[English] 日本語
Yorodumi
- PDB-1jqm: Fitting of L11 protein and elongation factor G (EF-G) in the cryo... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1jqm
TitleFitting of L11 protein and elongation factor G (EF-G) in the cryo-em map of e. coli 70S ribosome bound with EF-G, GDP and fusidic acid
Components
  • 50S Ribosomal protein L11
  • Elongation Factor GEF-G
KeywordsRIBOSOME / L11 / EF-G / cryo-EM / 70s E.coli ribosome / GDP state
Function / homology
Function and homology information


translational elongation / translation elongation factor activity / GDP binding / large ribosomal subunit rRNA binding / ribosome binding / cytosolic large ribosomal subunit / structural constituent of ribosome / translation / GTPase activity / GTP binding ...translational elongation / translation elongation factor activity / GDP binding / large ribosomal subunit rRNA binding / ribosome binding / cytosolic large ribosomal subunit / structural constituent of ribosome / translation / GTPase activity / GTP binding / magnesium ion binding / cytoplasm
Similarity search - Function
: / Translation elongation factor EFG/EF2 / Elongation factor G, domain III / EFG, domain V / Elongation Factor G, domain II / Elongation Factor G, domain III / Translation elongation factor EFG/EF2, domain IV / Elongation factor G, domain IV / Elongation factor G, domain IV / Elongation factor G C-terminus ...: / Translation elongation factor EFG/EF2 / Elongation factor G, domain III / EFG, domain V / Elongation Factor G, domain II / Elongation Factor G, domain III / Translation elongation factor EFG/EF2, domain IV / Elongation factor G, domain IV / Elongation factor G, domain IV / Elongation factor G C-terminus / Elongation factor EFG, domain V-like / Elongation factor G C-terminus / EF-G domain III/V-like / Tr-type G domain, conserved site / Translational (tr)-type guanine nucleotide-binding (G) domain signature. / Translation elongation factor EFTu-like, domain 2 / Elongation factor Tu domain 2 / Ribosomal protein L11, bacterial-type / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / Ribosomal protein L11, conserved site / Ribosomal protein L11 signature. / Ribosomal protein L11, N-terminal / Ribosomal protein L11, N-terminal domain / Ribosomal protein L11/L12 / Ribosomal protein L11, C-terminal / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein L11, RNA binding domain / Ribosomal protein L11/L12 / Small GTP-binding protein domain / Translation protein, beta-barrel domain superfamily / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Elongation factor G / Large ribosomal subunit protein uL11
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / Molecular Modeling based on crystal structures / cryo EM / Resolution: 18 Å
Model detailsThis structure was generated by fitting the X-ray crystal structure of L11 and EF-G into the 70S E. ...This structure was generated by fitting the X-ray crystal structure of L11 and EF-G into the 70S E. coli EF-G- (GDP form) bound ribosome map. L11 (linker region between N and C terminal) and EF-G positions of domains G' and V were modeled to accommodate the conformational changes. The structure is modeled as a C-alpha trace. Conformational changes occur in protein L11 and EF-G in two stpes due to the binding of EF-G to the 70S ribosome, and subsequent GTP hydrolysis. These changed conformations were modeled based on the fitting of the crystal coordinates to the low resolution ribosome map (factor-bound) and energy minimizing the fitted structures.
AuthorsAgrawal, R.K. / Linde, J. / Segupta, J. / Nierhaus, K.H. / Frank, J.
Citation
Journal: J Mol Biol / Year: 2001
Title: Localization of L11 protein on the ribosome and elucidation of its involvement in EF-G-dependent translocation.
Authors: R K Agrawal / J Linde / J Sengupta / K H Nierhaus / J Frank /
Abstract: L11 protein is located at the base of the L7/L12 stalk of the 50 S subunit of the Escherichia coli ribosome. Because of the flexible nature of the region, recent X-ray crystallographic studies of the ...L11 protein is located at the base of the L7/L12 stalk of the 50 S subunit of the Escherichia coli ribosome. Because of the flexible nature of the region, recent X-ray crystallographic studies of the 50 S subunit failed to locate the N-terminal domain of the protein. We have determined the position of the complete L11 protein by comparing a three-dimensional cryo-EM reconstruction of the 70 S ribosome, isolated from a mutant lacking ribosomal protein L11, with the three-dimensional map of the wild-type ribosome. Fitting of the X-ray coordinates of L11-23 S RNA complex and EF-G into the cryo-EM maps combined with molecular modeling, reveals that, following EF-G-dependent GTP hydrolysis, domain V of EF-G intrudes into the cleft between the 23 S ribosomal RNA and the N-terminal domain of L11 (where the antibiotic thiostrepton binds), causing the N-terminal domain to move and thereby inducing the formation of the arc-like connection with the G' domain of EF-G. The results provide a new insight into the mechanism of EF-G-dependent translocation.
#1: Journal: Cell(Cambridge,Mass.) / Year: 1999
Title: A Detailed View of a Ribosomal Active Site: The Structure of the L11-RNA Complex
Authors: Wimberly, B.T. / Guymon, R. / McCutcheon, J.P. / White, S.W. / Ramakrishnan, V.
#2: Journal: Embo J. / Year: 1994
Title: The Crystal Structure of Elongation Factor G Complexed with GDP, at 2.7A Resolution.
Authors: Czworkowski, J. / Wang, J. / Steitz, T.A. / Moore, P.B.
#3: Journal: Embo J. / Year: 1994
Title: Three-dimensional structure of the ribosomal translocase: Elongation factor G from Thermus thermophilus
Authors: AEvarsson, A. / Brazhnikov, E. / Garber, M. / Zheltonosova, J. / Chirgadze, Y. / al-Karadaghi, S. / Svensson, L.A. / Liljas, A.
#4: Journal: J.Mol.Biol. / Year: 2000
Title: Structure of a Mutant EF-G Reveals Domain III and Possibly the Fusidic Acid Binding Site
Authors: Laurberg, M. / Kristensen, O. / Martemyanov, K. / Gudkov, A.T. / Nagaev, I. / Hughes, D. / Liljas, A.
#5: Journal: Nat.Struct.Biol. / Year: 1999
Title: EF-G-dependent GTP hydrolysis induces translocation accompanied by large conformational changes in the 70S ribosome
Authors: Agrawal, R.K. / Heagle, A.B. / Penczek, P. / Grassucci, R.A. / Frank, J.
History
DepositionAug 7, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_image_scans / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 50S Ribosomal protein L11
B: Elongation Factor G


Theoretical massNumber of molelcules
Total (without water)91,8292
Polymers91,8292
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

-
Components

#1: Protein 50S Ribosomal protein L11 / / Coordinate model: Cα atoms only


Mass: 14865.637 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: L11 from E. coli 70S ribosome modeled by crystal structure of L11 from Thermatogoma maritima
Source: (natural) Escherichia coli (E. coli) / References: UniProt: P29395
#2: Protein Elongation Factor G / EF-G / EF-G / translation elongation factor EF-G / Coordinate model: Cα atoms only


Mass: 76963.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: EF-G from E. coli 70S ribosome modeled by crystal structure of EF-G from Thermus thermophilus
Source: (natural) Escherichia coli (E. coli) / References: UniProt: P13551

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction
NMR detailsText: This structure was generated by fitting the X-ray crystal structure of L11 and EF-G into the 70S E. coli EF-G (GDP form) bound ribosome map. L11 (linker region between N and C terminal) and EF- ...Text: This structure was generated by fitting the X-ray crystal structure of L11 and EF-G into the 70S E. coli EF-G (GDP form) bound ribosome map. L11 (linker region between N and C terminal) and EF-G positions of domains G' and V were modeled to accommodate the conformational changes.

-
Sample preparation

ComponentName: e. coli 70S ribosome bound with EF-G, GDP and fusidic acid
Type: RIBOSOME
Buffer solutionpH: 7.6
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Crystal grow
*PLUS
Method: electron microscopy

-
Electron microscopy imaging

MicroscopyModel: FEI/PHILIPS EM420
Electron gunElectron source: OTHER / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 52000 X
Specimen holderSpecimen holder model: GATAN LIQUID NITROGEN
Image recordingElectron dose: 10 e/Å2 / Film or detector model: GENERIC FILM

-
Processing

Particle selectionNum. of particles selected: 36113
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 18 Å / Resolution method: FSC 0.5 CUT-OFF / Num. of particles: 36113 / Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: REAL / Target criteria: VISUAL AGREEMENT
Details: REFINEMENT PROTOCOL--MANUAL DETAILS--This structure was generated by fitting the X-ray crystal structure of L11 and EF-G into the 70S E. coli EF-G (GDP form) bound ribosome electron ...Details: REFINEMENT PROTOCOL--MANUAL DETAILS--This structure was generated by fitting the X-ray crystal structure of L11 and EF-G into the 70S E. coli EF-G (GDP form) bound ribosome electron microscopy map. L11 (linker region between N and C terminal) and EF-G positions of domains G and V were modeled to accommodate the conformational changes. Conformational changes occur in protein L11 and EF-G in two steps due to the binding of EF-G to the 70S ribosome, and subsequent GTP hydrolysis. These changed conformations were modeled based on the fitting of the crystal coordinates to the low resolution ribosome map (factor-bound) and energy minimizing the fitted structures.
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms824 0 0 0 824
NMR software
NameVersionDeveloperClassification
IRIS Explorer3.5Numerical Algorithms Group, Inc.data analysis
O5.1Jones, Zou, Cowan, Kjeldgaarddata analysis
SPIDER4.48Frankprocessing
Insight II1998Biosym/MSI Inc.data analysis
RefinementMethod: Molecular Modeling based on crystal structures / Software ordinal: 1
Details: Conformational changes occur in protein L11 and EF-G in two stpes due to the binding of EF-G to the 70S ribosome, and subsequent GTP hydrolysis. These changed conformations were modeled ...Details: Conformational changes occur in protein L11 and EF-G in two stpes due to the binding of EF-G to the 70S ribosome, and subsequent GTP hydrolysis. These changed conformations were modeled based on the fitting of the crystal coordinates to the low resolution ribosome map (factor-bound) and energy minimizing the fitted structures.

+
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