3D Electron Microscopy (3D-EM) Data Navigator [English / [日本語]]
Top Gallery List Statistics Shape search Viewer
Movie pageYodrodumi (structure viewer)
PDBj>EM Navigator>Detail page - PDB-2akh

This page is a legacy version and will be discarded in future. The new page is here.

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: Deposited structure unit, Imaged by Jmol

#2: Superimposition on simplified surface model of EM map, EMDB-1143, Imaged by Jmol

#3: With , Imaged by Jmol

#4: Superimposition on EM map, EMDB-1143, + PDB-2aki, PDB-4v4w, Imaged 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, FSSP, SCOP
Structure Visualization
MoviesMovie Page

#1: Deposited structure unit, Imaged by Jmol

#2: Superimposition on simplified surface model of EM map, EMDB-1143, Imaged by Jmol

#3: With , Imaged by Jmol

#4: Superimposition on EM map, EMDB-1143, + PDB-2aki, PDB-4v4w, Imaged by UCSF CHIMERA

Structure viewersYorodumi, jV4, Jmol, Biological unit (Images, jV)
Related Structure Data
Related Entries

EMDB-1143

CiteFit

Cite: data citing same article

Fit: target map of fitting

Similar-shape strucutres
Search for similar-shape assemblies throgh:
EMDB + EM entries in PDB
all of EMDB & PDB (Omokage search)
Article
Citation - primary
ArticleNature, Vol. 438, Issue 7066, Page 318-324, 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), SEC Translocation Channels, SecE protein, E coli, SecG protein, E coli, SecY protein, E coli
LinksPubMed: 16292303, DOI: 10.1038/nature04133, PMC: PMC1351281
Components
ID 1 : Preprotein translocase band 1 subunit, P12
Image
DescriptionProtein-export membrane protein secG
Typepolypeptide(L)
Formula weight7906.356 Da
Number of molecules2
ID1
SourceMethod: Isolated from a genetically manipulated source
Src id: 1
Gene: Escherichia, secG, ID:562, Escherichia coli
Host: Escherichia, ID:562, Escherichia coli


Alt source flag: sample
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 weight43961.035 Da
Number of molecules2
ID2
SourceMethod: Isolated from a genetically manipulated source
Src id: 1
Gene: Escherichia, secY, prlA, ID:562, Escherichia coli
Host: Escherichia, ID:562, Escherichia coli
Alt source flag: sample
LinksUniProt: P03844, UniProt: P03844, Sequence view
ID 3 : Preprotein translocase secE subunit
Image
DescriptionPreprotein translocase secE subunit
Typepolypeptide(L)
Formula weight12095.701 Da
Number of molecules2
ID3
SourceMethod: Isolated from a genetically manipulated source
Src id: 1
Gene: Escherichia, secE, prlG, ID:562, Escherichia coli
Host: Escherichia, ID:562, Escherichia coli
Alt source flag: sample
LinksUniProt: P16920, Sequence view
Sample
Entity assembly
Nameprotein-conducting channel
TypeCOMPLEX
Entity assembly
Detailsdimer of SecYEG heterotrimer
Nameprotein translocase activity
Parent id1
Entity assembly
Detailsdimer of SecYEG heterotrimer
Nameprotein translocase activity
Parent id1
Entity assembly
Detailsdimer of SecYEG heterotrimer
Nameprotein translocase activity
Parent id1
Buffer
Specimen id1
Experiment
Aggregation statePARTICLE
Reconstruction methodSINGLE PARTICLE
Sample support
Specimen id1
Vitrification
Specimen id1
Cryogen nameETHANE
Humidity90
InstrumentHOMEMADE 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
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
Image scans
Image recording id1
Processing
Single particle entity
Image processing id1
Point symmetryC1
3D reconstruction
Image processing id1
DetailsThe resolution is based on FSC at 0.5 cut-off
Number of particles53325
Resolution14.9 A
Resolution methodFSC 0.5 CUT-OFF
Symmetry typePOINT
3D fitting
DetailsMETHOD--normal mode-based flexible fitting REFINEMENT PROTOCOL--normal mode-based flexible fitting, real space refinement
Refinement ProtocolFLEXIBLE FIT
Refinement SpaceREAL
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), 2.7 MB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.1 MB
.webm (WebM/VP8 format), 5.4 MB
movie #3
.mp4 (H.264/MPEG-4 AVC format), 3 MB
.webm (WebM/VP8 format), 2.7 MB
movie #4
.mp4 (H.264/MPEG-4 AVC format), 3.7 MB
.webm (WebM/VP8 format), 5.5 MB