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- EMDB-31484: Cryo-EM structure of human TMEM120B -

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Basic information

Entry
Database: EMDB / ID: EMD-31484
TitleCryo-EM structure of human TMEM120B
Map data
Sample
  • Complex: Dimeric human TMEM120B
    • Protein or peptide: MCherry fluorescent protein,Transmembrane protein 120B
KeywordsMembran protein / MEMBRANE PROTEIN
Function / homology
Function and homology information


protein heterooligomerization / nuclear inner membrane / fat cell differentiation / bioluminescence / generation of precursor metabolites and energy
Similarity search - Function
Ion channel TACAN/TMEM120B / TMPIT-like protein / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein
Similarity search - Domain/homology
Transmembrane protein 120B / MCherry fluorescent protein
Similarity search - Component
Biological speciesAnaplasma marginale (bacteria) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.0 Å
AuthorsKe M / Wu J
CitationJournal: Cell Discov / Year: 2021
Title: Cryo-EM structures of human TMEM120A and TMEM120B.
Authors: Meng Ke / Yue Yu / Changjian Zhao / Shirong Lai / Qiang Su / Weidan Yuan / Lina Yang / Dong Deng / Kun Wu / Weizheng Zeng / Jia Geng / Jianping Wu / Zhen Yan /
History
DepositionJun 27, 2021-
Header (metadata) releaseSep 1, 2021-
Map releaseSep 1, 2021-
UpdateJun 12, 2024-
Current statusJun 12, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.6
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.6
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7f73
  • Surface level: 0.6
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_31484.png

Downloads & links

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Map

FileDownload / File: emd_31484.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 220 pix.
= 239.14 Å		1.09 Å/pix.
x 220 pix.
= 239.14 Å		1.09 Å/pix.
x 220 pix.
= 239.14 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.087 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.6 / Movie #1: 0.6
Minimum - Maximum-3.4276173 - 4.1821017
Average (Standard dev.)0.007308725 (±0.08631343)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions220220220
Spacing220220220
CellA=B=C: 239.14 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0871.0871.087
M x/y/z220220220
origin x/y/z0.0000.0000.000
length x/y/z239.140239.140239.140
α/β/γ90.00090.00090.000
start NX/NY/NZ535455
NX/NY/NZ134138134
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS220220220
D min/max/mean-3.4284.1820.007

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Supplemental data

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Half map: #2

Fileemd_31484_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_31484_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 : Dimeric human TMEM120B

EntireName: Dimeric human TMEM120B
Components
  • Complex: Dimeric human TMEM120B
    • Protein or peptide: MCherry fluorescent protein,Transmembrane protein 120B

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Supramolecule #1: Dimeric human TMEM120B

SupramoleculeName: Dimeric human TMEM120B / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Anaplasma marginale (bacteria)

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Macromolecule #1: MCherry fluorescent protein,Transmembrane protein 120B

MacromoleculeName: MCherry fluorescent protein,Transmembrane protein 120B
type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 72.284109 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDYKDDDDKG SDYKDDDDKG SDYKDDDDKG SDEVDAMVSK GEEDNMAIIK EFMRFKVHME GSVNGHEFEI EGEGEGRPYE GTQTAKLKV TKGGPLPFAW DILSPQFMYG SKAYVKHPAD IPDYLKLSFP EGFKWERVMN FEDGGVVTVT QDSSLQDGEF I YKVKLRGT ...String:
MDYKDDDDKG SDYKDDDDKG SDYKDDDDKG SDEVDAMVSK GEEDNMAIIK EFMRFKVHME GSVNGHEFEI EGEGEGRPYE GTQTAKLKV TKGGPLPFAW DILSPQFMYG SKAYVKHPAD IPDYLKLSFP EGFKWERVMN FEDGGVVTVT QDSSLQDGEF I YKVKLRGT NFPSDGPVMQ KKTMGWEASS ERMYPEDGAL KGEIKQRLKL KDGGHYDAEV KTTYKAKKPV QLPGAYNVNI KL DITSHNE DYTIVEQYER AEGRHSTGGM DELYKLEVLF QGPEFMSGQL ERCEREWHEL EGEFQELQET HRIYKQKLEE LAA LQTLCS SSISKQKKHL KDLKLTLQRC KRHASREEAE LVQQMAANIK ERQDVFFDME AYLPKKNGLY LNLVLGNVNV TLLS NQAKF AYKDEYEKFK LYLTIILLLG AVACRFVLHY RVTDEVFNFL LVWYYCTLTI RESILISNGS RIKGWWVSHH YVSTF LSGV MLTWPNGPIY QKFRNQFLAF SIFQSCVQFL QYYYQRGCLY RLRALGERNH LDLTVEGFQS WMWRGLTFLL PFLFCG HFW QLYNAVTLFE LSSHEECREW QVFVLAFTFL ILFLGNFLTT LKVVHAKLQK NRGKTKQP

UniProtKB: MCherry fluorescent protein, Transmembrane protein 120B

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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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
EMDB ID:

30495

Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 137998
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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