9BW5 | pdb_00009bw5

Human Vault Cage


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural insights into the roles of PARP4 and NAD + binding in the human vault cage.

Lodwick, J.E.Shen, R.Erramilli, S.Xie, Y.Roganowicz, K.Ritchey, S.Kossiakoff, A.A.Zhao, M.

(2025) Nat Commun 16: 6724-6724

  • DOI: https://doi.org/10.1038/s41467-025-61981-x
  • Primary Citation of Related Structures:  
    9BW5, 9BW6, 9BW7, 9MXJ

  • PubMed Abstract: 

    Vault is a massive ribonucleoprotein complex found across Eukaryota. The major vault protein (MVP) oligomerizes into an ovular cage, which contains several minor vault components (MVCs) and is thought to transport transiently bound "cargo" molecules. Vertebrate vaults house a poly (ADP-ribose) polymerase (known as PARP4 in humans), which is the only MVC with known enzymatic activity. Despite being discovered decades ago, the molecular basis for PARP4's interaction with MVP remains unclear. In this study, we determined the structure of the human vault cage in complex with PARP4 and its enzymatic substrate NAD + . The structures reveal atomic-level details of the protein-binding interface, as well as unexpected binding sites for NAD + and related nucleotides within the interior of the vault cage. In addition, proteomics data show that human vaults purified from wild-type and PARP4-depleted cells interact with distinct subsets of proteins. Our results thereby support a model in which PARP4's specific incorporation into the vault cage helps to regulate vault's selection of cargo and its subcellular localization. Further, PARP4's proximity to MVP's NAD + -binding sites could support its enzymatic function within the vault.


  • Organizational Affiliation
    • Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Major vault protein
A, B
893Homo sapiensMutation(s): 0 
Gene Names: MVPLRP
UniProt & NIH Common Fund Data Resources
Find proteins for Q14764 (Homo sapiens)
Explore Q14764 
Go to UniProtKB:  Q14764
PHAROS:  Q14764
GTEx:  ENSG00000013364 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ14764
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.12
RECONSTRUCTIONcryoSPARC3.3.1

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35 GM143052

Revision History  (Full details and data files)

  • Version 1.0: 2025-02-05
    Type: Initial release
  • Version 1.1: 2025-08-06
    Changes: Data collection, Database references