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- EMDB-63427: TMEM164-substrate -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-63427
TitleTMEM164-substrate
Map data
Sample
  • Complex: TMEM164
    • Protein or peptide: Transmembrane protein 164
  • Ligand: ZINC ION
  • Ligand: CHOLESTEROL
  • Ligand: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine
  • Ligand: Petroselinic acid
  • Ligand: [1-MYRISTOYL-GLYCEROL-3-YL]PHOSPHONYLCHOLINE
  • Ligand: water
KeywordsTMEM164 / MEMBRANE PROTEIN
Function / homologyTransmembrane protein 164 / TMEM164 family / positive regulation of ferroptosis / membrane / Transmembrane protein 164
Function and homology information
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsZhang MF
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: TMEM164-substrate
Authors: Zhang MF
History
DepositionFeb 13, 2025-
Header (metadata) releaseMay 27, 2026-
Map releaseMay 27, 2026-
UpdateMay 27, 2026-
Current statusMay 27, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_63427.png

Downloads & links

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Map

FileDownload / File: emd_63427.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.57 Å/pix.
x 512 pix.
= 291.84 Å		0.57 Å/pix.
x 512 pix.
= 291.84 Å		0.57 Å/pix.
x 512 pix.
= 291.84 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.57 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.28901246 - 0.5215277
Average (Standard dev.)0.00004423405 (±0.008263466)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 291.84 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_63427_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_63427_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 : TMEM164

EntireName: TMEM164
Components
  • Complex: TMEM164
    • Protein or peptide: Transmembrane protein 164
  • Ligand: ZINC ION
  • Ligand: CHOLESTEROL
  • Ligand: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine
  • Ligand: Petroselinic acid
  • Ligand: [1-MYRISTOYL-GLYCEROL-3-YL]PHOSPHONYLCHOLINE
  • Ligand: water

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Supramolecule #1: TMEM164

SupramoleculeName: TMEM164 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Transmembrane protein 164

MacromoleculeName: Transmembrane protein 164 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 33.537695 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSRYSYQSLL DWLYGGVDPS FAGNGGPDCA AFLSWQQRLL ESVVVLTLAL LEILVALRHI LRQTKEDGRG SPGSQPEQVT QRPEEGKES LSKNLLLVAL CLTFGVEVGF KFATKTVIYL LNPCHLVTMM HIFLLACPPC RGAIVVFKLQ MHMLNGALLA L LFPVVNTR ...String:
MSRYSYQSLL DWLYGGVDPS FAGNGGPDCA AFLSWQQRLL ESVVVLTLAL LEILVALRHI LRQTKEDGRG SPGSQPEQVT QRPEEGKES LSKNLLLVAL CLTFGVEVGF KFATKTVIYL LNPCHLVTMM HIFLLACPPC RGAIVVFKLQ MHMLNGALLA L LFPVVNTR LLPFELEIYY IQHVMLYVVP IYLLWKGGAY TPEPLSSFRW ALLSTGLMFF YHFSVLQILG LVTEVNLNNM LC PAISDPF YGPWYRIWAS GHQTLMTMTH GKLVILFSYM AGPLCKYLLD LLRLPAKKID

UniProtKB: Transmembrane protein 164

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Macromolecule #2: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 2 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #3: CHOLESTEROL

MacromoleculeName: CHOLESTEROL / type: ligand / ID: 3 / Number of copies: 2 / Formula: CLR
Molecular weightTheoretical: 386.654 Da
Chemical component information

ChemComp-CLR:
CHOLESTEROL

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Macromolecule #4: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine

MacromoleculeName: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / type: ligand / ID: 4 / Number of copies: 2 / Formula: PEE
Molecular weightTheoretical: 744.034 Da
Chemical component information

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

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Macromolecule #5: Petroselinic acid

MacromoleculeName: Petroselinic acid / type: ligand / ID: 5 / Number of copies: 16 / Formula: 4I1
Molecular weightTheoretical: 282.461 Da
Chemical component information

ChemComp-4I1:
Petroselinic acid

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Macromolecule #6: [1-MYRISTOYL-GLYCEROL-3-YL]PHOSPHONYLCHOLINE

MacromoleculeName: [1-MYRISTOYL-GLYCEROL-3-YL]PHOSPHONYLCHOLINE / type: ligand / ID: 6 / Number of copies: 2 / Formula: LPC
Molecular weightTheoretical: 468.585 Da
Chemical component information

ChemComp-LPC:
[1-MYRISTOYL-GLYCEROL-3-YL]PHOSPHONYLCHOLINE

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Macromolecule #7: water

MacromoleculeName: water / type: ligand / ID: 7 / Number of copies: 4 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TECNAI F30
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 2.0 µm
Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING ONLY
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 47000
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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