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- PDB-2om7: Structural Basis for Interaction of the Ribosome with the Switch ... -

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Basic information

Entry
Database: PDB / ID: 2om7
TitleStructural Basis for Interaction of the Ribosome with the Switch Regions of GTP-bound Elongation Factors
Components
  • (30S ribosomal protein ...) x 2
  • (Fragment of 16S rRNA ...) x 3
  • (Fragment of23S rRNA ...) x 5
  • 16S ribosomal RNA (H5)
  • 50S ribosomal protein L1
  • Elongation factor GEF-G
  • p/E-tRNA
KeywordsRIBOSOME / RNA-Protein Complex
Function / homology
Function and homology information


translational elongation / translation elongation factor activity / GDP binding / regulation of translation / ribosome binding / large ribosomal subunit / small ribosomal subunit / tRNA binding / rRNA binding / structural constituent of ribosome ...translational elongation / translation elongation factor activity / GDP binding / regulation of translation / ribosome binding / large ribosomal subunit / small ribosomal subunit / tRNA binding / rRNA binding / structural constituent of ribosome / translation / response to antibiotic / 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 / Ribosomal protein L1, bacterial-type / Translation elongation factor EFG/EF2, domain IV / Elongation factor G, domain IV / Elongation factor G, domain IV ...: / Translation elongation factor EFG/EF2 / Elongation factor G, domain III / EFG, domain V / Elongation Factor G, domain II / Elongation Factor G, domain III / Ribosomal protein L1, bacterial-type / 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. / Ribosomal protein L1, conserved site / Ribosomal protein L1 / Ribosomal protein L1 signature. / Ribosomal protein L1, 3-layer alpha/beta-sandwich / Translation elongation factor EFTu-like, domain 2 / Ribosomal protein L1-like / Ribosomal protein L1/ribosomal biogenesis protein / Elongation factor Tu domain 2 / Ribosomal protein L1p/L10e family / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal protein S12, bacterial-type / Ribosomal protein S2 signature 1. / Ribosomal protein S2, conserved site / Ribosomal protein S2 / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S2 / Small GTP-binding protein domain / Ribosomal protein S12 signature. / Ribosomal protein S12/S23 / Ribosomal protein S12/S23 / Translation protein, beta-barrel domain superfamily / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold / Nucleic acid-binding, OB-fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
: / : / : / RNA / RNA (> 10) / RNA (> 100) / Elongation factor G / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS12 ...: / : / : / RNA / RNA (> 10) / RNA (> 100) / Elongation factor G / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS12 / Elongation factor G / Large ribosomal subunit protein uL1
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7.3 Å
AuthorsConnell, S.R. / Wilson, D.N. / Rost, M. / Schueler, M. / Giesebrecht, J. / Dabrowski, M. / Mielke, T. / Fucini, P. / Spahn, C.M.T.
CitationJournal: Mol Cell / Year: 2007
Title: Structural basis for interaction of the ribosome with the switch regions of GTP-bound elongation factors.
Authors: Sean R Connell / Chie Takemoto / Daniel N Wilson / Hongfei Wang / Kazutaka Murayama / Takaho Terada / Mikako Shirouzu / Maximilian Rost / Martin Schüler / Jan Giesebrecht / Marylena ...Authors: Sean R Connell / Chie Takemoto / Daniel N Wilson / Hongfei Wang / Kazutaka Murayama / Takaho Terada / Mikako Shirouzu / Maximilian Rost / Martin Schüler / Jan Giesebrecht / Marylena Dabrowski / Thorsten Mielke / Paola Fucini / Shigeyuki Yokoyama / Christian M T Spahn /
Abstract: Elongation factor G (EF-G) catalyzes tRNA translocation on the ribosome. Here a cryo-EM reconstruction of the 70S*EF-G ribosomal complex at 7.3 A resolution and the crystal structure of EF-G-2*GTP, ...Elongation factor G (EF-G) catalyzes tRNA translocation on the ribosome. Here a cryo-EM reconstruction of the 70S*EF-G ribosomal complex at 7.3 A resolution and the crystal structure of EF-G-2*GTP, an EF-G homolog, at 2.2 A resolution are presented. EF-G-2*GTP is structurally distinct from previous EF-G structures, and in the context of the cryo-EM structure, the conformational changes are associated with ribosome binding and activation of the GTP binding pocket. The P loop and switch II approach A2660-A2662 in helix 95 of the 23S rRNA, indicating an important role for these conserved bases. Furthermore, the ordering of the functionally important switch I and II regions, which interact with the bound GTP, is dependent on interactions with the ribosome in the ratcheted conformation. Therefore, a network of interaction with the ribosome establishes the active GTP conformation of EF-G and thus facilitates GTP hydrolysis and tRNA translocation.
History
DepositionJan 21, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 12, 2014Group: Derived calculations
Revision 1.3Jul 18, 2018Group: Data collection / Database references / Category: em_image_scans / em_software / struct_ref_seq
Item: _em_software.image_processing_id / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end
Revision 1.4Dec 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details

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Structure visualization

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Structure viewerMolecule:
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Assembly

Deposited unit
A: Fragment of 16S rRNA (h14)
B: Fragment of 16S rRNA (h15)
C: Fragment of 16S rRNA (h44)
D: 16S ribosomal RNA (H5)
F: Fragment of23S rRNA (H95)
G: Fragment of23S rRNA (H68)
H: Fragment of23S rRNA (H89)
I: Fragment of23S rRNA (H42-44)
J: Fragment of23S rRNA (H76)
M: p/E-tRNA
E: 30S ribosomal protein S12
K: 50S ribosomal protein L1
L: Elongation factor G
N: 30S ribosomal protein S2


Theoretical massNumber of molelcules
Total (without water)404,60214
Polymers404,60214
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
DetailsA model for the entire complex can be generated by aligning the 50s subunit, 30s Head and 30s body from PDB IDs 2j00 and 2j01 to the corresponding elements in this model

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Components

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Fragment of 16S rRNA ... , 3 types, 3 molecules ABC

#1: RNA chain Fragment of 16S rRNA (h14)


Mass: 3827.336 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: 16S rRNA / Source: (natural) Thermus thermophilus (bacteria)
#2: RNA chain Fragment of 16S rRNA (h15)


Mass: 9048.452 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: 16S rRNA / Source: (natural) Thermus thermophilus (bacteria)
#3: RNA chain Fragment of 16S rRNA (h44)


Mass: 31208.635 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: 16S rRNA / Source: (natural) Thermus thermophilus (bacteria) / References: GenBank: 118505352

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RNA chain , 2 types, 2 molecules DM

#4: RNA chain 16S ribosomal RNA (H5)


Mass: 98292.133 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: 16S rRNA / Source: (natural) Thermus thermophilus (bacteria) / References: GenBank: 48256
#10: RNA chain p/E-tRNA


Mass: 23728.123 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: tRNA / Source: (natural) Thermus thermophilus (bacteria)

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Fragment of23S rRNA ... , 5 types, 5 molecules FGHIJ

#5: RNA chain Fragment of23S rRNA (H95)


Mass: 9378.643 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: 23S rRNA / Source: (natural) Thermus thermophilus (bacteria)
#6: RNA chain Fragment of23S rRNA (H68)


Mass: 17631.637 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: 23S rRNA / Source: (natural) Thermus thermophilus (bacteria) / References: GenBank: 37223182
#7: RNA chain Fragment of23S rRNA (H89)


Mass: 13540.067 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: 23S rRNA / Source: (natural) Thermus thermophilus (bacteria)
#8: RNA chain Fragment of23S rRNA (H42-44)


Mass: 18710.129 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: 23S rRNA / Source: (natural) Thermus thermophilus (bacteria) / References: GenBank: 37223182
#9: RNA chain Fragment of23S rRNA (H76)


Mass: 33148.680 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: 23S rRNA / Source: (natural) Thermus thermophilus (bacteria) / References: GenBank: 37223182

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30S ribosomal protein ... , 2 types, 2 molecules EN

#11: Protein 30S ribosomal protein S12 /


Mass: 14920.754 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Small ribosomal subunit protein S12 / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P17293, UniProt: Q5SHN3*PLUS
#14: Protein 30S ribosomal protein S2 /


Mass: 29317.703 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Small ribosomal subunit protein S2 / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P80371

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Protein , 2 types, 2 molecules KL

#12: Protein 50S ribosomal protein L1 /


Mass: 24872.721 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Large ribosomal subunit protein L1 / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: Q5SLP7
#13: Protein Elongation factor G / EF-G / EF-G


Mass: 76977.102 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Gene: fusA, fus / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P13551, UniProt: Q5SHN5*PLUS

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeParent-ID
1complex of Thermus thermophilus 70S ribosomes and EF-G-GMPPNPRIBOSOME0
230S ribosomal protein S121
350S ribosomal protein L11
4Elongation factor GEF-G1
530S ribosomal protein S21
Buffer solutionName: 0.3 mM GMPPNP, 10 mM Hepes-KOH (pH 7.8), 10 mM Mg acetate, 60 mM NH4Cl, and 6 mM B-mercaptoethanol
pH: 7.8
Details: 0.3 mM GMPPNP, 10 mM Hepes-KOH (pH 7.8), 10 mM Mg acetate, 60 mM NH4Cl, and 6 mM B-mercaptoethanol
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F30
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 39000 X / Nominal defocus max: 4000 nm / Nominal defocus min: 800 nm
Specimen holderSpecimen holder type: Eucentric
Image recordingElectron dose: 19 e/Å2 / Film or detector model: KODAK SO-163 FILM

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Processing

SoftwareName: SPIDER / Classification: refinement
EM software
IDNameCategory
1Situsmodel fitting
2SPIDER3D reconstruction
CTF correctionDetails: defocus groups
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 7.3 Å / Num. of particles: 77038
Details: The geometry of linkages between some residues in chains J, M and L are distorted. They were not resolved based on the data used for solving this structure.
Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Details: METHOD--Rigid Body
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
12J00

2j00
PDB Unreleased entry

12J001PDBexperimental model
21GIX

1gix
PDB Unreleased entry

11GIX2PDBexperimental model
32J01

2j01
PDB Unreleased entry

12J013PDBexperimental model
41FNM11FNM4PDBexperimental model
51YL3

1yl3
PDB Unreleased entry

11YL35PDBexperimental model
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms9140 9891 0 0 19031

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