Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 161.20 kDa 
• Atom Count: 10322 
• Modelled Residue Count: 1242 
• Deposited Residue Count: 1436 
• Unique protein chains: 2

5IFS

Quantitative interaction mapping reveals an extended ubiquitin regulatory domain in ASPL that disrupts functional p97 hexamers and induces cell death

• PDB DOI: 10.2210/pdb5IFS/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-02-26 Released: 2016-10-26 
• Deposition Author(s): Roske, Y., Arumughan, A., Heinemann, U., Wanker, E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.46 Å
• R-Value Free: 0.251 
• R-Value Work: 0.201 
• R-Value Observed: 0.204 

Literature

Quantitative interaction mapping reveals an extended UBX domain in ASPL that disrupts functional p97 hexamers.

Arumughan, A., Roske, Y., Barth, C., Forero, L.L., Bravo-Rodriguez, K., Redel, A., Kostova, S., McShane, E., Opitz, R., Faelber, K., Rau, K., Mielke, T., Daumke, O., Selbach, M., Sanchez-Garcia, E., Rocks, O., Panakova, D., Heinemann, U., Wanker, E.E.

(2016) Nat Commun 7: 13047-13047

• PubMed: 27762274 
• DOI: 10.1038/ncomms13047
• Primary Citation of Related Structures:  
  5IFS, 5IFW


• PubMed Abstract: 
  

Interaction mapping is a powerful strategy to elucidate the biological function of protein assemblies and their regulators. Here, we report the generation of a quantitative interaction network, directly linking 14 human proteins to the AAA+ ATPase p97, an essential hexameric protein with multiple cellular functions. We show that the high-affinity interacting protein ASPL efficiently promotes p97 hexamer disassembly, resulting in the formation of stable p97:ASPL heterotetramers. High-resolution structural and biochemical studies indicate that an extended UBX domain (eUBX) in ASPL is critical for p97 hexamer disassembly and facilitates the assembly of p97:ASPL heterotetramers. This spontaneous process is accompanied by a reorientation of the D2 ATPase domain in p97 and a loss of its activity. Finally, we demonstrate that overproduction of ASPL disrupts p97 hexamer function in ERAD and that engineered eUBX polypeptides can induce cell death, providing a rationale for developing anti-cancer polypeptide inhibitors that may target p97 activity.

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Organizational Affiliation: 

Max Delbrück Center for Molecular Medicine, Robert-Rössle-Straße 10, 13125 Berlin, Germany.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tether containing UBX domain for GLUT4	A, C	237	Homo sapiens	Mutation(s): 0  Gene Names: ASPSCR1, ASPL, RCC17, TUG, UBXD9, UBXN9
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BZE9 (Homo sapiens) Explore Q9BZE9  Go to UniProtKB:  Q9BZE9
PHAROS:  Q9BZE9 GTEx:  ENSG00000169696

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Transitional endoplasmic reticulum ATPase	B, D	481	Homo sapiens	Mutation(s): 0  Gene Names: VCP EC: 3.6.4.6
UniProt & NIH Common Fund Data Resources
Find proteins for P55072 (Homo sapiens) Explore P55072  Go to UniProtKB:  P55072
PHAROS:  P55072 GTEx:  ENSG00000165280

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	E [auth B], K [auth D]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
SO4	G [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	J [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	H [auth B], I [auth B], M [auth D]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
MG	F [auth B], L [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.46 Å
• R-Value Free: 0.251 
• R-Value Work: 0.201 
• R-Value Observed: 0.204 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.844	α = 90
b = 132.914	β = 110.15
c = 96.121	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XSCALE	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2016-02-26 
• Released Date: 2016-10-26 
Deposition Author(s): Roske, Y., Arumughan, A., Heinemann, U., Wanker, E.

Revision History  

• Version 1.0: 2016-10-26
  Type: Initial release
  
• Version 1.1: 2016-11-02
  Changes: Database references