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- EMDB-26992: Cryo-EM structure of TMEM87A -

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Basic information

Entry
Database: EMDB / ID: EMD-26992
TitleCryo-EM structure of TMEM87A
Map data
Sample
  • Complex: TMEM87A in lipid nanodisc
    • Protein or peptide: Transmembrane protein 87ATransmembrane protein
  • Ligand: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine
Function / homology
Function and homology information


retrograde transport, endosome to Golgi / Golgi cisterna membrane / RHOA GTPase cycle / ruffle / cellular response to mechanical stimulus / Golgi membrane / Golgi apparatus / plasma membrane / cytosol
Similarity search - Function
Transmembrane protein GPR107/GPR108-like / Lung seven transmembrane receptor
Similarity search - Domain/homology
Transmembrane protein 87A
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.74 Å
AuthorsHoel CM / Zhang L / Brohawn SG
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)DP2GM123496 United States
CitationJournal: Elife / Year: 2022
Title: Structure of the GOLD-domain seven-transmembrane helix protein family member TMEM87A.
Authors: Christopher M Hoel / Lin Zhang / Stephen G Brohawn /
Abstract: TMEM87s are eukaryotic transmembrane proteins with two members (TMEM87A and TMEM87B) in humans. TMEM87s have proposed roles in protein transport to and from the Golgi, as mechanosensitive ion ...TMEM87s are eukaryotic transmembrane proteins with two members (TMEM87A and TMEM87B) in humans. TMEM87s have proposed roles in protein transport to and from the Golgi, as mechanosensitive ion channels, and in developmental signaling. TMEM87 disruption has been implicated in cancers and developmental disorders. To better understand TMEM87 structure and function, we determined a cryo-EM structure of human TMEM87A in lipid nanodiscs. TMEM87A consists of a Golgi-dynamics (GOLD) domain atop a membrane-spanning seven-transmembrane helix domain with a large cavity open to solution and the membrane outer leaflet. Structural and functional analyses suggest TMEM87A may not function as an ion channel or G-protein coupled receptor. We find TMEM87A shares its characteristic domain arrangement with seven other proteins in humans; three that had been identified as evolutionary related (TMEM87B, GPR107, and GPR108) and four previously unrecognized homologs (GPR180, TMEM145, TMEM181, and WLS). Among these structurally related LD domain even-ransmembrane helix (GOST) proteins, WLS is best characterized as a membrane trafficking and secretion chaperone for lipidated Wnt signaling proteins. We find key structural determinants for WLS function are conserved in TMEM87A. We propose TMEM87A and structurally homologous GOST proteins could serve a common role in trafficking membrane-associated cargo.
History
DepositionMay 15, 2022-
Header (metadata) releaseJul 20, 2022-
Map releaseJul 20, 2022-
UpdateNov 30, 2022-
Current statusNov 30, 2022Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_26992.png

Downloads & links

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Map

FileDownload / File: emd_26992.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.115 Å
Density
Contour LevelBy AUTHOR: 0.045
Minimum - Maximum-0.15236567 - 0.30564952
Average (Standard dev.)0.00016621614 (±0.005391474)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions180180180
Spacing180180180
CellA=B=C: 200.7 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_26992_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_26992_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : TMEM87A in lipid nanodisc

EntireName: TMEM87A in lipid nanodisc
Components
  • Complex: TMEM87A in lipid nanodisc
    • Protein or peptide: Transmembrane protein 87ATransmembrane protein
  • Ligand: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine

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Supramolecule #1: TMEM87A in lipid nanodisc

SupramoleculeName: TMEM87A in lipid nanodisc / type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 63 KDa

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Macromolecule #1: Transmembrane protein 87A

MacromoleculeName: Transmembrane protein 87A / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 64.512887 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MAAAAWLQVL PVILLLLGAH PSPLSFFSAG PATVAAADRS KWHIPIPSGK NYFSFGKILF RNTTIFLKFD GEPCDLSLNI TWYLKSADC YNEIYNFKAE EVELYLEKLK EKRGLSGKYQ TSSKLFQNCS ELFKTQTFSG DFMHRLPLLG EKQEAKENGT N LTFIGDKT ...String:
MAAAAWLQVL PVILLLLGAH PSPLSFFSAG PATVAAADRS KWHIPIPSGK NYFSFGKILF RNTTIFLKFD GEPCDLSLNI TWYLKSADC YNEIYNFKAE EVELYLEKLK EKRGLSGKYQ TSSKLFQNCS ELFKTQTFSG DFMHRLPLLG EKQEAKENGT N LTFIGDKT AMHEPLQTWQ DAPYIFIVHI GISSSKESSK ENSLSNLFTM TVEVKGPYEY LTLEDYPLMI FFMVMCIVYV LF GVLWLAW SACYWRDLLR IQFWIGAVIF LGMLEKAVFY AEFQNIRYKG ESVQGALILA ELLSAVKRSL ARTLVIIVSL GYG IVKPRL GVTLHKVVVA GALYLLFSGM EGVLRVTGAQ TDLASLAFIP LAFLDTALCW WIFISLTQTM KLLKLRRNIV KLSL YRHFT NTLILAVAAS IVFIIWTTMK FRIVTCQSDW RELWVDDAIW RLLFSMILFV IMVLWRPSAN NQRFAFSPLS EEEEE DEQK EPMLKESFEG MKMRSTKQEP NGNSKVNKAQ EDDLKWVEEN VPSSVTDVAL PALLDSDEER MITHFERSKM ESNSLE VLF Q

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Macromolecule #2: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine

MacromoleculeName: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / type: ligand / ID: 2 / Number of copies: 1 / Formula: PEE
Molecular weightTheoretical: 744.034 Da
Chemical component information

ChemComp-PEE:
1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / DOPE, phospholipid*YM / Discrete optimized protein energy

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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

BufferpH: 8
Component:
ConcentrationFormulaName
20.0 mMC4H11NO3Tris
150.0 mMNaClSodium chlorideNaClSodium chloride
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: OTHER / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.6 µm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.74 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 138217

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