[English] 日本語
Yorodumi
- PDB-2vda: Solution structure of the SecA-signal peptide complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2vda
TitleSolution structure of the SecA-signal peptide complex
Components
  • MALTOPORIN
  • TRANSLOCASE SUBUNIT SECA
KeywordsPROTEIN TRANSPORT / SUGAR TRANSPORT / PROTEIN TARGETING / TRANSMEMBRANE / OUTER MEMBRANE / SIGNAL PEPTIDE / PARAMAGNETIC RELAXATION ENHANCEMENT / TRANSLOCASE / ION TRANSPORT / TRANSLOCATION / PROTEIN SECRETION / NUCLEOTIDE-BINDING / SECA / PORIN / MEMBRANE / TRANSPORT / ATP-BINDING / HIGH MOLECULAR WEIGHT COMPLEX
Function / homology
Function and homology information


maltodextrin transmembrane transporter activity / maltose transporting porin activity / preprotein binding / protein-exporting ATPase activity / cell envelope Sec protein transport complex / protein-secreting ATPase / protein transport by the Sec complex / intracellular protein transmembrane transport / protein import / protein targeting to membrane ...maltodextrin transmembrane transporter activity / maltose transporting porin activity / preprotein binding / protein-exporting ATPase activity / cell envelope Sec protein transport complex / protein-secreting ATPase / protein transport by the Sec complex / intracellular protein transmembrane transport / protein import / protein targeting to membrane / pore complex / protein secretion / protein targeting / ribonucleoprotein complex binding / monoatomic ion transport / chaperone-mediated protein folding / cell outer membrane / cytoplasmic side of plasma membrane / protein transport / ribosome binding / zinc ion binding / ATP binding / identical protein binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Pre-protein croslinking domain of SecA / SecA, preprotein cross-linking domain / Maltoporin / Helical scaffold and wing domains of SecA / Helical scaffold and wing domains of SecA / Porin, LamB-type / Porin, LamB-type superfamily / LamB porin / SEC-C motif / SEC-C motif ...Pre-protein croslinking domain of SecA / SecA, preprotein cross-linking domain / Maltoporin / Helical scaffold and wing domains of SecA / Helical scaffold and wing domains of SecA / Porin, LamB-type / Porin, LamB-type superfamily / LamB porin / SEC-C motif / SEC-C motif / SecA P-loop domain / 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 / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleotide triphosphate hydrolases / Alpha-Beta Complex / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Protein translocase subunit SecA / Maltoporin
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodSOLUTION NMR / SEMIRIGID, FLEXIBLE SIMULATED ANNEALING
AuthorsGelis, I. / Bonvin, A.M.J.J. / Keramisanou, D. / Koukaki, M. / Gouridis, G. / Karamanou, S. / Economou, A. / Kalodimos, C.G.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2007
Title: Structural Basis for Signal-Sequence Recognition by the Translocase Motor Seca as Determined by NMR
Authors: Gelis, I. / Bonvin, A.M.J.J. / Keramisanou, D. / Koukaki, M. / Gouridis, G. / Karamanou, S. / Economou, A. / Kalodimos, C.G.
History
DepositionOct 1, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 27, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 24, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 1.4May 15, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_mr

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: TRANSLOCASE SUBUNIT SECA
B: MALTOPORIN


Theoretical massNumber of molelcules
Total (without water)96,9902
Polymers96,9902
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 200LOWEST ENERGY
RepresentativeModel #1

-
Components

#1: Protein TRANSLOCASE SUBUNIT SECA / SECA TRANSLOCASE ATPASE


Mass: 93999.711 Da / Num. of mol.: 1 / Fragment: RESIDUES 9-836
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Plasmid: PET16B / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / References: UniProt: P10408
#2: Protein/peptide MALTOPORIN / MALTOSE-INDUCIBLE PORIN


Mass: 2990.784 Da / Num. of mol.: 1 / Fragment: SIGNAL SEQUENCE, RESIDUES 1-25 / Source method: obtained synthetically / Source: (synth.) ESCHERICHIA COLI (E. coli) / References: UniProt: Q8CVI4

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 13C-HMQC
NMR detailsText: NONE

-
Sample preparation

DetailsContents: 100%D2O
Sample conditionsIonic strength: 50 mM / pH: 7.5 / Pressure: 1.0 atm / Temperature: 295.0 K

-
NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
HADDOCK-CNSBRUNGER,ADAMS,CLORE,DELANO,GROS, GROSSE- KUNSTLEVE,JIANG,KUSZEWSKI,NILGES, PANNU,READ, RICE,SIMONSON,WARRENrefinement
NMRPIPE; SPARKY; HADDOCK- CNSCNSstructure solution
RefinementMethod: SEMIRIGID, FLEXIBLE SIMULATED ANNEALING / Software ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE REFERENCE HADDOCK AUTH C. DOMIGUEZ, R. BOELENS, A.M.J.J. BONVIN TITLE HADDOCK A PROTEIN-PROTEIN DOCKING APPROACH BASED ON ...Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE REFERENCE HADDOCK AUTH C. DOMIGUEZ, R. BOELENS, A.M.J.J. BONVIN TITLE HADDOCK A PROTEIN-PROTEIN DOCKING APPROACH BASED ON BIOCHEMICAL OR BIOPHYSICAL INFORMATION REF J.AM. CHEM.SOC,V125,P1731,2003 COORDINATES FOR E. COLI SECA (RESIDUES 9-228, 349-836)WERE OBTAINED FROM PDB ENTRY 2FSF. THE PREPROTEIN BINDING DOMAIN (RESIDUES 229-348) WAS MODELLED BASED ON THE AVAILABLE STRUCTURE OF T. THERMOPHILUS, CSI DATA AND NOES ON THE ISOLATED DOMAIN. TWO SINGLE CYSTEINE VARIANTS (POSITIONS 7 AND 25) WERE PREPARED AND CROSSLINKED WITH MTSL. PARAMAGNETIC RELAXATION ENHANCEMENT (PRE) VALUES FOR METHYL PROTONS OF VAL, LEU, ILE AND MET RESIDUES WERE QUANTIFIED FROM TWO 13C-HMQC SPECTRA (PARAMAGNETIC AND DIAMAGNETIC). PRES WERE CONVERTED TO DISTANCE RESTRAINTS, WHICH WERE USED FOR SUBSEQUENT STRUCTURE CALCULATION OF THE SECA-SIGNAL PEPTIDE COMPLEX.
NMR ensembleConformer selection criteria: LOWEST ENERGY / Conformers calculated total number: 200 / Conformers submitted total number: 10

+
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://pdbjlvh1.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