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- PDB-9jjo: putative MgE1P-ADP of human TMEM94 -

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Basic information

Entry
Database: PDB / ID: 9jjo
Titleputative MgE1P-ADP of human TMEM94
ComponentsEndoplasmic reticulum magnesium-transporting P-type ATPase
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 / Chem-POV / Transmembrane protein 94
Function and homology information
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.24 Å
AuthorsGong, D.S.
Funding support1items
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, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jun 11, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Endoplasmic reticulum magnesium-transporting P-type ATPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,2424
Polymers155,6331
Non-polymers1,6093
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Endoplasmic reticulum magnesium-transporting P-type ATPase / ERMA / Endoplasmic reticulum magnesium ATPase / Transmembrane protein 94


Mass: 155632.641 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TMEM94, KIAA0195 / Production host: Homo sapiens (human) / References: UniProt: Q12767, P-type Mg2+ transporter
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-POV / (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate / POPC


Mass: 760.076 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C42H82NO8P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: putative MgE1P-ADP of TMEM94 / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 1300 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.20.1_4487: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.24 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 170219 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0028566
ELECTRON MICROSCOPYf_angle_d0.57111632
ELECTRON MICROSCOPYf_dihedral_angle_d7.5081176
ELECTRON MICROSCOPYf_chiral_restr0.0371371
ELECTRON MICROSCOPYf_plane_restr0.0041445

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