/mol
Surface area60260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.798, 127.798, 554.772
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

-
Components

-
Protein translocase subunit ... , 2 types, 2 molecules AY

#1: Protein Protein translocase subunit SecA, Insertion Peptide Chimera


Mass: 94360.195 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria), (gene. exp.) synthetic construct (others), (gene. exp.) Bacillus subtilis (bacteria)
Strain: 168 / Gene: secA, div+, BSU35300 / Production host: Escherichia coli (E. coli) / References: UniProt: P28366
#2: Protein Protein translocase subunit SecY


Mass: 46768.301 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus thermodenitrificans (strain NG80-2) (bacteria)
Strain: NG80-2 / Gene: secY, GTNG_0125 / Production host: Escherichia coli (E. coli) / References: UniProt: A4IJK8

-
Protein / Antibody , 2 types, 2 molecules EV

#3: Protein Preprotein translocase SecE subunit


Mass: 8249.600 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus thermodenitrificans (strain NG80-2) (bacteria)
Strain: NG80-2 / Gene: GTNG_0091 / Production host: Escherichia coli (E. coli) / References: UniProt: A4IJH4
#4: Antibody AYC08


Mass: 14475.136 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Escherichia coli (E. coli)

-
Non-polymers , 4 types, 21 molecules

#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: BeF3
#7: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#8: Chemical
ChemComp-TBR / HEXATANTALUM DODECABROMIDE / DODECABROMOHEXATANTALUM


Mass: 2044.535 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: Br12Ta6

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.89 Å3/Da / Density % sol: 68.35 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 21-24% polyethylene glycol 1500, 100mM Tris-HCl pH8.5, 50-100 mM MgAc2, 2% 2-methyl-2,4-pentandiol
PH range: 8.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.2782 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 18, 2015
RadiationMonochromator: Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2782 Å / Relative weight: 1
ReflectionResolution: 3.7→54 Å / Num. obs: 53847 / % possible obs: 99 % / Redundancy: 10.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.085 / Net I/σ(I): 9.3
Reflection shellResolution: 3.7→3.8 Å / Redundancy: 10.2 % / Mean I/σ(I) obs: 0.4 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
XDSdata reduction
XDSdata scaling
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 3.7→53.852 Å / SU ML: 0.71 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 42.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3148 2754 5.11 %Random selection
Rwork0.2952 ---
obs0.2962 53845 99.52 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.7→53.852 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10155 0 356 0 10511
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00611001
X-RAY DIFFRACTIONf_angle_d0.99417211
X-RAY DIFFRACTIONf_dihedral_angle_d16.9146339
X-RAY DIFFRACTIONf_chiral_restr0.0541607
X-RAY DIFFRACTIONf_plane_restr0.0051778
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.7001-3.76380.45111510.422584X-RAY DIFFRACTION100
3.7638-3.83230.44571330.41212518X-RAY DIFFRACTION100
3.8323-3.9060.431460.40552576X-RAY DIFFRACTION100
3.906-3.98570.40841480.39372581X-RAY DIFFRACTION100
3.9857-4.07230.45461310.37922513X-RAY DIFFRACTION99
4.0723-4.1670.38551200.35972554X-RAY DIFFRACTION99
4.167-4.27120.36821450.34462569X-RAY DIFFRACTION99
4.2712-4.38660.42131380.30842546X-RAY DIFFRACTION99
4.3866-4.51560.33691640.29152499X-RAY DIFFRACTION99
4.5156-4.66130.30661050.28552551X-RAY DIFFRACTION99
4.6613-4.82780.32681500.28532523X-RAY DIFFRACTION99
4.8278-5.02090.33931150.29172566X-RAY DIFFRACTION99
5.0209-5.24930.39841420.29372555X-RAY DIFFRACTION100
5.2493-5.52580.32571540.29512562X-RAY DIFFRACTION100
5.5258-5.87160.37281260.29662570X-RAY DIFFRACTION100
5.8716-6.32430.36891340.2922578X-RAY DIFFRACTION100
6.3243-6.95950.35021280.25752552X-RAY DIFFRACTION100
6.9595-7.96380.28541210.22472605X-RAY DIFFRACTION100
7.9638-10.0230.21291370.21172561X-RAY DIFFRACTION100
10.023-53.8580.30971660.33862528X-RAY DIFFRACTION100

+
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