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- PDB-8j0o: cryo-EM structure of human EMC and VDAC -

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Basic information

Entry
Database: PDB / ID: 8j0o
Titlecryo-EM structure of human EMC and VDAC
Components
  • (ER membrane protein complex subunit ...) x 9
  • Voltage-dependent anion-selective channel protein 1
KeywordsMEMBRANE PROTEIN / ER membrane protein complex
Function / homology
Function and homology information


negative regulation of calcium import into the mitochondrion / positive regulation of type 2 mitophagy / extrinsic component of endoplasmic reticulum membrane / inorganic cation transmembrane transporter activity / EMC complex / voltage-gated monoatomic anion channel activity / mitochondrial transmembrane transport / omegasome membrane / protein insertion into ER membrane by stop-transfer membrane-anchor sequence / neuron-neuron synaptic transmission ...negative regulation of calcium import into the mitochondrion / positive regulation of type 2 mitophagy / extrinsic component of endoplasmic reticulum membrane / inorganic cation transmembrane transporter activity / EMC complex / voltage-gated monoatomic anion channel activity / mitochondrial transmembrane transport / omegasome membrane / protein insertion into ER membrane by stop-transfer membrane-anchor sequence / neuron-neuron synaptic transmission / Mitochondrial calcium ion transport / magnesium ion transport / cobalt ion transmembrane transporter activity / tail-anchored membrane protein insertion into ER membrane / Miscellaneous transport and binding events / regulation of autophagy of mitochondrion / calcium import into the mitochondrion / ferrous iron transmembrane transporter activity / magnesium ion transmembrane transporter activity / ceramide binding / mitochondrial permeability transition pore complex / copper ion transport / Mitochondrial protein import / phosphatidylcholine binding / Pyruvate metabolism / oxysterol binding / monoatomic anion transport / pyruvate metabolic process / lipid transport / porin activity / cholesterol binding / pore complex / mitochondrial nucleoid / behavioral fear response / autophagosome assembly / RHOA GTPase cycle / negative regulation of reactive oxygen species metabolic process / epithelial cell differentiation / positive regulation of endothelial cell proliferation / positive regulation of endothelial cell migration / PINK1-PRKN Mediated Mitophagy / learning / mitochondrial membrane / positive regulation of angiogenesis / early endosome membrane / carbohydrate binding / angiogenesis / mitochondrial outer membrane / transmembrane transporter binding / early endosome / Ub-specific processing proteases / positive regulation of apoptotic process / membrane raft / Golgi membrane / synapse / endoplasmic reticulum membrane / negative regulation of apoptotic process / apoptotic process / protein kinase binding / Golgi apparatus / endoplasmic reticulum / protein-containing complex / mitochondrion / extracellular exosome / extracellular region / ATP binding / identical protein binding / membrane / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Eukaryotic mitochondrial porin signature. / Porin, eukaryotic type / : / ER membrane protein complex subunit 8/9 / Uncharacterised protein family (UPF0172) / EMC2 TPR-like repeat domain / 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 ...Eukaryotic mitochondrial porin signature. / Porin, eukaryotic type / : / ER membrane protein complex subunit 8/9 / Uncharacterised protein family (UPF0172) / EMC2 TPR-like repeat domain / 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 / Eukaryotic porin/Tom40 / Eukaryotic porin / Carbohydrate-binding-like fold / Pyrrolo-quinoline quinone repeat / PQQ-like domain / Porin domain superfamily / 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 8 / Non-selective voltage-gated ion channel VDAC1 / 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
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.32 Å
AuthorsLi, M. / Zhang, C. / Wu, J. / Lei, M.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31930063 China
CitationJournal: Aging (Albany NY) / Year: 2024
Title: Structural insights into human EMC and its interaction with VDAC.
Authors: Mingyue Li / Chunli Zhang / Yuntao Xu / Shaobai Li / Chenhui Huang / Jian Wu / Ming Lei /
Abstract: The endoplasmic reticulum (ER) membrane protein complex (EMC) is a conserved, multi-subunit complex acting as an insertase at the ER membrane. Growing evidence shows that the EMC is also involved in ...The endoplasmic reticulum (ER) membrane protein complex (EMC) is a conserved, multi-subunit complex acting as an insertase at the ER membrane. Growing evidence shows that the EMC is also involved in stabilizing and trafficking membrane proteins. However, the structural basis and regulation of its multifunctionality remain elusive. Here, we report cryo-electron microscopy structures of human EMC in apo- and voltage-dependent anion channel (VDAC)-bound states at resolutions of 3.47 Å and 3.32 Å, respectively. We discovered a specific interaction between VDAC proteins and the EMC at mitochondria-ER contact sites, which is conserved from yeast to humans. Moreover, we identified a gating plug located inside the EMC hydrophilic vestibule, the substrate-binding pocket for client insertion. Conformation changes of this gating plug during the apo-to-VDAC-bound transition reveal that the EMC unlikely acts as an insertase in the VDAC1-bound state. Based on the data analysis, the gating plug may regulate EMC functions by modifying the hydrophilic vestibule in different states. Our discovery offers valuable insights into the structural basis of EMC's multifunctionality.
History
DepositionApr 11, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 3, 2024Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2024Group: Database references / Category: citation / Item: _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 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: ER membrane protein complex subunit 5
F: ER membrane protein complex subunit 6
G: ER membrane protein complex subunit 7
H: ER membrane protein complex subunit 8
J: ER membrane protein complex subunit 10
K: Voltage-dependent anion-selective channel protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)328,24813
Polymers326,48910
Non-polymers1,7603
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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ER membrane protein complex subunit ... , 9 types, 9 molecules ABCDEFGHJ

#1: Protein ER membrane protein complex subunit 1


Mass: 111886.141 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q8N766
#2: Protein ER membrane protein complex subunit 2 / Tetratricopeptide repeat protein 35 / TPR repeat protein 35


Mass: 34882.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q15006
#3: Protein ER membrane protein complex subunit 3 / Transmembrane protein 111


Mass: 29981.924 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9P0I2
#4: Protein ER membrane protein complex subunit 4 / Cell proliferation-inducing gene 17 protein / Transmembrane protein 85


Mass: 20104.572 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q5J8M3
#5: Protein ER membrane protein complex subunit 5 / Membrane magnesium transporter 1 / Transmembrane protein 32


Mass: 14706.786 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q8N4V1
#6: Protein ER membrane protein complex subunit 6 / Transmembrane protein 93


Mass: 12029.248 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BV81
#7: Protein ER membrane protein complex subunit 7


Mass: 26501.586 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9NPA0
#8: Protein ER membrane protein complex subunit 8 / Neighbor of COX4 / Protein FAM158B


Mass: 23807.076 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O43402
#9: Protein ER membrane protein complex subunit 10 / Hematopoietic signal peptide-containing membrane domain-containing protein 1


Mass: 21781.484 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q5UCC4

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Protein / Sugars , 2 types, 4 molecules K

#10: Protein Voltage-dependent anion-selective channel protein 1 / VDAC-1 / hVDAC1 / Outer mitochondrial membrane protein porin 1 / Plasmalemmal porin / Porin 31HL / Porin 31HM


Mass: 30807.521 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P21796
#11: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE

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Details

Has ligand of interestN

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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: EMC_VDAC / Type: COMPLEX / Entity ID: #1-#10 / Source: NATURAL
Source (natural)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 FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.20.1_4487: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.32 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 455504 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.01421456
ELECTRON MICROSCOPYf_angle_d1.03629068
ELECTRON MICROSCOPYf_dihedral_angle_d3.7522911
ELECTRON MICROSCOPYf_chiral_restr0.0443279
ELECTRON MICROSCOPYf_plane_restr0.0083679

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