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- EMDB-45294: Structure of the human truncated BOS complex in GDN -

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Basic information

Entry
Database: EMDB / ID: EMD-45294
TitleStructure of the human truncated BOS complex in GDN
Map data
Sample
  • Complex: Human truncated BOS complex
    • Protein or peptide: Nicalin
    • Protein or peptide: BOS complex subunit NOMO2
    • Protein or peptide: Transmembrane protein 147
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Keywordsmembrane protein biogenesis / membrane protein complex / MEMBRANE PROTEIN
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.65 Å
AuthorsNguyen VN / Tomaleri GP / Voorhees RM
Funding support United States, 3 items
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, 2024-
Header (metadata) releaseAug 21, 2024-
Map releaseAug 21, 2024-
UpdateOct 16, 2024-
Current statusOct 16, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_45294.png

Downloads & links

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Map

FileDownload / File: emd_45294.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 448 pix.
= 372.736 Å		0.83 Å/pix.
x 448 pix.
= 372.736 Å		0.83 Å/pix.
x 448 pix.
= 372.736 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.832 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.112
Minimum - Maximum-0.5759834 - 1.0151747
Average (Standard dev.)-0.0000017234331 (±0.012070768)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions448448448
Spacing448448448
CellA=B=C: 372.73602 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Original unsharpened map of truncated BOS complex

Fileemd_45294_additional_1.map
AnnotationOriginal unsharpened map of truncated BOS complex
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_45294_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Half map: #2

Fileemd_45294_half_map_2.map
Projections & Slices
AxesZYX

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Sample components

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Entire : Human truncated BOS complex

EntireName: Human truncated BOS complex
Components
  • Complex: Human truncated BOS complex
    • Protein or peptide: Nicalin
    • Protein or peptide: BOS complex subunit NOMO2
    • Protein or peptide: Transmembrane protein 147
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Human truncated BOS complex

SupramoleculeName: Human truncated BOS complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Details: Human BOS complex of truncated NOMO (delta Ig 1-9), TMEM147, and NCLN
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Nicalin

MacromoleculeName: Nicalin / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 63.047145 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MLEEAGEVLE NMLKASCLPL GFIVFLPAVL LLVAPPLPAA DAAHEFTVYR MQQYDLQGQP YGTRNAVLNT EARTMAAEVL SRRCVLMRL LDFSYEQYQK ALRQSAGAVV IILPRAMAAV PQDVVRQFME IEPEMLAMET AVPVYFAVED EALLSIYKQT Q AASASQGS ...String:
MLEEAGEVLE NMLKASCLPL GFIVFLPAVL LLVAPPLPAA DAAHEFTVYR MQQYDLQGQP YGTRNAVLNT EARTMAAEVL SRRCVLMRL LDFSYEQYQK ALRQSAGAVV IILPRAMAAV PQDVVRQFME IEPEMLAMET AVPVYFAVED EALLSIYKQT Q AASASQGS ASAAEVLLRT ATANGFQMVT SGVQSKAVSD WLIASVEGRL TGLGGEDLPT IVIVAHYDAF GVAPWLSLGA DS NGSGVSV LLELARLFSR LYTYKRTHAA YNLLFFASGG GKFNYQGTKR WLEDNLDHTD SSLLQDNVAF VLCLDTVGRG SSL HLHVSK PPREGTLQHA FLRELETVAA HQFPEVRFSM VHKRINLAED VLAWEHERFA IRRLPAFTLS HLESHRDGQR SSIM DVRSR VDSKTLTRNT RIIAEALTRV IYNLTEKGTP PDMPVFTEQM QIQQEQLDSV MDWLTNQPRA AQLVDKDSTF LSTLE HHLS RYLKDVKQHH VKADKRDPEF VFYDQLKQVM NAYRVKPAVF DLLLAVGIAA YLGMAYVAVQ HFSLLYKTVQ RLLVKA KTQ

UniProtKB: BOS complex subunit NCLN

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Macromolecule #2: BOS complex subunit NOMO2

MacromoleculeName: BOS complex subunit NOMO2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 42.388957 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MLVGQGAGLL GPAVVTAAVV LLLSGVGPAH GSEDIVYALA GVSFEIKAED DQPLPGVLLS LSGGLFRSNL LTQDNGILTF SNLSPGQYY FKPMMKEFRF EPSSQMIEVQ EGQNLKITIT GYRTAYSCYG TVSSLNGEPE QGVAMEAVGQ NDCSIYGEDT V TDEEGKFR ...String:
MLVGQGAGLL GPAVVTAAVV LLLSGVGPAH GSEDIVYALA GVSFEIKAED DQPLPGVLLS LSGGLFRSNL LTQDNGILTF SNLSPGQYY FKPMMKEFRF EPSSQMIEVQ EGQNLKITIT GYRTAYSCYG TVSSLNGEPE QGVAMEAVGQ NDCSIYGEDT V TDEEGKFR LRGLLPGCVY HVQLKAEGND HIERALPHHR VIEVGNNDID DVNIIVFRQI NQFDLSGNVI TSSEYLPTLW VK LYKSENL DNPIQTVSLG QSLFFHFPPL LRDGENYVVL LDSTLPRSQY DYILPQVSFT AVGYHKHITL IFNPTRKLPE QDI AQGSYI ALPLTLLVLL AGYNHDKLIP LLLQLTSRLQ GVGALGQAAS DNSGPEDAKR QAKKQKTRRT

UniProtKB: BOS complex subunit NOMO2, BOS complex subunit NOMO2

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Macromolecule #3: Transmembrane protein 147

MacromoleculeName: Transmembrane protein 147 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.279848 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MTLFHFGNCF ALAYFPYFIT YKCSGLSEYN AFWKCVQAGV TYLFVQLCKM LFLATFFPTW EGGIYDFIGE FMKASVDVAD LIGLNLVMS RNAGKGEYKI MVAALGWATA ELIMSRCIPL WVGARGIEFD WKYIQMSIDS NISLVHYIVA SAQVWMITRY D LYHTFRPA ...String:
MTLFHFGNCF ALAYFPYFIT YKCSGLSEYN AFWKCVQAGV TYLFVQLCKM LFLATFFPTW EGGIYDFIGE FMKASVDVAD LIGLNLVMS RNAGKGEYKI MVAALGWATA ELIMSRCIPL WVGARGIEFD WKYIQMSIDS NISLVHYIVA SAQVWMITRY D LYHTFRPA VLLLMFLSVY KAFVMETFVH LCSLGSWAAL LARAVVTGLL ALSTLALYVA VVNVHS

UniProtKB: BOS complex subunit TMEM147

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Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 1 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration4 mg/mL
BufferpH: 7.5
Component:
ConcentrationNameFormula
50.0 mM4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid
200.0 mMsodium chlorideNaCl
2.0 mMmagnesium acetate
1.0 mMdithiothreitol
0.0105 % (w/v)glyco-diosgenin
0.005 % (w/v)3-([3-Cholamidopropyl]dimethylammonio)-2-hydroxy-1-propanesulfonate
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 279 K / Instrument: FEI VITROBOT MARK IV
DetailsSample solubilized and purified in GDN.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 15929 / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: DARK FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.65 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.3) / Number images used: 115841
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3)
Final 3D classificationSoftware - Name: cryoSPARC (ver. 3.3)

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Atomic model buiding 1

Initial model
PDB IDChain

69v3

chain_id: A, source_name: AlphaFold, initial_model_type: in silico model

jpe7

chain_id: B, source_name: AlphaFold, initial_model_type: in silico model

bvk8

chain_id: C, source_name: AlphaFold, initial_model_type: in silico model
Output model

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

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