6IQE | pdb_00006iqe

Human prohibitin 2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 
    0.239 (Depositor), 0.246 (DCC) 
  • R-Value Work: 
    0.216 (Depositor), 0.224 (DCC) 
  • R-Value Observed: 
    0.217 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6IQE

This is version 1.1 of the entry. See complete history

Literature

Structural Basis of Mitochondrial Scaffolds by Prohibitin Complexes: Insight into a Role of the Coiled-Coil Region.

Yoshinaka, T.Kosako, H.Yoshizumi, T.Furukawa, R.Hirano, Y.Kuge, O.Tamada, T.Koshiba, T.

(2019) iScience 19: 1065-1078

  • DOI: https://doi.org/10.1016/j.isci.2019.08.056
  • Primary Citation Related Structures: 
    6IQE

  • PubMed Abstract: 

    The coiled-coil motif mediates subunit oligomerization and scaffolding and underlies several fundamental biologic processes. Prohibitins (PHBs), mitochondrial inner membrane proteins involved in mitochondrial homeostasis and signal transduction, are predicted to have a coiled-coil motif, but their structural features are poorly understood. Here we solved the crystal structure of the heptad repeat (HR) region of PHB2 at 1.7-Å resolution, showing that it assembles into a dimeric, antiparallel coiled-coil with a unique negatively charged area essential for the PHB interactome in mitochondria. Disruption of the HR coiled-coil abolishes well-ordered PHB complexes and the mitochondrial tubular networks accompanying PHB-dependent signaling. Using a proximity-dependent biotin identification (BioID) technique in live cells, we mapped a number of mitochondrial intermembrane space proteins whose association with PHB2 relies on the HR coiled-coil region. Elucidation of the PHB complex structure in mitochondria provides insight into essential PHB interactomes required for mitochondrial dynamics as well as signal transduction.


  • Organizational Affiliation
    • Department of Biology, Faculty of Science, Kyushu University, Fukuoka 819-0395, Japan.

Macromolecule Content 

  • Total Structure Weight: 9.82 kDa 
  • Atom Count: 553 
  • Modeled Residue Count: 59 
  • Deposited Residue Count: 87 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Prohibitin-287Homo sapiensMutation(s): 0 
Gene Names: PHB2BAPREA
UniProt & NIH Common Fund Data Resources
Find proteins for Q99623 (Homo sapiens)
Explore Q99623 
Go to UniProtKB:  Q99623
PHAROS:  Q99623
GTEx:  ENSG00000215021 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ99623
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free:  0.239 (Depositor), 0.246 (DCC) 
  • R-Value Work:  0.216 (Depositor), 0.224 (DCC) 
  • R-Value Observed: 0.217 (Depositor) 
Space Group: P 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.142α = 90
b = 65.142β = 90
c = 62.288γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-09-25
    Type: Initial release
  • Version 1.1: 2023-11-22
    Changes: Data collection, Database references, Refinement description