[English] 日本語
Yorodumi
- SASDDY9: Protein translocase subunit SecA (full length, amino acids 1-901) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: SASBDB / ID: SASDDY9
SampleProtein translocase subunit SecA (full length, amino acids 1-901)
  • Protein translocase subunit SecA (protein), Escherichia coli (strain K12)
Function / homology
Function and homology information


preprotein binding / 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 targeting to membrane / protein secretion / protein targeting ...preprotein binding / 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 targeting to membrane / protein secretion / protein targeting / ribonucleoprotein complex binding / chaperone-mediated protein folding / cytoplasmic side of plasma membrane / ribosome binding / protein transport / zinc ion binding / ATP binding / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
SecA P-loop domain / SEC-C motif / 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 P-loop domain / SEC-C motif / 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 / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Protein translocase subunit SecA
Similarity search - Component
Biological speciesEscherichia coli (strain K12) (bacteria)
CitationDate: 2019 Jun 27
Title: The C-terminal tail of the bacterial translocation ATPase SecA modulates its activity
Authors: Jamshad M / Knowles T / White S / Ward D / Mohammed F / Rahman K / Wynne M / Hughes G / Kramer G / Bukau B
Contact author
  • Timothy Knowles (University of Birmingham, Birmingham, UK)

-
Structure visualization

Downloads & links

-
Models

-
Sample

SampleName: Protein translocase subunit SecA (full length, amino acids 1-901)
Specimen concentration: 5 mg/ml
BufferName: 20mM HEPES, 100mM NaCl, 1mM TCEP / pH: 8
Entity #1174Type: protein / Description: Protein translocase subunit SecA / Formula weight: 102.022 / Num. of mol.: 2 / Source: Escherichia coli (strain K12) / References: UniProt: P10408
Sequence: MLIKLLTKVF GSRNDRTLRR MRKVVNIINA MEPEMEKLSD EELKGKTAEF RARLEKGEVL ENLIPEAFAV VREASKRVFG MRHFDVQLLG GMVLNERCIA EMRTGEGKTL TATLPAYLNA LTGKGVHVVT VNDYLAQRDA ENNRPLFEFL GLTVGINLPG MPAPAKREAY ...Sequence:
MLIKLLTKVF GSRNDRTLRR MRKVVNIINA MEPEMEKLSD EELKGKTAEF RARLEKGEVL ENLIPEAFAV VREASKRVFG MRHFDVQLLG GMVLNERCIA EMRTGEGKTL TATLPAYLNA LTGKGVHVVT VNDYLAQRDA ENNRPLFEFL GLTVGINLPG MPAPAKREAY AADITYGTNN EYGFDYLRDN MAFSPEERVQ RKLHYALVDE VDSILIDEAR TPLIISGPAE DSSEMYKRVN KIIPHLIRQE KEDSETFQGE GHFSVDEKSR QVNLTERGLV LIEELLVKEG IMDEGESLYS PANIMLMHHV TAALRAHALF TRDVDYIVKD GEVIIVDEHT GRTMQGRRWS DGLHQAVEAK EGVQIQNENQ TLASITFQNY FRLYEKLAGM TGTADTEAFE FSSIYKLDTV VVPTNRPMIR KDLPDLVYMT EAEKIQAIIE DIKERTAKGQ PVLVGTISIE KSELVSNELT KAGIKHNVLN AKFHANEAAI VAQAGYPAAV TIATNMAGRG TDIVLGGSWQ AEVAALENPT AEQIEKIKAD WQVRHDAVLE AGGLHIIGTE RHESRRIDNQ LRGRSGRQGD AGSSRFYLSM EDALMRIFAS DRVSGMMRKL GMKPGEAIEH PWVTKAIANA QRKVESRNFD IRKQLLEYDD VANDQRRAIY SQRNELLDVS DVSETINSIR EDVFKATIDA YIPPQSLEEM WDIPGLQERL KNDFDLDLPI AEWLDKEPEL HEETLRERIL AQSIEVYQRK EEVVGAEMMR HFEKGVMLQT LDSLWKEHLA AMDYLRQGIH LRGYAQKDPK QEYKRESFSM FAAMLESLKY EVISTLSKVQ VRMPEEVEEL EQQRRMEAER LAQMQQLSHQ DDDSAAAAAL AAQTGERKVG RNDPCPCGSG KKYKQCHGRL Q

-
Experimental information

BeamInstrument name: ESRF BM29 / City: Grenoble / 国: France / Type of source: X-ray synchrotronSynchrotron / Wavelength: 0.0919 Å / Dist. spec. to detc.: 2.867 mm
DetectorName: Pilatus 1M / Type: Dectris / Pixsize x: 172 mm
Scan
Title: Protein translocase subunit SecA (full length, amino acids 1-901)
Measurement date: Jul 18, 2016 / Storage temperature: 4 °C / Cell temperature: 20 °C / Exposure time: 1 sec. / Number of frames: 45 / Unit: 1/nm /
MinMax
Q0.0278 4.9518
Distance distribution function P(R)
Sofotware P(R): GNOM 5.0 / Number of points: 366 /
MinMax
Q0.1696 1.89442
P(R) point1 366
R0 14.89
Result
Type of curve: sec
Comments: Additional SEC parameters: Column type, S200 10/300 GL (GE Lifesciences); Flow rate, 1.0mL/min; Sample injection concentration, 5mg/mL; Injection volume, 0.5mL
ExperimentalStandardPorod
MW232.267 kDa224.7 kDa-
Volume--424 nm3

P(R)GuinierGuinier error
Forward scattering, I0144 144.47 0.076
Radius of gyration, Rg4.186 nm4.22 nm-

MinMax
D-14.89
Guinier point23 60

+
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