8OQH | pdb_00008oqh

Structure of the cytosolic domain of lysosome-associated TMEM55B

• PDB DOI: https://doi.org/10.2210/pdb8OQH/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-04-12 Released: 2023-11-29 
• Deposition Author(s): Waschbusch, D., Khan, A.R.
• Funding Organization(s): Science Foundation Ireland

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free: 
  0.224 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.194 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.196 (Depositor) 

Starting Model: in silico

Literature

Structure of the cytosolic domain of lysosome-associated TMEM55B

Washcbusch, D., Khan, A.R.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: light scattering

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 19.88 kDa 
• Atom Count: 1,281 
• Modeled Residue Count: 159 
• Deposited Residue Count: 182 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Type 1 phosphatidylinositol 4,5-bisphosphate 4-phosphatase	A, B	91	Homo sapiens	Mutation(s): 0  Gene Names: PIP4P1, C14orf9, TMEM55B EC: 3.1.3.78
UniProt & NIH Common Fund Data Resources
Find proteins for Q86T03 (Homo sapiens) Explore Q86T03  Go to UniProtKB:  Q86T03
PHAROS:  Q86T03 GTEx:  ENSG00000165782

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	C [auth A], D [auth A], E [auth B], F [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free:  0.224 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.194 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.196 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 29.412	α = 90
b = 84.445	β = 98.32
c = 32.177	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-11-29 
Deposition Author(s): Waschbusch, D., Khan, A.R.

---

Funding Organization	Location	Grant Number
Science Foundation Ireland	Ireland	20/FFP-A/8446

Revision History  

• Version 1.0: 2023-11-29
  Type: Initial release