7CYZ | pdb_00007cyz

The structure of human ORP3 OSBP-related domain

• PDB DOI: https://doi.org/10.2210/pdb7CYZ/pdb

• Classification: LIPID BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2020-09-05 Released: 2020-10-28 
• Deposition Author(s): Dong, X.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.219 (Depositor), 0.229 (DCC) 
• R-Value Work: 
  0.173 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.175 (Depositor) 

Starting Model: experimental

Literature

The crystal structure of ORP3 reveals the conservative PI4P binding pattern.

Dong, X., Wang, Z., Ye, S., Zhang, R.

(2020) Biochem Biophys Res Commun 529: 1005-1010

• PubMed: 32819557 
• DOI: https://doi.org/10.1016/j.bbrc.2020.06.090
• Primary Citation Related Structures: 
  7CYZ


• PubMed Abstract: 
  

  Oxysterol-binding protein (OSBP) and its related protein (ORP) constitute a conserved family of lipid transfer proteins (LTPs). ORPs have been implicated as intracellular lipid exchanger and sensor in recent years, which regulate the lipid homeostasis and signal pathway. OSBP-related protein 3 plays key role in controlling cell adhesion and migration and could be developed as the drug target for cancer therapy. Here, we report the crystal structures of human ORP3 ORD to 2.1 Å and ORD-PI4P complex to 3.2 Å. The binding assay in vitro confirms the ORP3 has the capability of PI4P binding. This study further verifies that the PI4P is the common ligand of all ORPs and ORPs should be the lipid exchanger in membrane contact sites(MCS).

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Organizational Affiliation: 
• National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China. Electronic address: [e-mail].
National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China.
National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China. Electronic address: [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 88.65 kDa 
• Atom Count: 6,588 
• Modeled Residue Count: 732 
• Deposited Residue Count: 754 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Oxysterol-binding protein-related protein 3	A, B	377	Homo sapiens	Mutation(s): 2  Gene Names: OSBPL3, KIAA0704, ORP3, OSBP3
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H4L5 (Homo sapiens) Explore Q9H4L5  Go to UniProtKB:  Q9H4L5
PHAROS:  Q9H4L5 GTEx:  ENSG00000070882

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CAF	A, B	L-PEPTIDE LINKING	C5 H12 As N O3 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.219 (Depositor), 0.229 (DCC) 
• R-Value Work:  0.173 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.175 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.336	α = 90
b = 95.336	β = 90
c = 185.251	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
PDB_EXTRACT	data extraction
HKL-3000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-10-28 
Deposition Author(s): Dong, X.

Revision History  

• Version 1.0: 2020-10-28
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-10-09
  Changes: Structure summary