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- PDB-5abb: Visualization of a polytopic membrane protein during SecY-mediate... -

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Entry
Database: PDB / ID: 5abb
TitleVisualization of a polytopic membrane protein during SecY-mediated membrane insertion
DescriptorPROTEIN TRANSLOCASE SUBUNIT SECY
PROTEIN TRANSLOCASE SUBUNIT SECE
GREEN-LIGHT ABSORBING PROTEORHODOPSIN
KeywordsTRANSLATION / RIBOSOME / MEMBRANE PROTEIN / TRANSLOCON
Specimen sourceEscherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
MethodElectron microscopy (8 Å resolution / Particle / Single particle)
AuthorsBischoff, L. / Wickles, S. / Berninghausen, O. / vanderSluis, E. / Beckmann, R.
CitationNat Commun, 2014, 5, 4103-4103

Nat Commun, 2014, 5, 4103-4103 Yorodumi Papers
Visualization of a polytopic membrane protein during SecY-mediated membrane insertion.
Lukas Bischoff / Stephan Wickles / Otto Berninghausen / Eli O van der Sluis / Roland Beckmann

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Aug 5, 2015 / Release: Aug 19, 2015
RevisionDateData content typeGroupCategoryItemProviderType
1.0Aug 19, 2015Structure modelrepositoryInitial release
1.1Aug 30, 2017Structure modelData collectionem_image_scans / em_software_em_software.image_processing_id

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Structure visualization

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Assembly

Deposited unit
A: PROTEIN TRANSLOCASE SUBUNIT SECY
B: PROTEIN TRANSLOCASE SUBUNIT SECE
Z: GREEN-LIGHT ABSORBING PROTEORHODOPSIN


Theoretical massNumber of molelcules
Total (without water)68,8113
Polyers68,8113
Non-polymers00
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Polypeptide(L)PROTEIN TRANSLOCASE SUBUNIT SECY


Mass: 48553.375 Da / Num. of mol.: 1
Source: (natural) Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
References: UniProt: B7MCR5

Cellular component

Molecular function

Biological process

  • intracellular protein transmembrane transport (GO: 0065002)
  • intracellular protein transport (GO: 0006886)
  • protein insertion into membrane from inner side (GO: 0032978)
  • protein transport by the Sec complex (GO: 0043952)
  • SRP-dependent cotranslational protein targeting to membrane, translocation (GO: 0006616)
#2: Polypeptide(L)PROTEIN TRANSLOCASE SUBUNIT SECE


Mass: 12623.296 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 12-127
Source: (natural) Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
References: UniProt: B7MIW7

Cellular component

Molecular function

  • P-P-bond-hydrolysis-driven protein transmembrane transporter activity (GO: 0015450)

Biological process

#3: Polypeptide(L)GREEN-LIGHT ABSORBING PROTEORHODOPSIN / GPR


Mass: 7634.684 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 19-83
Source: (natural) Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
References: UniProt: Q9F7P4

Cellular component

Molecular function

Biological process

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE

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Sample preparation

ComponentName: TnaC stalled E.coli ribosome in complex with SecYE / Type: RIBOSOME
Buffer solutionName: 20 MM TRIS 150 MM NH4CL 10 MM MGCL2 0.05%DDM 125 MM SUCROSE
Details: 20 MM TRIS 150 MM NH4CL 10 MM MGCL2 0.05%DDM 125 MM SUCROSE
pH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: HOLEY CARBON
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS / Date: May 21, 2012
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal magnification: 148721 / Nominal defocus max: 3500 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 20 e/Å2 / Film or detector model: TVIPS TEMCAM-F416 (4k x 4k)
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameCategoryImage processing ID
1CootMODEL FITTING
2SPIDERRECONSTRUCTION1
SymmetryPoint symmetry: C1
3D reconstructionMethod: REAL / Resolution: 8 Å / Number of particles: 47471 / Symmetry type: POINT
Least-squares processHighest resolution: 8 Å
Refine hist #LASTHighest resolution: 8 Å
Number of atoms included #LASTProtein: 2512 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 2512

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