6Z3E | pdb_00006z3e

Crystal structure of GDP-bound human GIMAP5, amino acid residues 1-276


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 
    0.268 (Depositor), 0.263 (DCC) 
  • R-Value Work: 
    0.215 (Depositor), 0.212 (DCC) 
  • R-Value Observed: 
    0.218 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

GIMAP5 deficiency reveals a mammalian ceramide-driven longevity assurance pathway.

Park, A.Y.Leney-Greene, M.Lynberg, M.Gabrielski, J.Q.Xu, X.Schwarz, B.Zheng, L.Balasubramaniyam, A.Ham, H.Chao, B.Zhang, Y.Matthews, H.F.Cui, J.Yao, Y.Kubo, S.Chanchu, J.M.Morawski, A.R.Cook, S.A.Jiang, P.Ravell, J.C.Cheng, Y.H.George, A.Faruqi, A.Pagalilauan, A.M.Bergerson, J.R.E.Ganesan, S.Chauvin, S.D.Aluri, J.Edwards-Hicks, J.Bohrnsen, E.Tippett, C.Omar, H.Xu, L.Butcher, G.W.Pascall, J.Karakoc-Aydiner, E.Kiykim, A.Maecker, H.Tezcan, I.Esenboga, S.Heredia, R.J.Akata, D.Tekin, S.Kara, A.Kuloglu, Z.Unal, E.Kendirli, T.Dogu, F.Karabiber, E.Atkinson, T.P.Cochet, C.Filhol, O.Bosio, C.M.Davis, M.M.Lifton, R.P.Pearce, E.L.Daumke, O.Aytekin, C.Sahin, G.E.Aksu, A.U.Uzel, G.Koneti Rao, V.Sari, S.Dalgic, B.Boztug, K.Cagdas, D.Haskologlu, S.Ikinciogullari, A.Schwefel, D.Vilarinho, S.Baris, S.Ozen, A.Su, H.C.Lenardo, M.J.

(2024) Nat Immunol 25: 282-293

  • DOI: https://doi.org/10.1038/s41590-023-01691-y
  • Primary Citation Related Structures: 
    6Z3E

  • PubMed Abstract: 

    Preserving cells in a functional, non-senescent state is a major goal for extending human healthspans. Model organisms reveal that longevity and senescence are genetically controlled, but how genes control longevity in different mammalian tissues is unknown. Here, we report a new human genetic disease that causes cell senescence, liver and immune dysfunction, and early mortality that results from deficiency of GIMAP5, an evolutionarily conserved GTPase selectively expressed in lymphocytes and endothelial cells. We show that GIMAP5 restricts the pathological accumulation of long-chain ceramides (CERs), thereby regulating longevity. GIMAP5 controls CER abundance by interacting with protein kinase CK2 (CK2), attenuating its ability to activate CER synthases. Inhibition of CK2 and CER synthase rescues GIMAP5-deficient T cells by preventing CER overaccumulation and cell deterioration. Thus, GIMAP5 controls longevity assurance pathways crucial for immune function and healthspan in mammals.


  • Organizational Affiliation
    • Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.

Macromolecule Content 

  • Total Structure Weight: 31.61 kDa 
  • Atom Count: 1,947 
  • Modeled Residue Count: 237 
  • Deposited Residue Count: 278 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
GTPase IMAP family member 5278Homo sapiensMutation(s): 0 
Gene Names: GIMAP5IAN4L1IAN5IMAP3
UniProt & NIH Common Fund Data Resources
Find proteins for Q96F15 (Homo sapiens)
Explore Q96F15 
Go to UniProtKB:  Q96F15
PHAROS:  Q96F15
GTEx:  ENSG00000196329 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96F15
Sequence Annotations
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Reference Sequence

Small Molecules

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free:  0.268 (Depositor), 0.263 (DCC) 
  • R-Value Work:  0.215 (Depositor), 0.212 (DCC) 
  • R-Value Observed: 0.218 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.28α = 90
b = 57.23β = 90
c = 106.76γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Helmholtz AssociationGermany--

Revision History  (Full details and data files)

  • Version 1.0: 2021-12-01
    Type: Initial release
  • Version 1.1: 2024-01-24
    Changes: Data collection, Refinement description
  • Version 1.2: 2025-07-16
    Changes: Database references, Structure summary