4HYD | pdb_00004hyd

Structure of a presenilin family intramembrane aspartate protease in C2221 space group

• PDB DOI: https://doi.org/10.2210/pdb4HYD/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Methanoculleus marisnigri JR1
• Expression System: Escherichia coli
• Mutation(s): Yes 
• Membrane Protein: Yes  PDBTMMemProtMDmpstruc


• Deposited: 2012-11-13 Released: 2012-12-19 
• Deposition Author(s): Li, X., Dang, S., Yan, C., Wang, J., Shi, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.80 Å
• R-Value Free: 
  0.308 (Depositor), 0.315 (DCC) 
• R-Value Work: 
  0.307 (Depositor), 0.311 (DCC) 
• R-Value Observed: 
  0.307 (Depositor) 

Literature

Structure of a presenilin family intramembrane aspartate protease

Li, X., Dang, S., Yan, C., Gong, X., Wang, J., Shi, Y.

(2013) Nature 493: 56-61

• PubMed: 23254940 
• DOI: https://doi.org/10.1038/nature11801
• Primary Citation Related Structures: 
  4HYC, 4HYD, 4HYG


• PubMed Abstract: 
  

  Presenilin and signal peptide peptidase (SPP) are intramembrane aspartyl proteases that regulate important biological functions in eukaryotes. Mechanistic understanding of presenilin and SPP has been hampered by lack of relevant structural information. Here we report the crystal structure of a presenilin/SPP homologue (PSH) from the archaeon Methanoculleus marisnigri JR1. The protease, comprising nine transmembrane segments (TMs), adopts a previously unreported protein fold. The amino-terminal domain, consisting of TM1-6, forms a horseshoe-shaped structure, surrounding TM7-9 of the carboxy-terminal domain. The two catalytic aspartate residues are located on the cytoplasmic side of TM6 and TM7, spatially close to each other and approximately 8 Å into the lipid membrane surface. Water molecules gain constant access to the catalytic aspartates through a large cavity between the amino- and carboxy-terminal domains. Structural analysis reveals insights into the presenilin/SPP family of intramembrane proteases.

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Organizational Affiliation: 
• Ministry of Education Key Laboratory of Protein Science, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China.

Biological Assembly 1  

Global Symmetry: Cyclic - C4  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content 

• Total Structure Weight: 127.52 kDa 
• Atom Count: 7,199 
• Modeled Residue Count: 984 
• Deposited Residue Count: 1,204 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative uncharacterized protein	A, B, C, D	301	Methanoculleus marisnigri JR1	Mutation(s): 5  Gene Names: Memar_1924 Membrane Entity: Yes
UniProt
Find proteins for A3CWV0 (Methanoculleus marisnigri (strain ATCC 35101 / DSM 1498 / JR1)) Explore A3CWV0  Go to UniProtKB:  A3CWV0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.80 Å
• R-Value Free:  0.308 (Depositor), 0.315 (DCC) 
• R-Value Work:  0.307 (Depositor), 0.311 (DCC) 
• R-Value Observed: 0.307 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 114.077	α = 90
b = 170.025	β = 90
c = 181.397	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-12-19 
Deposition Author(s): Li, X., Dang, S., Yan, C., Wang, J., Shi, Y.

Revision History  

• Version 1.0: 2012-12-19
  Type: Initial release
  
• Version 1.1: 2013-01-02
  Changes: Database references, Structure summary
• Version 1.2: 2024-03-20
  Changes: Data collection, Database references