[English] 日本語
Yorodumi
- EMDB-10266: Homo sapiens WRB/CAML heterotetramer in complex with a TRC40 dimer -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-10266
TitleHomo sapiens WRB/CAML heterotetramer in complex with a TRC40 dimer
Map data
Sample
  • Complex: Homo sapiens WRB/CAML heterotetramer in complex with a TRC40 dimer
    • Complex: ATPase ASNA1
      • Protein or peptide: ATPase ASNA1
    • Complex: Tail-anchored protein insertion receptor WRB and calcium signal-modulating cyclophilin ligand
      • Protein or peptide: Tail-anchored protein insertion receptor WRB
      • Protein or peptide: Calcium signal-modulating cyclophilin ligand
  • Ligand: ZINC ION
Function / homology
Function and homology information


arsenite transmembrane transporter activity / receptor recycling / membrane insertase activity / GET complex / 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 / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / B cell homeostasis ...arsenite transmembrane transporter activity / receptor recycling / membrane insertase activity / GET complex / 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 / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / B cell homeostasis / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / protein-membrane adaptor activity / negative regulation of protein ubiquitination / vesicle-mediated transport / defense response / epidermal growth factor receptor signaling pathway / protein stabilization / ubiquitin protein ligase binding / endoplasmic reticulum membrane / nucleolus / endoplasmic reticulum / signal transduction / ATP hydrolysis activity / extracellular exosome / nucleoplasm / ATP binding / membrane / metal ion binding / nucleus / cytoplasm
Similarity search - Function
Guided entry of tail-anchored proteins factor CAMLG / Get2-like / Get1 family / CHD5-like protein / Arsenical pump ATPase, ArsA/GET3, eukaryotic / Arsenical pump ATPase, ArsA/GET3 / Anion-transporting ATPase-like domain / Anion-transporting ATPase / Helix hairpin bin domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Guided entry of tail-anchored proteins factor 1 / ATPase GET3 / Guided entry of tail-anchored proteins factor CAMLG
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsMcDowell MA / Heimes M / Wild K / Flemming D / Sinning I
Funding support Germany, 3 items
OrganizationGrant numberCountry
German Research Foundation (DFG)Leibniz SI 586/6-1 Germany
European Molecular Biology Organization (EMBO)ALTF 1230-2013 Germany
German Research Foundation (DFG)TRR83 TP22 Germany
CitationJournal: Mol Cell / Year: 2020
Title: Structural Basis of Tail-Anchored Membrane Protein Biogenesis by the GET Insertase Complex.
Authors: Melanie A McDowell / Michael Heimes / Francesco Fiorentino / Shahid Mehmood / Ákos Farkas / Javier Coy-Vergara / Di Wu / Jani Reddy Bolla / Volker Schmid / Roger Heinze / Klemens Wild / ...Authors: Melanie A McDowell / Michael Heimes / Francesco Fiorentino / Shahid Mehmood / Ákos Farkas / Javier Coy-Vergara / Di Wu / Jani Reddy Bolla / Volker Schmid / Roger Heinze / Klemens Wild / Dirk Flemming / Stefan Pfeffer / Blanche Schwappach / Carol V Robinson / Irmgard Sinning /
Abstract: Membrane protein biogenesis faces the challenge of chaperoning hydrophobic transmembrane helices for faithful membrane insertion. The guided entry of tail-anchored proteins (GET) pathway targets and ...Membrane protein biogenesis faces the challenge of chaperoning hydrophobic transmembrane helices for faithful membrane insertion. The guided entry of tail-anchored proteins (GET) pathway targets and inserts tail-anchored (TA) proteins into the endoplasmic reticulum (ER) membrane with an insertase (yeast Get1/Get2 or mammalian WRB/CAML) that captures the TA from a cytoplasmic chaperone (Get3 or TRC40, respectively). Here, we present cryo-electron microscopy reconstructions, native mass spectrometry, and structure-based mutagenesis of human WRB/CAML/TRC40 and yeast Get1/Get2/Get3 complexes. Get3 binding to the membrane insertase supports heterotetramer formation, and phosphatidylinositol binding at the heterotetramer interface stabilizes the insertase for efficient TA insertion in vivo. We identify a Get2/CAML cytoplasmic helix that forms a "gating" interaction with Get3/TRC40 important for TA insertion. Structural homology with YidC and the ER membrane protein complex (EMC) implicates an evolutionarily conserved insertion mechanism for divergent substrates utilizing a hydrophilic groove. Thus, we provide a detailed structural and mechanistic framework to understand TA membrane insertion.
History
DepositionAug 29, 2019-
Header (metadata) releaseSep 11, 2019-
Map releaseSep 9, 2020-
UpdateFeb 17, 2021-
Current statusFeb 17, 2021Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.014
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.014
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6so5
  • Surface level: 0.014
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6so5
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10266.png

Downloads & links

-
Map

FileDownload / File: emd_10266.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.81 Å
Density
Contour LevelBy AUTHOR: 0.014 / Movie #1: 0.014
Minimum - Maximum-0.037962444 - 0.057236042
Average (Standard dev.)0.00016846736 (±0.0021505535)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 233.28 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.810.810.81
M x/y/z288288288
origin x/y/z0.0000.0000.000
length x/y/z233.280233.280233.280
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS288288288
D min/max/mean-0.0380.0570.000

-
Supplemental data

-
Mask #1

Fileemd_10266_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: #1

Fileemd_10266_additional.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Homo sapiens WRB/CAML heterotetramer in complex with a TRC40 dimer

EntireName: Homo sapiens WRB/CAML heterotetramer in complex with a TRC40 dimer
Components
  • Complex: Homo sapiens WRB/CAML heterotetramer in complex with a TRC40 dimer
    • Complex: ATPase ASNA1
      • Protein or peptide: ATPase ASNA1
    • Complex: Tail-anchored protein insertion receptor WRB and calcium signal-modulating cyclophilin ligand
      • Protein or peptide: Tail-anchored protein insertion receptor WRB
      • Protein or peptide: Calcium signal-modulating cyclophilin ligand
  • Ligand: ZINC ION

-
Supramolecule #1: Homo sapiens WRB/CAML heterotetramer in complex with a TRC40 dimer

SupramoleculeName: Homo sapiens WRB/CAML heterotetramer in complex with a TRC40 dimer
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Molecular weightExperimental: 150 KDa

-
Supramolecule #2: ATPase ASNA1

SupramoleculeName: ATPase ASNA1 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)

-
Supramolecule #3: Tail-anchored protein insertion receptor WRB and calcium signal-m...

SupramoleculeName: Tail-anchored protein insertion receptor WRB and calcium signal-modulating cyclophilin ligand
type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)

-
Macromolecule #1: ATPase ASNA1

MacromoleculeName: ATPase ASNA1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: Hydrolases; Acting on acid anhydrides
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 40.14607 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GAMAAGVAGW GVEAEEFEDA PDVEPLEPTL SNIIEQRSLK WIFVGGKGGV GKTTCSCSLA VQLSKGRESV LIISTDPAHN ISDAFDQKF SKVPTKVKGY DNLFAMEIDP SLGVAELPDE FFEEDNMLSM GKKMMQEAMS AFPGIDEAMS YAEVMRLVKG M NFSVVVFD ...String:
GAMAAGVAGW GVEAEEFEDA PDVEPLEPTL SNIIEQRSLK WIFVGGKGGV GKTTCSCSLA VQLSKGRESV LIISTDPAHN ISDAFDQKF SKVPTKVKGY DNLFAMEIDP SLGVAELPDE FFEEDNMLSM GKKMMQEAMS AFPGIDEAMS YAEVMRLVKG M NFSVVVFD TAPTGHTLRL LNFPTIVERG LGRLMQIKNQ ISPFISQMCN MLGLGDMNAD QLASKLEETL PVIRSVSEQF KD PEQTTFI CVCIAEFLSL YETERLIQEL AKCKIDTHNI IVNQLVFPDP EKPCKMCEAR HKIQAKYLDQ MEDLYEDFHI VKL PLLPHE VRGADKVNTF SALLLEPYKP PSAQGSWSHP QFEK

-
Macromolecule #2: Tail-anchored protein insertion receptor WRB

MacromoleculeName: Tail-anchored protein insertion receptor WRB / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 20.821668 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
MSSAAADHWA WLLVLSFVFG CNVLRILLPS FSSFMSRVLQ KDAEQESQMR AEIQDMKQEL STVNMMDEFA RYARLERKIN KMTDKLKTH VKARTAQLAK IKWVISVAFY VLQAALMISL IWKYYSVPVA VVPSKWITPL DRLVAFPTRV AGGVGITCWI L VCNKVVAI VLHPFSGSGS LEVLFQ

-
Macromolecule #3: Calcium signal-modulating cyclophilin ligand

MacromoleculeName: Calcium signal-modulating cyclophilin ligand / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 14.279671 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
MDSFRIFRLV GCALLALGVR AFVCKYLSIF APFLTLQLAY MGLYKYFPKS EKKIKTTVLT AALLLSGIPA EVINRSMDTY SKMGEVFTD LCVYFFTFIF CHELLDYWGS EVPGSGSENL YFQSGSGS

-
Macromolecule #4: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 4 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration1.8 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormula
20.0 mMHEPES
200.0 mMNaClSodium chloride
GridModel: Quantifoil R2/1 / Material: COPPER/RHODIUM / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 279 K / Instrument: FEI VITROBOT MARK IV
Detailscomplex stabilised in PMAL-C8 amphipol

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Sample stageCooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 9470 / Average exposure time: 12.0 sec. / Average electron dose: 45.6 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Particle selectionNumber selected: 1698096
CTF correctionSoftware - Name: RELION (ver. 3.0)
Initial angle assignmentType: NOT APPLICABLE
Final 3D classificationNumber classes: 5 / Software - Name: RELION (ver. 3.0)
Final angle assignmentType: NOT APPLICABLE
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 225244
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelPDB ID:

3sja

Details3SJA
RefinementProtocol: RIGID BODY FIT
Output model

PDB-6so5:
Homo sapiens WRB/CAML heterotetramer in complex with a TRC40 dimer

-
Atomic model buiding 2

RefinementSpace: REAL / Protocol: BACKBONE TRACE
Output model

PDB-6so5:
Homo sapiens WRB/CAML heterotetramer in complex with a TRC40 dimer

+
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