[English] 日本語
Yorodumi
- PDB-4pwx: Crystal structure of an ATP-bound Get3-Get4-Get5 complex from S.c... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4pwx
TitleCrystal structure of an ATP-bound Get3-Get4-Get5 complex from S.cerevisiae
Components
  • ATPase GET3
  • Golgi to ER traffic protein 4
  • Ubiquitin-like protein MDY2
KeywordsTRANSPORT PROTEIN / Tail-anchored targeting
Function / homology
Function and homology information


cell morphogenesis involved in conjugation with cellular fusion / GET complex / TRC complex / pheromone-dependent signal transduction involved in conjugation with cellular fusion / tail-anchored membrane protein insertion into ER membrane / Hydrolases; Acting on acid anhydrides / protein insertion into ER membrane / post-translational protein targeting to endoplasmic reticulum membrane / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / response to arsenic-containing substance ...cell morphogenesis involved in conjugation with cellular fusion / GET complex / TRC complex / pheromone-dependent signal transduction involved in conjugation with cellular fusion / tail-anchored membrane protein insertion into ER membrane / Hydrolases; Acting on acid anhydrides / protein insertion into ER membrane / post-translational protein targeting to endoplasmic reticulum membrane / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / response to arsenic-containing substance / response to metal ion / vesicle-mediated transport / protein folding chaperone / guanyl-nucleotide exchange factor activity / cytoplasmic stress granule / unfolded protein binding / response to heat / cellular response to oxidative stress / protein-macromolecule adaptor activity / endoplasmic reticulum membrane / endoplasmic reticulum / Golgi apparatus / ATP hydrolysis activity / ATP binding / metal ion binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Mdy2, Get4 binding domain / Get5, C-terminal domain / Binding domain to Get4 on Get5, Golgi to ER traffic protein / Ubiquitin-like protein MDY2, C-terminal domain / Golgi to ER traffic protein 4 / Golgi to ER traffic protein 4 / : / Arsenical pump ATPase, ArsA/GET3, eukaryotic / Arsenical pump ATPase, ArsA/GET3 / Anion-transporting ATPase-like domain ...Mdy2, Get4 binding domain / Get5, C-terminal domain / Binding domain to Get4 on Get5, Golgi to ER traffic protein / Ubiquitin-like protein MDY2, C-terminal domain / Golgi to ER traffic protein 4 / Golgi to ER traffic protein 4 / : / Arsenical pump ATPase, ArsA/GET3, eukaryotic / Arsenical pump ATPase, ArsA/GET3 / Anion-transporting ATPase-like domain / Anion-transporting ATPase / Ubiquitin family / Ubiquitin homologues / Tetratricopeptide-like helical domain superfamily / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Golgi to ER traffic protein 4 / ATPase GET3 / Ubiquitin-like protein MDY2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 5.4 Å
AuthorsGristick, H.B. / Clemons Jr., W.M.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2014
Title: Crystal structure of ATP-bound Get3-Get4-Get5 complex reveals regulation of Get3 by Get4.
Authors: Gristick, H.B. / Rao, M. / Chartron, J.W. / Rome, M.E. / Shan, S.O. / Clemons, W.M.
History
DepositionMar 21, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 9, 2014Provider: repository / Type: Initial release
Revision 1.1May 21, 2014Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
Revision 1.3Sep 20, 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 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ATPase GET3
B: ATPase GET3
E: Golgi to ER traffic protein 4
F: Ubiquitin-like protein MDY2
C: Golgi to ER traffic protein 4
D: Ubiquitin-like protein MDY2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,90411
Polymers158,7766
Non-polymers1,1285
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)166.341, 134.501, 84.060
Angle α, β, γ (deg.)90.00, 113.37, 90.00
Int Tables number5
Space group name H-MC121

-
Components

-
Protein , 3 types, 6 molecules ABECFD

#1: Protein ATPase GET3 / Arsenical pump-driving ATPase / Arsenite-stimulated ATPase / Golgi to ER traffic protein 3 / Guided ...Arsenical pump-driving ATPase / Arsenite-stimulated ATPase / Golgi to ER traffic protein 3 / Guided entry of tail-anchored proteins 3


Mass: 39547.738 Da / Num. of mol.: 2 / Fragment: UNP residues 2-354 / Mutation: D57V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: ARR4, D2371, GET3, Get3 YDL100C, YDL100C / Plasmid: pET33b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21Gold(DE3)
References: UniProt: Q12154, Hydrolases; Acting on acid anhydrides
#2: Protein Golgi to ER traffic protein 4 / Guided entry of tail-anchored proteins 4


Mass: 33806.137 Da / Num. of mol.: 2 / Fragment: UNP residues 11-290 / Mutation: K258A, K260A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: GET4, GET4 YOR164C, O3580, YOR164C / Plasmid: pET33b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21Gold(DE3) / References: UniProt: Q12125
#3: Protein Ubiquitin-like protein MDY2 / Golgi to ER traffic protein 5 / Mating-deficient protein 2 / Translation machinery-associated protein 24


Mass: 6034.042 Da / Num. of mol.: 2 / Fragment: UNP residues 1-54
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: GET5, GET5 MDY2 YOL111C, MDY2, TMA24, YOL111C / Plasmid: pET33b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21Gold(DE3) / References: UniProt: Q12285

-
Non-polymers , 3 types, 5 molecules

#4: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.72 Å3/Da / Density % sol: 54.75 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 18% PEG 3350, 0.2M potassium thiocyanate, 0.1M bis-tris propane, 5% DMSO, pH 9.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Type: OTHER / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 22, 2013
RadiationMonochromator: Liquid nitrogen-cooled double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 5.4→30 Å / Num. all: 5529 / Num. obs: 5529 / % possible obs: 93.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.05
Reflection shellResolution: 5.4→6 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 2 / Num. unique all: 1597 / % possible all: 95.9

-
Processing

Software
NameVersionClassification
Blu-Icedata collection
Web-Icedata collection
PHASERphasing
REFMACv6.3refinement
CNS1.2refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 2WOJ AND 3LKU

2woj

3lku


Resolution: 5.4→30 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.328 537 Random
Rwork0.27 --
all-5529 -
obs-4992 -
Refinement stepCycle: LAST / Resolution: 5.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10094 0 65 0 10159

+
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