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- PDB-6z3w: Human ER membrane protein complex -

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Basic information

Entry
Database: PDB / ID: 6z3w
TitleHuman ER membrane protein complex
Components
  • (ER membrane protein complex subunit ...Endoplasmic reticulum) x 8
  • Membrane magnesium transporter 1
KeywordsMEMBRANE PROTEIN / Complex / insertase / PROTEIN TRANSPORT
Function / homology
Function and homology information


inorganic cation transmembrane transporter activity / extrinsic component of endoplasmic reticulum membrane / EMC complex / omegasome membrane / protein insertion into ER membrane by stop-transfer membrane-anchor sequence / magnesium ion transport / cobalt ion transmembrane transporter activity / Miscellaneous transport and binding events / tail-anchored membrane protein insertion into ER membrane / magnesium ion transmembrane transporter activity ...inorganic cation transmembrane transporter activity / extrinsic component of endoplasmic reticulum membrane / EMC complex / omegasome membrane / protein insertion into ER membrane by stop-transfer membrane-anchor sequence / magnesium ion transport / cobalt ion transmembrane transporter activity / Miscellaneous transport and binding events / tail-anchored membrane protein insertion into ER membrane / magnesium ion transmembrane transporter activity / ferrous iron transmembrane transporter activity / protein folding in endoplasmic reticulum / copper ion transport / 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) / TMEM85/ER membrane protein complex subunit 4 / Protein of unknown function (DUF1077) / 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 ...ER membrane protein complex subunit 8/9 / Uncharacterised protein family (UPF0172) / TMEM85/ER membrane protein complex subunit 4 / Protein of unknown function (DUF1077) / 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 / Tetratricopeptide repeat / Quinoprotein alcohol dehydrogenase-like superfamily / TPR repeat region circular profile. / TPR repeat profile. / MPN domain / MPN domain 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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6.4 Å
AuthorsHegde, R.S. / O'Donnell, J.P.
Funding support United Kingdom, Germany, 2items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MC_UP_A022_1007 United Kingdom
European Molecular Biology Organization (EMBO)ALTF-18-2018 Germany
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 22, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 15, 2020Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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Assembly

Deposited unit
A: ER membrane protein complex subunit 1,ER membrane protein complex subunit 1,ER membrane protein complex subunit 1,ER membrane protein complex subunit 1
B: ER membrane protein complex subunit 2
C: ER membrane protein complex subunit 3
D: ER membrane protein complex subunit 4
E: Membrane magnesium transporter 1
F: ER membrane protein complex subunit 6
G: ER membrane protein complex subunit 7
H: ER membrane protein complex subunit 9
I: ER membrane protein complex subunit 10


Theoretical massNumber of molelcules
Total (without water)275,3349
Polymers275,3349
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: cross-linking
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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ER membrane protein complex subunit ... , 8 types, 8 molecules ABCDFGHI

#1: Protein ER membrane protein complex subunit 1,ER membrane protein complex subunit 1,ER membrane protein complex subunit 1,ER membrane protein complex subunit 1 / Endoplasmic reticulum


Mass: 86666.734 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EMC1, KIAA0090, PSEC0263 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q8N766
#2: Protein ER membrane protein complex subunit 2 / Endoplasmic reticulum / Tetratricopeptide repeat protein 35 / TPR repeat protein 35


Mass: 34882.531 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: HEK293 / Gene: EMC2, KIAA0103, TTC35 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q15006
#3: Protein ER membrane protein complex subunit 3 / Endoplasmic reticulum / Transmembrane protein 111


Mass: 29981.924 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EMC3, TMEM111 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q9P0I2
#4: Protein ER membrane protein complex subunit 4 / Endoplasmic reticulum / Cell proliferation-inducing gene 17 protein / Transmembrane protein 85


Mass: 20104.572 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EMC4, TMEM85, HSPC184, PIG17 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q5J8M3
#6: Protein ER membrane protein complex subunit 6 / Endoplasmic reticulum / Transmembrane protein 93


Mass: 12029.248 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EMC6, TMEM93 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q9BV81
#7: Protein ER membrane protein complex subunit 7 / Endoplasmic reticulum


Mass: 26501.586 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EMC7, C11orf3, C15orf24, HT022, UNQ905/PRO1926 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q9NPA0
#8: Protein ER membrane protein complex subunit 9 / Endoplasmic reticulum / Protein FAM158A


Mass: 23084.434 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EMC9, C14orf122, FAM158A, CGI-112 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q9Y3B6
#9: Protein ER membrane protein complex subunit 10 / Endoplasmic reticulum / Hematopoietic signal peptide-containing membrane domain-containing protein 1


Mass: 27375.797 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EMC10, C19orf63, HSM1, INM02, UNQ764/PRO1556 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q5UCC4

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Protein , 1 types, 1 molecules E

#5: Protein Membrane magnesium transporter 1 / ER membrane protein complex subunit 5 / Transmembrane protein 32


Mass: 14706.786 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MMGT1, EMC5, TMEM32 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q8N4V1

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Human ER membrane protein complexEndoplasmic reticulum
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weight
IDEntity assembly-IDExperimental value
11NO
21NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

Software
NameVersionClassification
phenix.real_space_refine1.17.1_3660refinement
PHENIX1.17.1_3660refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 6.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 167294 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 200 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00519384
ELECTRON MICROSCOPYf_angle_d1.021413022
ELECTRON MICROSCOPYf_chiral_restr0.04731788
ELECTRON MICROSCOPYf_plane_restr0.00551878
ELECTRON MICROSCOPYf_dihedral_angle_d10.05981878

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