7E1T | pdb_00007e1t

Crystal structure of Rab9A-GTP-Nde1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 
    0.244 (Depositor), 0.246 (DCC) 
  • R-Value Work: 
    0.194 (Depositor), 0.199 (DCC) 
  • R-Value Observed: 
    0.196 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Nde1 is a Rab9 effector for loading late endosomes to cytoplasmic dynein motor complex.

Zhang, Y.Chen, Z.Wang, F.Sun, H.Zhu, X.Ding, J.Zhang, T.

(2022) Structure 30: 386-395.e5

  • DOI: https://doi.org/10.1016/j.str.2021.10.013
  • Primary Citation Related Structures: 
    7E1T

  • PubMed Abstract: 

    Rab9 is mainly located on late endosomes and required for their intracellular transport to trans-Golgi network (TGN). The cytoplasmic dynein motor, together with its regulatory proteins Nde1/Ndel1 and Lis1, controls intracellular retrograde transport of membranous organelles along the microtubule network. How late endosomes are tethered to the microtubule-based motor dynein for their retrograde transport remains unclear. Here, we demonstrate that the guanosine triphosphate (GTP)-bound Rab9A/B specifically uses Nde1/Ndel1 as an effector to interact with the dynein motor complex. We determined the crystal structure of Rab9A-GTP in complex with the Rab9-binding region of Nde1. The functional roles of key residues involved in the Rab9A-Nde1 interaction are verified using biochemical and cell biology assays. Rab9A mutants unable to bind to Nde1 also failed to associate with dynein, Lis1, and dynactin. Therefore, Nde1 is a Rab9 effector that tethers Rab9-associated late endosomes to the dynein motor for their retrograde transport to the TGN.


  • Organizational Affiliation
    • Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai 200031, China.

Macromolecule Content 

  • Total Structure Weight: 64.15 kDa 
  • Atom Count: 3,447 
  • Modeled Residue Count: 402 
  • Deposited Residue Count: 550 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Ras-related protein Rab-9A
A, B
203Homo sapiensMutation(s): 1 
Gene Names: RAB9ARAB9
EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for P51151 (Homo sapiens)
Explore P51151 
Go to UniProtKB:  P51151
PHAROS:  P51151
GTEx:  ENSG00000123595 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP51151
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Isoform 2 of Nuclear distribution protein nudE homolog 1
C, D
72Homo sapiensMutation(s): 0 
Gene Names: NDE1NUDE
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NXR1 (Homo sapiens)
Explore Q9NXR1 
Go to UniProtKB:  Q9NXR1
PHAROS:  Q9NXR1
GTEx:  ENSG00000072864 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NXR1
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free:  0.244 (Depositor), 0.246 (DCC) 
  • R-Value Work:  0.194 (Depositor), 0.199 (DCC) 
  • R-Value Observed: 0.196 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.421α = 90
b = 67.646β = 90
c = 118.516γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PDB_EXTRACTdata extraction
PHENIXphasing

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)China31530013 and 31870722

Revision History  (Full details and data files)

  • Version 1.0: 2021-10-27
    Type: Initial release
  • Version 1.1: 2022-05-18
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Refinement description