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Normal mode-based flexible fitted coordinates of a non-translocating SecYEG protein-conducting channel into the cryo-EM map of a SecYEG-nascent chain-70S ribosome complex from E. coli

by single particle reconstruction, at 14.9 A resolution

Movie

Orientation:

#1: Depositted structure unit, Made by Jmol

#2: Superimposing with simplified surface model of EM map, EMDB-1143, Made by Jmol

#3: With PDB-2aki, PDB-2gyb, PDB-2gyc, Made by Jmol

#4: Superimposing with EM 3D map: EMDB-1143 (with PDB-2aki, PDB-2gyb, PDB-2gyc), Made by UCSF CHIMERA

Entry
Summary
Database / IDPORTEIN DATA BANK (PDB) / 2akh
TitleNormal mode-based flexible fitted coordinates of a non-translocating SecYEG protein-conducting channel into the cryo-EM map of a SecYEG-nascent chain-70S ribosome complex from E. coli
DescriptorProtein-export membrane protein secG
Preprotein translocase secY subunit
Preprotein translocase secE subunit
KeywordsPROTEIN TRANSPORT, Protein transport, Translocation, Transmembrane, Transport
AuthorsMitra, K.M., Schaffitzel, C., Shaikh, T., Tama, F., Jenni, S., Brooks III, C.L., Ban, N., Frank, J.
DateDeposition: 2005-08-03, Release: 2005-11-15
PDBj Mine pagesSummary, Structural Details, Experimental Details, Functional Details
Other databasesRCSB-PDB, PDBe, CATH, CE, FSSP, SCOP, VAST
Structure Visualization
MoviesMovie Page

#1: Depositted structure unit, Made by Jmol

#2: Superimposing with simplified surface model of EM map, EMDB-1143, Made by Jmol

#3: With PDB-2aki, PDB-2gyb, PDB-2gyc, Made by Jmol

#4: Superimposing with EM 3D map: EMDB-1143 (with PDB-2aki, PDB-2gyb, PDB-2gyc), Made by UCSF CHIMERA

Structure viewersYorodumi, jV4, Jmol, Biological unit (Images, jV)
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EMDB-1143

CiteFit

Cite: data citing same article

Fit: target map of fitting

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List of similar structure data about Omokage system
Article
Citation - primary
ArticleNature, Vol. 438, Issue 7066, Page 318-24, Year 2005
TitleStructure of the E. coli protein-conducting channel bound to a translating ribosome.
AuthorsKakoli Mitra, Christiane Schaffitzel, Tanvir Shaikh, Florence Tama, Simon Jenni, Charles L Brooks, Nenad Ban, Joachim Frank
Howard Hughes Medical Institute, Health Research Inc. at the Wadsworth Center, Empire State Plaza, Albany, New York 12201-0509, USA.
KeywordsCell Membrane (chemistry), Cryoelectron Microscopy, Escherichia coli Proteins (biosynthesis), Membrane Proteins (chemistry), Models, Molecular, Multiprotein Complexes (chemistry), Pliability, Protein Binding, Protein Biosynthesis, Protein Structure, Quaternary, Protein Transport, Ribosomes (metabolism), SecE protein, E coli, SecG protein, E coli, SecY protein, E coli
LinksDOI: 10.1038/nature04133, PubMed: 16292303, PMC: PMC1351281
Components
ID 1 : Preprotein translocase band 1 subunit, P12
Image
DescriptionProtein-export membrane protein secG
Typepolypeptide(L)
Formula weight7906.411 Da
Number of molecules2
ID1
SourceMethod: Isolated from a genetically manipulated source
Gene: Escherichia, secG, ID:562, Escherichia coli
Host: Escherichia, ID:562, Escherichia coli

LinksUniProt: P33582, Sequence view
ID 2 : Preprotein translocase secY subunit
Image
DescriptionPreprotein translocase secY subunit
Typepolypeptide(L)
Fragmentplug TMH 2a deleted
MutationDEL(40-75)
Formula weight43961.500 Da
Number of molecules2
ID2
SourceMethod: Isolated from a genetically manipulated source
Gene: Escherichia, secY, prlA, ID:562, Escherichia coli
Host: Escherichia, ID:562, Escherichia coli
LinksUniProt: P03844, UniProt: P03844, Sequence view
ID 3 : Preprotein translocase secE subunit
Image
DescriptionPreprotein translocase secE subunit
Typepolypeptide(L)
Formula weight12095.814 Da
Number of molecules2
ID3
SourceMethod: Isolated from a genetically manipulated source
Gene: Escherichia, secE, prlG, ID:562, Escherichia coli
Host: Escherichia, ID:562, Escherichia coli
LinksUniProt: P16920, Sequence view
Sample
Assembly
Aggregation statePARTICLE
Nameprotein-conducting channel
Entity assembly
Assembly-ID1
Detailsdimer of SecYEG heterotrimer
GO-IDGO:0015450
InterPro-IDIPR:004692
Nameprotein translocase activity
Entity assembly
Assembly-ID1
Detailsdimer of SecYEG heterotrimer
GO-IDGO:0015450
InterPro-IDIPR:002208
Nameprotein translocase activity
Entity assembly
Assembly-ID1
Detailsdimer of SecYEG heterotrimer
GO-IDGO:0015450
InterPro-IDIPR:005807
Nameprotein translocase activity
Experiment
Reconstruction methodSINGLE PARTICLE
Specimen typeVITREOUS ICE (CRYO EM)
Vitrification
Cryogen nameETHANE
Humidity90
Instrumenttwo sided blotting plunger
MethodBlot for 2 seconds before plunging
Temp93 Kelvin
Experiment
MethodELECTRON MICROSCOPY
Electron Microscopy
Imaging
MicroscopeModel: FEI TECNAI F30
Date2004-03-09
Electron gun
Electron sourceFIELD EMISSION GUN
Accelerating voltage300 kV
Electron dose11 e/A**2
Illumination modeFLOOD BEAM
Lens
ModeBRIGHT FIELD
MagnificationCalibrated: 39000 X, Nominal: 39000 X
CsNominal: 2.26 mm
Nominal defocusMax: 4300 nm, Min: 1500 nm
Specimen holder
Specimen holderModel: OTHER, Type: Cryo Stage
Temperature93 Kelvin
Detector
TypeKodak SO163 film
Processing
2D projection selection
Software nameRSR2000
Single particle entity
Symmetry typeASYMMETRIC
3D reconstruction
CTF correction methoddefocus groups
DetailsThe resolution is based on FSC at 0.5 cut-off
Resolution14.9 A
3D fitting
Methodnormal mode-based flexible fitting
Refinement Protocolnormal mode-based flexible fitting, real space refinement
Refinement SpaceREAL
Software nameRSR2000
Target criteriacorrelation coefficient, R-factor
Refine hist
Cycle idLAST
Refine idELECTRON MICROSCOPY
Total atoms1176
Protein atoms1176
Download
PDB format
Allpdb2akh.ent.gz
pdb2akh.ent (uncompressed file)
Header onlypdb2akh.ent.gz
mmCIF format
mmCIF2akh.cif.gz
XML format
All2akh.xml.gz
No-atom2akh-noatom.xml.gz
Ext-atom2akh-extatom.xml.gz
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 2.7 MB
.webm (WebM/VP8 format), 3.6 MB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.4 MB
.webm (WebM/VP8 format), 4.4 MB
movie #3
.mp4 (H.264/MPEG-4 AVC format), 2.9 MB
.webm (WebM/VP8 format), 3.6 MB
movie #4
.mp4 (H.264/MPEG-4 AVC format), 3.7 MB
.webm (WebM/VP8 format), 5.5 MB