8HSI

Cryo-EM structure of human TMEM87A, PE-bound

• PDB DOI: https://doi.org/10.2210/pdb8HSI/pdb
• EM Map EMD-34998: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 
• Membrane Protein: Yes  PDBTMMemProtMD


• Deposited: 2022-12-19 Released: 2023-12-27 
• Deposition Author(s): Han, A., Kim, H.M.
• Funding Organization(s): Other government

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.10 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Cryo-EM structure of human TMEM87A, PE-bound

Han, A., Kim, H.M.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 66.45 kDa 
• Atom Count: 3,516 
• Modelled Residue Count: 405 
• Deposited Residue Count: 555 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transmembrane protein 87A	A	555	Homo sapiens	Mutation(s): 0  Gene Names: TMEM87A, PSEC0094 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q8NBN3 (Homo sapiens) Explore Q8NBN3  Go to UniProtKB:  Q8NBN3
PHAROS:  Q8NBN3 GTEx:  ENSG00000103978

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B, C	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE GlyCosmos:  G15407YE GlyGen:  G15407YE

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
L9Q (Subject of Investigation/LOI)	E [auth A]	(1S)-2-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(octadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate C41 H80 N O8 P JQKOHRZNEOQNJE-VYCVAHKRSA-N
CLR (Subject of Investigation/LOI)	F [auth A], G [auth A]	CHOLESTEROL C27 H46 O HVYWMOMLDIMFJA-DPAQBDIFSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.10 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	3.3.2
MODEL REFINEMENT	PHENIX	1.19.2

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-12-27 
Deposition Author(s): Han, A., Kim, H.M.

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Funding Organization	Location	Grant Number
Other government	Korea, Republic Of	IBS-R030-C1

Revision History  

• Version 1.0: 2023-12-27
  Type: Initial release