4X8Y

Crystal structure of human PGRMC1 cytochrome b5-like domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.183 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Haem-dependent dimerization of PGRMC1/Sigma-2 receptor facilitates cancer proliferation and chemoresistance

Kabe, Y.Nakane, T.Koike, I.Yamamoto, T.Sugiura, Y.Harada, E.Sugase, K.Shimamura, T.Ohmura, M.Muraoka, K.Yamamoto, A.Uchida, T.Iwata, S.Yamaguchi, Y.Krayukhina, E.Noda, M.Handa, H.Ishimori, K.Uchiyama, S.Kobayashi, T.Suematsu, M.

(2016) Nat Commun 7: 11030-11030

  • DOI: 10.1038/ncomms11030

  • PubMed Abstract: 
  • Progesterone-receptor membrane component 1 (PGRMC1/Sigma-2 receptor) is a haem-containing protein that interacts with epidermal growth factor receptor (EGFR) and cytochromes P450 to regulate cancer proliferation and chemoresistance; its structural ba ...

    Progesterone-receptor membrane component 1 (PGRMC1/Sigma-2 receptor) is a haem-containing protein that interacts with epidermal growth factor receptor (EGFR) and cytochromes P450 to regulate cancer proliferation and chemoresistance; its structural basis remains unknown. Here crystallographic analyses of the PGRMC1 cytosolic domain at 1.95 Å resolution reveal that it forms a stable dimer through stacking interactions of two protruding haem molecules. The haem iron is five-coordinated by Tyr113, and the open surface of the haem mediates dimerization. Carbon monoxide (CO) interferes with PGRMC1 dimerization by binding to the sixth coordination site of the haem. Haem-mediated PGRMC1 dimerization is required for interactions with EGFR and cytochromes P450, cancer proliferation and chemoresistance against anti-cancer drugs; these events are attenuated by either CO or haem deprivation in cancer cells. This study demonstrates protein dimerization via haem-haem stacking, which has not been seen in eukaryotes, and provides insights into its functional significance in cancer.


    Organizational Affiliation

    JST, CREST, Kyoto 606-8501, Japan.,Okazaki Institute for Integrative Bioscience, National Institutes of Natural Sciences, Okazaki 444-8787, Japan.,Bioorganic Research Institute, Suntory Foundation for Life Sciences, Kyoto 619-0284, Japan.,Department of Statistical Genetics, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan.,Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama 226-8501, Japan.,Department of Medical Chemistry and Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan.,Department of Biotechnology, Graduate School of Engineering, Osaka University, Osaka 565-0871, Japan.,Department of Nanoparticle Translational Research, Tokyo Medical University, Tokyo 160-8402, Japan.,Department of Biochemistry, Keio University School of Medicine, and Japan Science and Technology Agency (JST), Core Research for Evolutional Science and Technology (CREST), Tokyo 160-8582, Japan.,Platform for Drug Discovery, Informatics, and Structural Life Science, JST, Kyoto 606-8501, Japan.,Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan.,Department of Biochemistry, Keio University School of Medicine, JST, Exploratory Research for Advanced Technology (ERATO), Suematsu Gas Biology Project, Tokyo 160-8582, Japan.,JST, Research Acceleration Program, Membrane Protein Crystallography Project, Kyoto 606-8501, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Membrane-associated progesterone receptor component 1
A, B
132Homo sapiensMutation(s): 0 
Gene Names: PGRMC1 (HPR6.6, PGRMC)
Find proteins for O00264 (Homo sapiens)
Go to Gene View: PGRMC1
Go to UniProtKB:  O00264
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download SDF File 
Download CCD File 
A, B
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.183 
  • Space Group: I 41 2 2
Unit Cell:
Length (Å)Angle (°)
a = 167.230α = 90.00
b = 167.230β = 90.00
c = 63.460γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
BSSdata collection
PHENIXmodel building
XDSdata reduction
XSCALEdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Science and Technology AgencyJapanExploratory Research for Advanced Technology (ERATO) Suematsu Gas Biology Project

Revision History 

  • Version 1.0: 2016-03-23
    Type: Initial release
  • Version 1.1: 2016-03-30
    Type: Database references