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- PDB-7f73: Cryo-EM structure of human TMEM120B -

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Basic information

Entry
Database: PDB / ID: 7f73
TitleCryo-EM structure of human TMEM120B
ComponentsMCherry fluorescent protein,Transmembrane protein 120B
KeywordsMEMBRANE PROTEIN / Membran 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 / TMEM120A/B / 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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4 Å
AuthorsKe, M. / Wu, J. / Yan, Z.
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, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 1, 2021Provider: repository / Type: Initial release
Revision 1.0Sep 1, 2021Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Sep 1, 2021Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
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Revision 1.0Sep 1, 2021Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Sep 1, 2021Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
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Revision 1.1Mar 2, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jun 12, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.3Jun 18, 2025Group: Data collection / Structure summary / Category: em_admin / em_software / pdbx_entry_details / Item: _em_admin.last_update / _em_software.name
Revision 1.1Jun 18, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Structure visualization

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  • Imaged by UCSF Chimera
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Assembly

Deposited unit
A: MCherry fluorescent protein,Transmembrane protein 120B
B: MCherry fluorescent protein,Transmembrane protein 120B


Theoretical massNumber of molelcules
Total (without water)144,5682
Polymers144,5682
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein MCherry fluorescent protein,Transmembrane protein 120B / TMEM120B


Mass: 72284.109 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anaplasma marginale (bacteria), (gene. exp.) Homo sapiens (human)
Gene: mCherry, TMEM120B / Production host: Homo sapiens (human) / References: UniProt: X5DSL3, UniProt: A0PK00
Has protein modificationN

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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: Dimeric human TMEM120B / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
11Anaplasma marginale (bacteria)770
21Homo sapiens (human)9606
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
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.18.1_3865: / Classification: refinement
EM softwareName: PHENIX / Category: model refinement
CTF correctionType: NONE
3D reconstructionResolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 137998 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0055064
ELECTRON MICROSCOPYf_angle_d0.966844
ELECTRON MICROSCOPYf_dihedral_angle_d29.102638
ELECTRON MICROSCOPYf_chiral_restr0.05748
ELECTRON MICROSCOPYf_plane_restr0.005844

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