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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


multi-pass transmembrane protein insertion into ER membrane / multi-pass translocon complex / regulation of protein complex stability / regulation of protein-containing complex assembly / regulation of signal transduction / ribosome binding / carbohydrate binding / membrane => GO:0016020 / protein stabilization / endoplasmic reticulum membrane ...multi-pass transmembrane protein insertion into ER membrane / multi-pass translocon complex / regulation of protein complex stability / regulation of protein-containing complex assembly / regulation of signal transduction / ribosome binding / carbohydrate binding / membrane => GO:0016020 / protein stabilization / endoplasmic reticulum membrane / protein-containing complex / membrane / plasma membrane
Similarity search - Function
: / Nicalin / Transmembrane protein 147 / Predicted membrane protein (DUF2053) / Carboxypeptidase regulatory-like domain / Prealbumin-like fold domain / Prealbumin-like fold domain / Carboxypeptidase-like, regulatory domain superfamily / Carbohydrate-binding-like fold / Peptidase M28 ...: / Nicalin / Transmembrane protein 147 / Predicted membrane protein (DUF2053) / Carboxypeptidase regulatory-like domain / Prealbumin-like fold domain / Prealbumin-like fold domain / Carboxypeptidase-like, regulatory domain superfamily / Carbohydrate-binding-like fold / Peptidase M28 / Peptidase family M28 / Immunoglobulin-like fold
Similarity search - Domain/homology
BOS complex subunit NOMO2 / Nicalin / Transmembrane protein 147
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: 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
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

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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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