8ZQ3

Structure of ORP1L-RAB7A in the presence of GDP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.43 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.198 

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Ligand Structure Quality Assessment 


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Literature

Structure of GDP-bound Rab7 Q67L in complex with ORP1L.

Lu, Q.Zhu, Z.Zhang, J.Xu, C.

(2024) Biochem Biophys Res Commun 725: 150232-150232

  • DOI: https://doi.org/10.1016/j.bbrc.2024.150232
  • Primary Citation of Related Structures:  
    8ZQ3

  • PubMed Abstract: 

    Molecular processes are orchestrated by various proteins that promote early endosomes to become late endosomes and eventually fuse with lysosomes, guaranteeing the degradation of the content. Rab7, which is localized to late endosomes, is one of the most well-known GTPases. ORP1L is recruited by Rab7 to facilitate the fusion of late endosomes and lysosomes. Here, we present the structure of GDP-bound Rab7 Q67L with ORP1L. Structural analysis, supported by biochemical and ITC binding experiments, not only provides structural insight into the interactions between the ORP1L ANK domain and Rab7 but also suggests that the GTPase activity of Rab7 does not interfere with its ORP1L-binding capacity.


  • Organizational Affiliation

    Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, PR China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ras-related protein Rab-7a207Homo sapiensMutation(s): 1 
Gene Names: RAB7ARAB7
EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for P51149 (Homo sapiens)
Explore P51149 
Go to UniProtKB:  P51149
PHAROS:  P51149
GTEx:  ENSG00000075785 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP51149
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Oxysterol-binding protein-related protein 1205Homo sapiensMutation(s): 0 
Gene Names: OSBPL1AORP1OSBP8OSBPL1OSBPL1B
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BXW6 (Homo sapiens)
Explore Q9BXW6 
Go to UniProtKB:  Q9BXW6
PHAROS:  Q9BXW6
GTEx:  ENSG00000141447 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9BXW6
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GDP (Subject of Investigation/LOI)
Query on GDP

Download Ideal Coordinates CCD File 
C [auth A]GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.43 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.198 
  • Space Group: P 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.42α = 90
b = 80.42β = 90
c = 134.16γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China--

Revision History  (Full details and data files)

  • Version 1.0: 2024-06-26
    Type: Initial release