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- PDB-37np: Tetrameric structure of TM6SF2 -

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Basic information

Entry
Database: PDB / ID: 37np
TitleTetrameric structure of TM6SF2
ComponentsTransmembrane 6 superfamily member 2
KeywordsLIPID TRANSPORT / Membrane protein / Cholesterol-binding protein / Lipid metabolism / VLDL secretion
Function / homology
Function and homology information


regulation of lipid metabolic process / endoplasmic reticulum-Golgi intermediate compartment membrane / endoplasmic reticulum membrane / identical protein binding
Similarity search - Function
: / : / Transmembrane 6 superfamily member 2-like, transmembrane domain / EXPERA (EXPanded EBP superfamily) / EXPERA domain / EXPERA domain profile.
Similarity search - Domain/homology
CHOLESTEROL / Transmembrane 6 superfamily member 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.64 Å
AuthorsHong, S. / Li, X.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)NIH-R01DK090066 United States
CitationJournal: To Be Published
Title: Tetrameric structure of TM6SF2
Authors: Hong, S. / Li, X.
History
DepositionJul 28, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2026Provider: repository / Type: Initial release
Revision 1.0Oct 14, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transmembrane 6 superfamily member 2
B: Transmembrane 6 superfamily member 2
C: Transmembrane 6 superfamily member 2
D: Transmembrane 6 superfamily member 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,9168
Polymers172,3704
Non-polymers1,5474
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Transmembrane 6 superfamily member 2


Mass: 43092.465 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Tm6sf2 / Production host: Homo sapiens (human) / References: UniProt: E9QM19
#2: Chemical
ChemComp-CLR / CHOLESTEROL


Mass: 386.654 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H46O / Feature type: SUBJECT OF INVESTIGATION
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: Tetrameric structure of TM6SF2 in complex with cholesterol
Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.042 MDa / Experimental value: NO
Source (natural)Organism: Mus musculus (house mouse)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
SpecimenConc.: 10 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyModel: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: DIFFRACTION / Nominal defocus max: 1800 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategoryDetails (eV)
1RELION3.1.4particle selection
2PHENIX1.21_5207model refinement
13cryoSPARCV4.4.13D reconstruction3DFlex
CTF correctionType: NONE
3D reconstructionResolution: 3.64 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 69049 / Symmetry type: POINT
RefinementHighest resolution: 3.64 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00410256
ELECTRON MICROSCOPYf_angle_d0.60214009
ELECTRON MICROSCOPYf_dihedral_angle_d13.0183777
ELECTRON MICROSCOPYf_chiral_restr0.0711538
ELECTRON MICROSCOPYf_plane_restr0.0061697

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