9G71 | pdb_00009g71

Cryo-EM structure of TTYH2 in complex with lipids in GDN


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.74 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

Interactions between TTYH2 and APOE facilitate endosomal lipid transfer.

Sukalskaia, A.Karner, A.Pugnetti, A.Weber, F.Plochberger, B.Dutzler, R.

(2025) Nature 644: 273-279

  • DOI: https://doi.org/10.1038/s41586-025-09200-x
  • Primary Citation of Related Structures:  
    9G6X, 9G71, 9QNR

  • PubMed Abstract: 

    The Tweety homologues (TTYHs) constitute a family of eukaryotic membrane proteins that, on the basis of structural features, were recently proposed to contribute to lipid transfer between soluble carriers and cellular membranes 1 . However, in the absence of supporting data, this function was hypothetical. Here through pull-down of endogenous proteins, we identify APOE as the interaction partner of human TTYH2. Subcellular fractionation and immunocytochemistry assays showed that both proteins colocalize in endosomal compartments. Characterization of the specific interaction between APOE and TTYH2 through binding assays and structural studies enabled us to identify an epitope in an extended domain of TTYH2 that faces the endosomal lumen. Structures of complexes with APOE-containing lipoprotein particles revealed a binding mode that places lipids in a suitable position to facilitate their diffusion into the membrane. Moreover, in vitro studies revealed that lipid transfer is accelerated by TTYH2. Collectively, our findings indicate that TTYH2 has a role in the unloading of APOE-containing lipoproteins after they are endocytosed. These results define a new protein class that facilitates the extraction of lipids from and their insertion into cellular membranes. Although ubiquitous, this process could be of particular relevance in the brain, where APOE is involved in the transfer of lipids between astrocytes and neurons.


  • Organizational Affiliation
    • Department of Biochemistry University of Zurich, Zurich, Switzerland.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein tweety homolog 2
A, B
599Homo sapiensMutation(s): 0 
Gene Names: TTYH2C17orf29
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BSA4 (Homo sapiens)
Explore Q9BSA4 
Go to UniProtKB:  Q9BSA4
PHAROS:  Q9BSA4
GTEx:  ENSG00000141540 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9BSA4
Glycosylation
Glycosylation Sites: 4Go to GlyGen: Q9BSA4-1
Sequence Annotations
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
C, D, E, F
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CPL (Subject of Investigation/LOI)
Query on CPL

Download Ideal Coordinates CCD File 
P [auth A],
Q [auth A],
Y [auth B]
1-PALMITOYL-2-LINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
C42 H80 N O8 P
JLPULHDHAOZNQI-ZTIMHPMXSA-N
PLC (Subject of Investigation/LOI)
Query on PLC

Download Ideal Coordinates CCD File 
AA [auth B]
BA [auth B]
CA [auth B]
DA [auth B]
EA [auth B]
AA [auth B],
BA [auth B],
CA [auth B],
DA [auth B],
EA [auth B],
HA [auth B],
I [auth A],
IA [auth B],
J [auth A],
JA [auth B],
M [auth A],
R [auth A],
S [auth A],
T [auth A],
U [auth A],
V [auth A],
Z [auth B]
DIUNDECYL PHOSPHATIDYL CHOLINE
C32 H65 N O8 P
IJFVSSZAOYLHEE-SSEXGKCCSA-O
CLR (Subject of Investigation/LOI)
Query on CLR

Download Ideal Coordinates CCD File 
FA [auth B]
GA [auth B]
K [auth A]
L [auth A]
N [auth A]
FA [auth B],
GA [auth B],
K [auth A],
L [auth A],
N [auth A],
O [auth A]
CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
NAG (Subject of Investigation/LOI)
Query on NAG

Download Ideal Coordinates CCD File 
G [auth A],
H [auth A],
W [auth B],
X [auth B]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.74 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21.1_5286

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swiss National Science FoundationSwitzerland--

Revision History  (Full details and data files)

  • Version 1.0: 2025-05-21
    Type: Initial release
  • Version 1.1: 2025-06-11
    Changes: Data collection, Structure summary
  • Version 1.2: 2025-06-25
    Changes: Data collection, Database references
  • Version 1.3: 2025-07-09
    Changes: Data collection, Database references
  • Version 1.4: 2025-08-20
    Changes: Data collection, Database references
  • Version 1.5: 2025-12-03
    Changes: Data collection, Database references