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- EMDB-11058: Human ER Membrane protein Complex (EMC) -

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Basic information

Entry
Database: EMDB / ID: EMD-11058
TitleHuman ER Membrane protein Complex (EMC)
Map data3D reconstruction of the human ER-Membrane Complex produced by single particle cryo-electron microscopy.
Sample
  • Complex: Human ER Membrane protein Complex (EMC)
Function / homology
Function and homology information


extrinsic component of endoplasmic reticulum membrane / inorganic cation transmembrane transporter activity / EMC complex / omegasome membrane / protein insertion into ER membrane by stop-transfer membrane-anchor sequence / magnesium ion transport / tail-anchored membrane protein insertion into ER membrane / Miscellaneous transport and binding events / cobalt ion transmembrane transporter activity / copper ion transport ...extrinsic component of endoplasmic reticulum membrane / inorganic cation transmembrane transporter activity / EMC complex / omegasome membrane / protein insertion into ER membrane by stop-transfer membrane-anchor sequence / magnesium ion transport / tail-anchored membrane protein insertion into ER membrane / Miscellaneous transport and binding events / cobalt ion transmembrane transporter activity / copper ion transport / magnesium ion transmembrane transporter activity / ferrous iron transmembrane transporter activity / autophagosome assembly / RHOA GTPase cycle / positive regulation of endothelial cell proliferation / positive regulation of endothelial cell migration / positive regulation of angiogenesis / early endosome membrane / carbohydrate binding / angiogenesis / early endosome / Golgi membrane / apoptotic process / endoplasmic reticulum membrane / Golgi apparatus / endoplasmic reticulum / protein-containing complex / extracellular region / membrane / plasma membrane / cytoplasm
Similarity search - Function
: / ER membrane protein complex subunit 8/9 / : / Uncharacterised protein family (UPF0172) / EMC2 TPR-like repeat domain / TMEM85/ER membrane protein complex subunit 4 / ER membrane protein complex subunit 4 / ER membrane protein complex subunit 7, beta-sandwich domain / ER membrane protein complex subunit 7 / ER membrane protein complex subunit 7, beta-sandwich domain ...: / ER membrane protein complex subunit 8/9 / : / Uncharacterised protein family (UPF0172) / EMC2 TPR-like repeat domain / TMEM85/ER membrane protein complex subunit 4 / ER membrane protein complex subunit 4 / ER membrane protein complex subunit 7, beta-sandwich domain / ER membrane protein complex subunit 7 / ER membrane protein complex subunit 7, beta-sandwich domain / ER membrane protein complex subunit 6 / ER membrane protein complex subunit 3 / ER membrane protein complex subunit 1, C-terminal / Membrane magnesium transporter / ER membrane protein complex subunit 1 / ER membrane protein complex subunit 6-like / EMC6 / ER membrane protein complex subunit 1, C-terminal / Membrane magnesium transporter / ER membrane protein complex subunit 10 / ER membrane protein complex subunit 2-like / Integral membrane protein EMC3/TMCO1-like / Integral membrane protein EMC3/TMCO1-like / Integral membrane protein DUF106 / Carbohydrate-binding-like fold / Pyrrolo-quinoline quinone repeat / PQQ-like domain / Quinoprotein alcohol dehydrogenase-like superfamily / TPR repeat region circular profile. / MPN domain / MPN domain profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
ER membrane protein complex subunit 2 / ER membrane protein complex subunit 4 / ER membrane protein complex subunit 10 / ER membrane protein complex subunit 5 / ER membrane protein complex subunit 1 / ER membrane protein complex subunit 6 / Endoplasmic reticulum membrane protein complex subunit 7 / ER membrane protein complex subunit 3 / ER membrane protein complex subunit 9
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.4 Å
AuthorsPhillips BP / O'Donnell JP
Funding support United Kingdom, 3 items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MC_UP_1201/10 United Kingdom
European Molecular Biology Organization (EMBO)ALTF-18-2018 United Kingdom
Medical Research Council (MRC, United Kingdom)MC_UP_A022_1007 United Kingdom
CitationJournal: Elife / Year: 2020
Title: The architecture of EMC reveals a path for membrane protein insertion.
Authors: John P O'Donnell / Ben P Phillips / Yuichi Yagita / Szymon Juszkiewicz / Armin Wagner / Duccio Malinverni / Robert J Keenan / Elizabeth A Miller / Ramanujan S Hegde /
Abstract: Approximately 25% of eukaryotic genes code for integral membrane proteins that are assembled at the endoplasmic reticulum. An abundant and widely conserved multi-protein complex termed EMC has been ...Approximately 25% of eukaryotic genes code for integral membrane proteins that are assembled at the endoplasmic reticulum. An abundant and widely conserved multi-protein complex termed EMC has been implicated in membrane protein biogenesis, but its mechanism of action is poorly understood. Here, we define the composition and architecture of human EMC using biochemical assays, crystallography of individual subunits, site-specific photocrosslinking, and cryo-EM reconstruction. Our results suggest that EMC's cytosolic domain contains a large, moderately hydrophobic vestibule that can bind a substrate's transmembrane domain (TMD). The cytosolic vestibule leads into a lumenally-sealed, lipid-exposed intramembrane groove large enough to accommodate a single substrate TMD. A gap between the cytosolic vestibule and intramembrane groove provides a potential path for substrate egress from EMC. These findings suggest how EMC facilitates energy-independent membrane insertion of TMDs, explain why only short lumenal domains are translocated by EMC, and constrain models of EMC's proposed chaperone function.
History
DepositionMay 20, 2020-
Header (metadata) releaseJun 17, 2020-
Map releaseJun 17, 2020-
UpdateJun 17, 2020-
Current statusJun 17, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.21
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.21
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6z3w
  • Surface level: 0.21
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11058.png

Downloads & links

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Map

FileDownload / File: emd_11058.map.gz / Format: CCP4 / Size: 42.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation3D reconstruction of the human ER-Membrane Complex produced by single particle cryo-electron microscopy.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.38 Å/pix.
x 224 pix.
= 309.12 Å		1.38 Å/pix.
x 224 pix.
= 309.12 Å		1.38 Å/pix.
x 224 pix.
= 309.12 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.38 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.21 / Movie #1: 0.21
Minimum - Maximum0 - 1
Average (Standard dev.)0.09072395 (±0.27806097)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions224224224
Spacing224224224
CellA=B=C: 309.12 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.381.381.38
M x/y/z224224224
origin x/y/z0.0000.0000.000
length x/y/z309.120309.120309.120
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS224224224
D min/max/mean-0.3750.7370.003

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Supplemental data

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Mask #1

Fileemd_11058_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A, produced during local resolution estimation...

Fileemd_11058_half_map_1.map
AnnotationHalf map A, produced during local resolution estimation in CryoSPARC and used to calculate FSC for human ER-Membrane Complex 3D reconstruction.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B, produced during local resolution estimation...

Fileemd_11058_half_map_2.map
AnnotationHalf map B, produced during local resolution estimation in CryoSPARC and used to calculate FSC for human ER-Membrane Complex 3D reconstruction.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Human ER Membrane protein Complex (EMC)

EntireName: Human ER Membrane protein Complex (EMC)
Components
  • Complex: Human ER Membrane protein Complex (EMC)

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Supramolecule #1: Human ER Membrane protein Complex (EMC)

SupramoleculeName: Human ER Membrane protein Complex (EMC) / type: complex / ID: 1 / Parent: 0 / Details: 9-subunit human ER Membrane protein Complex (EMC)
Source (natural)Organism: Homo sapiens (human) / Tissue: Embryonic Kidney / Organelle: Endoplasmic Reticulum / Location in cell: Endoplasmic Reticulum
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant strain: HEK293 / Recombinant cell: Embryonic Kidney / Recombinant plasmid: pcDNA5/FRT
Molecular weightExperimental: 330 KDa

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.85 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
400.0 mMNaClsodium chloride
50.0 mMHEPESHEPES pH 7.4
2.0 mMMgCl2magnesium chloride
0.01 %LMNGLauryl Maltose Neopentyl Glycol
GridModel: Quantifoil R2/2 / Material: GOLD / Mesh: 200 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Atmosphere: OTHER / Pretreatment - Pressure: 4e-05 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: LEICA PLUNGER
DetailsThis sample was purified from suspension adapted human HEK293 cells and was monodisperse on EM grids.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
TemperatureMin: 84.0 K / Max: 93.0 K
Specialist opticsPhase plate: VOLTA PHASE PLATE / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3710 pixel / Digitization - Dimensions - Height: 3710 pixel / Digitization - Sampling interval: 5.0 µm / Digitization - Frames/image: 1-44 / Number grids imaged: 5 / Number real images: 11626 / Average exposure time: 11.0 sec. / Average electron dose: 39.36 e/Å2
Details: Data collected across 5 independent sessions using two different FEI Titan Krios Microscopes, both equipped with a Gatan K2 Summit detector and volta phase plate. Volta phase plate used ...Details: Data collected across 5 independent sessions using two different FEI Titan Krios Microscopes, both equipped with a Gatan K2 Summit detector and volta phase plate. Volta phase plate used without charging between exposures. Phase plate evolution varied between different microscopes used to collect data but positions were shifted once phase evolution progressed past 120 degrees.
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: -1.5 µm / Nominal defocus min: -0.5 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 2560511 / Details: Template-based autopicking in CryoSPARC v2.12.4.
CTF correctionSoftware - Name: cryoSPARC (ver. 2.12.4) / Software - details: Patch CTF correction (Multi)
Details: Patch CTF correction (Multi) implemented in CryoSPARC
Startup modelType of model: INSILICO MODEL / In silico model: Ab initio model generation in CryoSPARC.
Details: 4 classes generated and best class used as a initial model for refinement.
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 6.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2.12.4)
Software - details: Local resolution estimation and filtering
Details: Resolution calculated from half maps produced during local resolution estimation in CryoSPARC following non-uniform refinement.
Number images used: 167294
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2.12.4) / Software - details: Ab Initio Model generation
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2.12.4) / Software - details: Non-Uniform Refinement / Details: Non-uniform refinement in CryoSPARC.
Final 3D classificationNumber classes: 4 / Avg.num./class: 85780 / Software - Name: cryoSPARC (ver. 2.12.4) / Software - details: Ab Initio 3D classification / Details: Ab Initio classification in CryoSPARC
FSC plot (resolution estimation)

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