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- PDB-9c7u: Structure of the human truncated BOS complex in GDN -

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Basic information

Entry
Database: PDB / ID: 9c7u
TitleStructure of the human truncated BOS complex in GDN
Components
  • BOS complex subunit NOMO2
  • Nicalin
  • Transmembrane protein 147
KeywordsMEMBRANE PROTEIN / membrane protein biogenesis / membrane protein complex
Function / homology
Function and homology information


negative regulation of nodal signaling pathway / multi-pass transmembrane protein insertion into ER membrane / multi-pass translocon complex / determination of left/right asymmetry in lateral mesoderm / protein localization to nuclear inner membrane / regulation of protein complex stability / regulation of signal transduction / regulation of protein-containing complex assembly / ribosome binding / carbohydrate binding ...negative regulation of nodal signaling pathway / multi-pass transmembrane protein insertion into ER membrane / multi-pass translocon complex / determination of left/right asymmetry in lateral mesoderm / protein localization to nuclear inner membrane / regulation of protein complex stability / regulation of signal transduction / regulation of protein-containing complex assembly / ribosome binding / carbohydrate binding / nuclear membrane / protein stabilization / endoplasmic reticulum membrane / protein-containing complex / membrane / plasma membrane
Similarity search - Function
: / : / : / : / : / : / : / : / : / : ...: / : / : / : / : / : / : / : / : / : / BOS complex subunit NOMO1-like, first beta sandwich domain / BOS complex subunit NOMO1-like, beta sandwich domain / BOS complex subunit NOMO1-like, second beta sandwich domain / NOMO Ig-like domain / NOMO C-terminal transthyretin-like domain / NOMO third transthyretin-like domain / NOMO fifth transthyretin-like domain / NOMO sixth transthyretin-like domain / NOMO eighth prealbumin-like domain / Nicalin / Transmembrane protein 147 / Predicted membrane protein (DUF2053) / Carboxypeptidase regulatory-like domain / Carboxypeptidase-like, regulatory domain superfamily / Prealbumin-like fold domain / Prealbumin-like fold domain / Carbohydrate-binding-like fold / Peptidase M28 / Peptidase family M28 / Immunoglobulin-like fold
Similarity search - Domain/homology
BOS complex subunit NOMO2 / BOS complex subunit NCLN / BOS complex subunit TMEM147
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.65 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: Mol Cell / Year: 2024
Title: Role of a holo-insertase complex in the biogenesis of biophysically diverse ER membrane proteins.
Authors: Katharine R Page / Vy N Nguyen / Tino Pleiner / Giovani Pinton Tomaleri / Maxine L Wang / Alina Guna / Masami Hazu / Ting-Yu Wang / Tsui-Fen Chou / Rebecca M Voorhees /
Abstract: Mammalian membrane proteins perform essential physiologic functions that rely on their accurate insertion and folding at the endoplasmic reticulum (ER). Using forward and arrayed genetic screens, we ...Mammalian membrane proteins perform essential physiologic functions that rely on their accurate insertion and folding at the endoplasmic reticulum (ER). Using forward and arrayed genetic screens, we systematically studied the biogenesis of a panel of membrane proteins, including several G-protein-coupled receptors (GPCRs). We observed a central role for the insertase, the ER membrane protein complex (EMC), and developed a dual-guide approach to identify genetic modifiers of the EMC. We found that the back of Sec61 (BOS) complex, a component of the multipass translocon, was a physical and genetic interactor of the EMC. Functional and structural analysis of the EMC⋅BOS holocomplex showed that characteristics of a GPCR's soluble domain determine its biogenesis pathway. In contrast to prevailing models, no single insertase handles all substrates. We instead propose a unifying model for coordination between the EMC, the multipass translocon, and Sec61 for the biogenesis of diverse membrane proteins in human cells.
History
DepositionJun 11, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2024Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2024Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name / _em_admin.last_update
Revision 1.2Sep 18, 2024Group: Data collection / Database references / Category: citation / em_admin
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _em_admin.last_update
Revision 1.3Sep 25, 2024Group: Data collection / Database references / Category: citation / em_admin / Item: _citation.page_last / _em_admin.last_update
Revision 1.4Oct 16, 2024Group: Data collection / Structure summary
Category: em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nicalin
B: BOS complex subunit NOMO2
C: Transmembrane protein 147
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,9374
Polymers130,7163
Non-polymers2211
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Nicalin / Nicastrin-like protein / BOS complex subunit NCLN


Mass: 63047.145 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NCLN / Production host: Homo sapiens (human) / References: UniProt: Q969V3
#2: Protein BOS complex subunit NOMO2 / Nodal modulator 2 / pM5 protein 2


Mass: 42388.957 Da / Num. of mol.: 1
Fragment: UNP residues 1-36,873-1222 (Ig domains 1-9 deleted)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NOMO2 / Production host: Homo sapiens (human) / References: UniProt: Q5JPE7
#3: Protein Transmembrane protein 147 / Protein NIFIE 14 / BOS complex subunit TMEM147


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
#4: 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.: 1 / 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
Has ligand of interestN
Has protein modificationY

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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 truncated BOS complex / Type: COMPLEX
Details: Human BOS complex of truncated NOMO (delta Ig 1-9), TMEM147, and NCLN
Entity ID: #1-#3 / Source: RECOMBINANT
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
60.005 % (w/v)3-([3-Cholamidopropyl]dimethylammonio)-2-hydroxy-1-propanesulfonate1
SpecimenConc.: 4 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: 15929
EM imaging opticsEnergyfilter name: GIF Quantum LS / Energyfilter slit width: 20 eV

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Processing

EM software
IDNameVersionCategory
4cryoSPARC3.3CTF correction
7UCSF ChimeraX1.6.1model fitting
10cryoSPARC3.3final Euler assignment
11cryoSPARC3.3classification
12cryoSPARC3.33D reconstruction
13PHENIX1.20.1-4487model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.65 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 115841 / Num. of class averages: 1 / Symmetry type: POINT
Atomic model building
ID 3D fitting-IDAccession codeChain-IDInitial refinement model-IDSource nameType
11Q969V3A1AlphaFoldin silico model
21Q5JPE7B2AlphaFoldin silico model
31Q9BVK8C3AlphaFoldin silico model

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