[English] 日本語
Yorodumi
- PDB-3p27: Crystal structure of S. cerevisiae Hbs1 protein (GDP-bound form),... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3p27
TitleCrystal structure of S. cerevisiae Hbs1 protein (GDP-bound form), a translational GTPase involved in RNA quality control pathways and interacting with Dom34/Pelota
ComponentsElongation factor 1 alpha-like protein
KeywordsSIGNALING PROTEIN / GDP/GTP binding domain / beta-barrel / translational GTPase / Structural Genomics / Paris-Sud Yeast Structural Genomics / YSG
Function / homology
Function and homology information


Eukaryotic Translation Elongation / Dom34-Hbs1 complex / nuclear-transcribed mRNA catabolic process, no-go decay / HSF1 activation / nonfunctional rRNA decay / ribosome disassembly / Protein methylation / positive regulation of translational initiation / translation elongation factor activity / Neutrophil degranulation ...Eukaryotic Translation Elongation / Dom34-Hbs1 complex / nuclear-transcribed mRNA catabolic process, no-go decay / HSF1 activation / nonfunctional rRNA decay / ribosome disassembly / Protein methylation / positive regulation of translational initiation / translation elongation factor activity / Neutrophil degranulation / rescue of stalled ribosome / positive regulation of translation / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / translation / GTPase activity / GTP binding / cytoplasm / cytosol
Similarity search - Function
HBS1-like protein, N-terminal / HBS1 N-terminus / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / Translation factors / Tr-type G domain, conserved site / Translational (tr)-type guanine nucleotide-binding (G) domain signature. / Elongation Factor Tu (Ef-tu); domain 3 / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. ...HBS1-like protein, N-terminal / HBS1 N-terminus / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / Translation factors / Tr-type G domain, conserved site / Translational (tr)-type guanine nucleotide-binding (G) domain signature. / Elongation Factor Tu (Ef-tu); domain 3 / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / Translation protein, beta-barrel domain superfamily / P-loop containing nucleotide triphosphate hydrolases / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / Elongation factor 1 alpha-like protein
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
Authorsvan den Elzen, A. / Henri, J. / Lazar, N. / Gas, M.E. / Durand, D. / Lacroute, F. / Nicaise, M. / van Tilbeurgh, H. / Sraphin, B. / Graille, M. / Paris-Sud Yeast Structural Genomics (YSG)
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2010
Title: Dissection of Dom34-Hbs1 reveals independent functions in two RNA quality control pathways.
Authors: van den Elzen, A.M. / Henri, J. / Lazar, N. / Gas, M.E. / Durand, D. / Lacroute, F. / Nicaise, M. / van Tilbeurgh, H. / Seraphin, B. / Graille, M.
History
DepositionOct 1, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 17, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 14, 2012Group: Structure summary

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Elongation factor 1 alpha-like protein
B: Elongation factor 1 alpha-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,5744
Polymers109,6872
Non-polymers8862
Water1,15364
1
A: Elongation factor 1 alpha-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,2872
Polymers54,8441
Non-polymers4431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Elongation factor 1 alpha-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,2872
Polymers54,8441
Non-polymers4431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)109.964, 109.964, 188.199
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 139:204 OR RESSEQ 231:254 OR RESSEQ...
211CHAIN B AND (RESSEQ 139:204 OR RESSEQ 231:254 OR RESSEQ...

-
Components

#1: Protein Elongation factor 1 alpha-like protein


Mass: 54843.676 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: HBS1, YKR084C, YKR404 / Production host: Escherichia coli (E. coli) / References: UniProt: P32769
#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.59 Å3/Da / Density % sol: 52.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7
Details: 50mM MOPS, 12% PEG 4000, 20% Glycerol, 500mM KCl, pH 7.0, VAPOR DIFFUSION, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1.5418 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 18, 2009
RadiationMonochromator: Channel cut cryogenically cooled monochromator crystal
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.95→19.98 Å / Num. all: 46226 / Num. obs: 45371 / % possible obs: 98.15 % / Observed criterion σ(F): 50 / Observed criterion σ(I): 2
Reflection shell
Resolution (Å)Diffraction-ID% possible all
2.95-3.02197
3.02-3.09199
3.09-3.2199
3.2-3.3199
3.3-3.4199
3.4-19.98198

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
PHENIX(phenix.refine)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.95→19.98 Å / SU ML: 0.37 / σ(F): 1.22 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2775 2306 5.08 %RANDOM
Rwork0.2142 ---
obs0.2173 45371 98.15 %-
all-46226 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 21.818 Å2 / ksol: 0.301 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.9156 Å20 Å2-0 Å2
2--0.9156 Å20 Å2
3----1.8312 Å2
Refinement stepCycle: LAST / Resolution: 2.95→19.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6923 0 56 64 7043
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0117112
X-RAY DIFFRACTIONf_angle_d1.3589618
X-RAY DIFFRACTIONf_dihedral_angle_d19.4212637
X-RAY DIFFRACTIONf_chiral_restr0.0891097
X-RAY DIFFRACTIONf_plane_restr0.0051217
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A3340X-RAY DIFFRACTIONPOSITIONAL
12B3340X-RAY DIFFRACTIONPOSITIONAL0.043
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.95-3.01550.35421430.33012646X-RAY DIFFRACTION97
3.0155-3.08540.341380.32512726X-RAY DIFFRACTION99
3.0854-3.16220.41191460.29512736X-RAY DIFFRACTION99
3.1622-3.24740.35911460.2692717X-RAY DIFFRACTION99
3.2474-3.34250.33991510.26322698X-RAY DIFFRACTION99
3.3425-3.44990.31541320.262704X-RAY DIFFRACTION98
3.4499-3.57250.31121450.2352727X-RAY DIFFRACTION99
3.5725-3.71470.28121370.21052688X-RAY DIFFRACTION98
3.7147-3.88260.24721670.19962681X-RAY DIFFRACTION98
3.8826-4.08560.22491690.18952672X-RAY DIFFRACTION98
4.0856-4.33910.22421600.15542655X-RAY DIFFRACTION98
4.3391-4.67020.22231430.14522695X-RAY DIFFRACTION98
4.6702-5.13290.19471350.15372694X-RAY DIFFRACTION98
5.1329-5.85920.24111450.18212712X-RAY DIFFRACTION98
5.8592-7.32120.28831370.20322673X-RAY DIFFRACTION97
7.3212-19.98050.22711120.19132641X-RAY DIFFRACTION95

+
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://pdbjlvh1.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