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- PDB-9c7v: Structure of the human BOS:human EMC complex in GDN -

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Basic information

Entry
Database: PDB / ID: 9c7v
TitleStructure of the human BOS:human EMC complex in GDN
Components
  • (ER membrane protein complex subunit ...) x 8
  • BOS complex subunit NOMO2
  • Membrane magnesium transporter 1
  • Nicalin
  • Transmembrane protein 147
KeywordsMEMBRANE PROTEIN / membrane protein biogenesis / membrane protein complex
Function / homology
Function and homology information


multi-pass transmembrane protein insertion into ER membrane / multi-pass translocon complex / 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 / cobalt ion transmembrane transporter activity / tail-anchored membrane protein insertion into ER membrane ...multi-pass transmembrane protein insertion into ER membrane / multi-pass translocon complex / 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 / cobalt ion transmembrane transporter activity / tail-anchored membrane protein insertion into ER membrane / Miscellaneous transport and binding events / ferrous iron transmembrane transporter activity / magnesium ion transmembrane transporter activity / copper ion transport / regulation of protein complex stability / autophagosome assembly / RHOA GTPase cycle / regulation of protein-containing complex assembly / regulation of signal transduction / positive regulation of endothelial cell proliferation / positive regulation of endothelial cell migration / positive regulation of angiogenesis / ribosome binding / early endosome membrane / carbohydrate binding / angiogenesis / membrane => GO:0016020 / early endosome / protein stabilization / Golgi membrane / endoplasmic reticulum membrane / apoptotic process / Golgi apparatus / endoplasmic reticulum / protein-containing complex / extracellular region / membrane / plasma membrane / cytoplasm
Similarity search - Function
: / Nicalin / Transmembrane protein 147 / Predicted membrane protein (DUF2053) / Carboxypeptidase regulatory-like domain / : / ER membrane protein complex subunit 8/9 / Uncharacterised protein family (UPF0172) / TMEM85/ER membrane protein complex subunit 4 / Protein of unknown function (DUF1077) ...: / Nicalin / Transmembrane protein 147 / Predicted membrane protein (DUF2053) / Carboxypeptidase regulatory-like domain / : / 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 / Prealbumin-like fold domain / Prealbumin-like fold domain / Carboxypeptidase-like, regulatory domain superfamily / Carbohydrate-binding-like fold / Pyrrolo-quinoline quinone repeat / PQQ-like domain / Tetratricopeptide repeat / Peptidase M28 / Peptidase family M28 / 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 / Immunoglobulin-like fold
Similarity search - Domain/homology
ER membrane protein complex subunit 8 / ER membrane protein complex subunit 2 / ER membrane protein complex subunit 4 / BOS complex subunit NOMO2 / ER membrane protein complex subunit 10 / ER membrane protein complex subunit 5 / ER membrane protein complex subunit 1 / Nicalin / ER membrane protein complex subunit 6 / Transmembrane protein 147 ...ER membrane protein complex subunit 8 / ER membrane protein complex subunit 2 / ER membrane protein complex subunit 4 / BOS complex subunit NOMO2 / ER membrane protein complex subunit 10 / ER membrane protein complex subunit 5 / ER membrane protein complex subunit 1 / Nicalin / ER membrane protein complex subunit 6 / Transmembrane protein 147 / 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: 6.6 Å
AuthorsNguyen, V.N. / Tomaleri, G.P. / Voorhees, R.M.
Funding support United States, 3items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)DP2 GM137412 United States
Heritage Medical Research Institute United States
CitationJournal: To Be Published
Title: Role of a holo-insertase complex in the biogenesis of biophysically diverse ER membrane proteins
Authors: Page, K.R. / Nguyen, V.N. / Pleiner, T. / Tomaleri, G.P. / Wang, M.L. / Guna, A. / Hazu, M. / Wang, T. / Chou, T. / Voorhees, R.M.
History
DepositionJun 11, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
10: ER membrane protein complex subunit 10
1: ER membrane protein complex subunit 1
2: ER membrane protein complex subunit 2
3: ER membrane protein complex subunit 3
4: ER membrane protein complex subunit 4
5: Membrane magnesium transporter 1
6: ER membrane protein complex subunit 6
7: ER membrane protein complex subunit 7
8: ER membrane protein complex subunit 8
A: Nicalin
B: BOS complex subunit NOMO2
C: Transmembrane protein 147
hetero molecules


Theoretical massNumber of molelcules
Total (without water)530,47416
Polymers529,18312
Non-polymers1,2914
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: cross-linking, electron microscopy, gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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ER membrane protein complex subunit ... , 8 types, 8 molecules 101234678

#1: Protein ER membrane protein complex subunit 10 / Hematopoietic signal peptide-containing membrane domain-containing protein 1


Mass: 27375.797 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q5UCC4
#2: 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
#3: 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 genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EMC2, KIAA0103, TTC35 / Production host: Homo sapiens (human) / References: UniProt: Q15006
#4: 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
#5: 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
#7: 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
#8: 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
#9: 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

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Protein , 4 types, 4 molecules 5ABC

#6: 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 natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q8N4V1
#10: Protein Nicalin / Nicastrin-like protein


Mass: 63047.145 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q969V3
#11: Protein BOS complex subunit NOMO2 / Nodal modulator 2 / pM5 protein 2


Mass: 139580.234 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q5JPE7
#12: Protein Transmembrane protein 147 / Protein NIFIE 14


Mass: 25279.848 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TMEM147 / Production host: Homo sapiens (human) / References: UniProt: Q9BVK8

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Sugars , 2 types, 4 molecules

#13: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#14: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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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: Human BOS complex / Type: COMPLEX / Details: Human BOS complex of NOMO, TMEM147, and NCLN / Entity ID: #1-#12 / Source: MULTIPLE SOURCES
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
150.0 mM4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid1
2200.0 mMsodium chlorideNaCl1
32.0 mMmagnesium acetate1
41.0 mMdithiothreitol1
50.0105 % (w/v)glyco-diosgenin1
SpecimenConc.: 2.53 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: Sample solubilized and purified in GDN.
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 279 K

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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: SPOT SCAN
Electron lensMode: DARK FIELD / Nominal magnification: 105000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 17978
EM imaging opticsEnergyfilter name: GIF Quantum LS / Energyfilter slit width: 20 eV

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.2.1particle selection
4cryoSPARC4.2.1CTF correction
7UCSF ChimeraX1.6.1model fitting
10cryoSPARC4.2.1final Euler assignment
11cryoSPARC4.2.1classification
12cryoSPARC4.2.13D reconstruction
13PHENIX1.21-5207-000model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 6.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 45703 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
18S9S

8s9s

18S9S1PDBexperimental model
29C7U

9c7u

19C7U2PDBexperimental model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 105.92 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.004325069
ELECTRON MICROSCOPYf_angle_d0.829834048
ELECTRON MICROSCOPYf_chiral_restr0.04713873
ELECTRON MICROSCOPYf_plane_restr0.00524356
ELECTRON MICROSCOPYf_dihedral_angle_d16.93099085

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