[English] 日本語
Yorodumi
- PDB-2iwh: Structure of yeast Elongation Factor 3 in complex with ADPNP -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2iwh
TitleStructure of yeast Elongation Factor 3 in complex with ADPNP
ComponentsELONGATION FACTOR 3A
KeywordsTRANSLATION / PROTEIN BIOSYNTHESIS / PHOSPHORYLATION / ELONGATION FACTOR / NUCLEOTIDE-BINDING / RNA-BINDING / ACETYLATION / ATP-BINDING / RRNA-BINDING
Function / homology
Function and homology information


translational elongation / translational termination / translation elongation factor activity / cytosolic ribosome / negative regulation of protein phosphorylation / : / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / negative regulation of protein kinase activity / cytoplasmic stress granule / ribosome ...translational elongation / translational termination / translation elongation factor activity / cytosolic ribosome / negative regulation of protein phosphorylation / : / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / negative regulation of protein kinase activity / cytoplasmic stress granule / ribosome / rRNA binding / ATP hydrolysis activity / ATP binding
Similarity search - Function
PWI domain - #20 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #990 / PWI domain / Elongation Factor 3 / Four helical bundle domain / : / : / Four helical bundle domain / HEAT repeat profile. / HEAT, type 2 ...PWI domain - #20 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #990 / PWI domain / Elongation Factor 3 / Four helical bundle domain / : / : / Four helical bundle domain / HEAT repeat profile. / HEAT, type 2 / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / Armadillo-like helical / Alpha Horseshoe / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Armadillo-type fold / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Up-down Bundle / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Elongation factor 3A
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsAndersen, C.B.F. / Becker, T. / Blau, M. / Anand, M. / Halic, M. / Balar, B. / Mielke, T. / Boesen, T. / Pedersen, J.S. / Spahn, C.M.T. ...Andersen, C.B.F. / Becker, T. / Blau, M. / Anand, M. / Halic, M. / Balar, B. / Mielke, T. / Boesen, T. / Pedersen, J.S. / Spahn, C.M.T. / Kinzy, T.G. / Andersen, G.R. / Beckmann, R.
CitationJournal: Nature / Year: 2006
Title: Structure of eEF3 and the mechanism of transfer RNA release from the E-site.
Authors: Christian B F Andersen / Thomas Becker / Michael Blau / Monika Anand / Mario Halic / Bharvi Balar / Thorsten Mielke / Thomas Boesen / Jan Skov Pedersen / Christian M T Spahn / Terri Goss ...Authors: Christian B F Andersen / Thomas Becker / Michael Blau / Monika Anand / Mario Halic / Bharvi Balar / Thorsten Mielke / Thomas Boesen / Jan Skov Pedersen / Christian M T Spahn / Terri Goss Kinzy / Gregers R Andersen / Roland Beckmann /
Abstract: Elongation factor eEF3 is an ATPase that, in addition to the two canonical factors eEF1A and eEF2, serves an essential function in the translation cycle of fungi. eEF3 is required for the binding of ...Elongation factor eEF3 is an ATPase that, in addition to the two canonical factors eEF1A and eEF2, serves an essential function in the translation cycle of fungi. eEF3 is required for the binding of the aminoacyl-tRNA-eEF1A-GTP ternary complex to the ribosomal A-site and has been suggested to facilitate the clearance of deacyl-tRNA from the E-site. Here we present the crystal structure of Saccharomyces cerevisiae eEF3, showing that it consists of an amino-terminal HEAT repeat domain, followed by a four-helix bundle and two ABC-type ATPase domains, with a chromodomain inserted in ABC2. Moreover, we present the cryo-electron microscopy structure of the ATP-bound form of eEF3 in complex with the post-translocational-state 80S ribosome from yeast. eEF3 uses an entirely new factor binding site near the ribosomal E-site, with the chromodomain likely to stabilize the ribosomal L1 stalk in an open conformation, thus allowing tRNA release.
History
DepositionJun 30, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 9, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ELONGATION FACTOR 3A
B: ELONGATION FACTOR 3A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)221,50216
Polymers219,3362
Non-polymers2,16514
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)98.729, 107.551, 207.240
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein ELONGATION FACTOR 3A / ELONGATION FACTOR 3 / EF-3A / EF-3 / TRANSLATION ELONGATION FACTOR 3A / EUKARYOTIC ELONGATION ...ELONGATION FACTOR 3 / EF-3A / EF-3 / TRANSLATION ELONGATION FACTOR 3A / EUKARYOTIC ELONGATION FACTOR 3 / EEF3 / YEAST ELONGATION FACTOR 3


Mass: 109668.180 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-980
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Production host: SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P16521
#2: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.51 Å3/Da / Density % sol: 50 %
Crystal growpH: 5.2 / Details: pH 5.20

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.995
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.995 Å / Relative weight: 1
ReflectionResolution: 3→20 Å / Num. obs: 45221 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 6.3
Reflection shellResolution: 3→3.16 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 3.1 / % possible all: 99.5

-
Processing

Software
NameVersionClassification
CNS1.1refinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→58.12 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2368757.8 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.276 2219 5 %RANDOM
Rwork0.24 ---
obs0.24 44587 99.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 23.9133 Å2 / ksol: 0.366448 e/Å3
Displacement parametersBiso mean: 38.8 Å2
Baniso -1Baniso -2Baniso -3
1--8.55 Å20 Å20 Å2
2---5.15 Å20 Å2
3---13.7 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.48 Å0.39 Å
Luzzati d res low-5 Å
Luzzati sigma a0.58 Å0.47 Å
Refinement stepCycle: LAST / Resolution: 3→58.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15226 0 122 0 15348
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d2.63
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 3→3.19 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.365 367 5 %
Rwork0.316 6957 -
obs--99.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4SO4_XPLOR_PAR.TXTSO4_XPLOR_TOP.TXT
X-RAY DIFFRACTION5ANP_CNS.PARANP_CNS.TOP

+
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