[English] 日本語
Yorodumi
- EMDB-61533: putative MgE1-ATP of human TMEM94 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-61533
Titleputative MgE1-ATP of human TMEM94
Map data
Sample
  • Organelle or cellular component: putative MgE1-ATP of TMEM94
    • Organelle or cellular component: humam TMEM94
      • Protein or peptide: Endoplasmic reticulum magnesium-transporting P-type ATPase
  • Ligand: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
KeywordsMEMBRANE PROTEIN
Function / homologymagnesium ion transport from cytosol to endoplasmic reticulum / Transmembrane protein 94 / P-type magnesium transporter activity / intracellular magnesium ion homeostasis / P-type ATPase, transmembrane domain superfamily / endoplasmic reticulum membrane / Transmembrane protein 94
Function and homology information
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.49 Å
AuthorsGong DS
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Cell Discov / Year: 2025
Title: Structural analysis of full-length human transmembrane protein 94 argues against its classification as a P-type Mg ATPase.
Authors: Yuqi Li / Ye Cong / Xinyao Lou / Weiping Li / Runhao Wang / Mingyu Gong / Jiaxian Xiao / Dandan Qian / Chuangye Yan / Deshun Gong /
History
DepositionSep 14, 2024-
Header (metadata) releaseJun 11, 2025-
Map releaseJun 11, 2025-
UpdateJun 11, 2025-
Current statusJun 11, 2025Processing site: PDBc / Status: Released

-
Structure visualization

Supplemental images

emd_61533.png

Downloads & links

-
Map

FileDownload / File: emd_61533.map.gz / Format: CCP4 / Size: 178 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 360 pix.
= 298.8 Å		0.83 Å/pix.
x 360 pix.
= 298.8 Å		0.83 Å/pix.
x 360 pix.
= 298.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.499
Minimum - Maximum-2.3863337 - 3.6339052
Average (Standard dev.)-0.0010760528 (±0.07037286)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 298.8 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_61533_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_61533_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : putative MgE1-ATP of TMEM94

EntireName: putative MgE1-ATP of TMEM94
Components
  • Organelle or cellular component: putative MgE1-ATP of TMEM94
    • Organelle or cellular component: humam TMEM94
      • Protein or peptide: Endoplasmic reticulum magnesium-transporting P-type ATPase
  • Ligand: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate

-
Supramolecule #1: putative MgE1-ATP of TMEM94

SupramoleculeName: putative MgE1-ATP of TMEM94 / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1

-
Supramolecule #3: humam TMEM94

SupramoleculeName: humam TMEM94 / type: organelle_or_cellular_component / ID: 3 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

-
Macromolecule #1: Endoplasmic reticulum magnesium-transporting P-type ATPase

MacromoleculeName: Endoplasmic reticulum magnesium-transporting P-type ATPase
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: P-type Mg2+ transporter
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 155.632641 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDLKEKHLGE PPSALGLSTR KALSVLKEQL EAVLEGHLRE RKKCLTWKEV WRSSFLHHSN RCSCFHWPGA SLMLLAVLLL LGCCGGQPA GSRGVGLVNA SALFLLLLLN LVLIGRQDRL KRREVERRLR GIIDQIQDAL RDGREIQWPS AMYPDLHMPF A PSWSLHWA ...String:
MDLKEKHLGE PPSALGLSTR KALSVLKEQL EAVLEGHLRE RKKCLTWKEV WRSSFLHHSN RCSCFHWPGA SLMLLAVLLL LGCCGGQPA GSRGVGLVNA SALFLLLLLN LVLIGRQDRL KRREVERRLR GIIDQIQDAL RDGREIQWPS AMYPDLHMPF A PSWSLHWA YRDGHLVNLP VSLLVEGDII ALRPGQESFA SLRGIKDDEH IVLEPGDLFP PFSPPPSPRG EVERGPQSPQ QH RLFRVLE TPVIDNIRWC LDMALSRPVT ALDNERFTVQ SVMLHYAVPV VLAGFLITNA LRFIFSAPGV TSWQYTLLQL QVN GVLPIL PLLFPVLWVL ATACGEARVL AQMSKASPSS LLAKFSEDTL SSYTEAVSSQ EMLRCIWGHF LRVLGGTSPT LSHS SSLLH SLGSVTVLCC VDKQGILSWP NPSPETVLFF SGKVEPPHSS HEDLTDGLST RSFCHPEPHE RDALLAGSLN NTLHL SNEQ ERGDWPGEAP KPPEPYSHHK AHGRSKHPSG SNVSFSRDTE GGEEEPSKTQ PGMESDPYEA EDFVCDYHLE MLSLSQ DQQ NPSCIQFDDS NWQLHLTSLK PLGLNVLLNL CDASVTERLC RFSDHLCNIA LQESHSAVLP VHVPWGLCEL ARLIGFT PG AKELFKQENH LALYRLPSAE TMKETSLGRL SCVTKRRPPL SHMISLFIKD TTTSTEQMLS HGTADVVLEA CTDFWDGA D IYPLSGSDRK KVLDFYQRAC LSGYCSAFAY KPMNCALSSQ LNGKCIELVQ VPGQSSIFTM CELPSTIPIK QNARRSSWS SDEGIGEVLE KEDCMQALSG QIFMGMVSSQ YQARLDIVRL IDGLVNACIR FVYFSLEDEL KSKVFAEKMG LETGWNCHIS LTPNGDMPG SEIPPSSPSH AGSLHDDLNQ VSRDDAEGLL LMEEEGHSDL ISFQPTDSDI PSFLEDSNRA KLPRGIHQVR P HLQNIDNV PLLVPLFTDC TPETMCEMIK IMQEYGEVTC CLGSSANLRN SCLFLQSDIS IALDPLYPSR CSWETFGYAT SI SMAQASD GLSPLQLSGQ LNSLPCSLTF RQEETISIIR LIEQARHATY GIRKCFLFLL QCQLTLVVIQ FLSCLVQLPP LLS TTDILW LSCFCYPLLS ISLLGKPPHS SIMSMATGKN LQSIPKKTQH YFLLCFLLKF SLTISSCLIC FGFTLQSFCD SSRD RNLTN CSSVMLPSND DRAPAWFEDF ANGLLSAQKL TAALIVLHTV FISITHVHRT KPLWRKSPLT NLWWAVTVPV VLLGQ VVQT AVDLQLWTHR DSHVHFGLED VPLLTWLLGC LSLVLVVVTN EIVKLHEIRV RVRYQKRQKL QFETKLGMNS PFLEGS DEV DAGSHHHHHH HHHHGSVEDY KDDDDKVIAE P

UniProtKB: Transmembrane protein 94

-
Macromolecule #3: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(tri...

MacromoleculeName: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
type: ligand / ID: 3 / Number of copies: 1 / Formula: POV
Molecular weightTheoretical: 760.076 Da
Chemical component information

ChemComp-POV:
(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate / phospholipid*YM

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k 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 / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.3 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.49 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 394712
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more