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- EMDB-13035: Cryo-EM structure of human TMEM45A -

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Basic information

Entry
Database: EMDB / ID: EMD-13035
TitleCryo-EM structure of human TMEM45A
Map datasharpened 3D reconstruction
Sample
  • Organelle or cellular component: Transmembrane Protein 45ATransmembrane protein
    • Protein or peptide: Transmembrane protein 45ATransmembrane protein
  • Ligand: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
Function / homologyProtein of unknown function DUF716 / Transmembrane protein 45 / Family of unknown function (DUF716) / membrane => GO:0016020 / Transmembrane protein 45A
Function and homology information
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.27 Å
AuthorsGrieben M / Pike ACW / Evans A / Shrestha L / Venkaya S / Mukhopadhyay SMM / Moreira T / Chalk R / MacLean EM / Marsden BD ...Grieben M / Pike ACW / Evans A / Shrestha L / Venkaya S / Mukhopadhyay SMM / Moreira T / Chalk R / MacLean EM / Marsden BD / Burgess-Brown NA / Bountra C / Carpenter EP
Funding support United Kingdom, 2 items
OrganizationGrant numberCountry
Wellcome Trust106169/Z/14/Z United Kingdom
European Commission115766 United Kingdom
CitationJournal: To Be Published
Title: CryoEM structure of human TMEM45A
Authors: Grieben M / Pike ACW / Evans A / Shrestha L / Venkaya S / Mukhopadhyay SMM / Moreira T / Marsden BD / Burgess-Brown NA / Carpenter EP
History
DepositionJun 4, 2021-
Header (metadata) releaseJun 16, 2021-
Map releaseJun 16, 2021-
UpdateJun 30, 2021-
Current statusJun 30, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.23
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.23
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7oqz
  • Surface level: 0.23
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_13035.png

Downloads & links

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Map

FileDownload / File: emd_13035.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened 3D reconstruction
Voxel sizeX=Y=Z: 1.09 Å
Density
Contour LevelBy AUTHOR: 0.2 / Movie #1: 0.23
Minimum - Maximum-0.4878575 - 0.8272719
Average (Standard dev.)0.0017005677 (±0.03662648)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions220220220
Spacing220220220
CellA=B=C: 239.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.091.091.09
M x/y/z220220220
origin x/y/z0.0000.0000.000
length x/y/z239.800239.800239.800
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ380380380
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS220220220
D min/max/mean-0.4880.8270.002

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Supplemental data

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Mask #1

Fileemd_13035_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half A

Fileemd_13035_half_map_1.map
Annotationhalf A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half B

Fileemd_13035_half_map_2.map
Annotationhalf B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Transmembrane Protein 45A

EntireName: Transmembrane Protein 45ATransmembrane protein
Components
  • Organelle or cellular component: Transmembrane Protein 45ATransmembrane protein
    • Protein or peptide: Transmembrane protein 45ATransmembrane protein
  • Ligand: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE

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Supramolecule #1: Transmembrane Protein 45A

SupramoleculeName: Transmembrane Protein 45A / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)

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Macromolecule #1: Transmembrane protein 45A

MacromoleculeName: Transmembrane protein 45A / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 32.51833 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MNFRGHALPG TFFFIIGLWW CTKSILKYIC KKQKRTCYLG SKTLFYRLEI LEGITIVGMA LTGMAGEQFI PGGPHLMLYD YKQGHWNQL LGWHHFTMYF FFGLLGVADI LCFTISSLPV SLTKLMLSNA LFVEAFIFYN HTHGREMLDI FVHQLLVLVV F LTGLVAFL ...String:
MNFRGHALPG TFFFIIGLWW CTKSILKYIC KKQKRTCYLG SKTLFYRLEI LEGITIVGMA LTGMAGEQFI PGGPHLMLYD YKQGHWNQL LGWHHFTMYF FFGLLGVADI LCFTISSLPV SLTKLMLSNA LFVEAFIFYN HTHGREMLDI FVHQLLVLVV F LTGLVAFL EFLVRNNVLL ELLRSSLILL QGSWFFQIGF VLYPPSGGPA WDLMDHENIL FLTICFCWHY AVTIVIVGMN YA FITWLVK SRLKRLCSSE VGLLKNAERE QESEEEMAEN LYFQ

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Macromolecule #2: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE

MacromoleculeName: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / type: ligand / ID: 2 / Number of copies: 16 / Formula: PC1
Molecular weightTheoretical: 790.145 Da
Chemical component information

ChemComp-PC1:
1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / phospholipid*YM / Phosphatidylcholine

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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: 7.5
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.6 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 81000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Average electron dose: 45.9 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC / Details: Patch CTF routine in cryoSPARC
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C4 (4 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.27 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 94268
FSC plot (resolution estimation)

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