3NZI

Substrate induced remodeling of the active site regulates HtrA1 activity

• PDB DOI: https://doi.org/10.2210/pdb3NZI/pdb

• Classification: hydrolase/hydrolase substrate
• Organism(s): Homo sapiens, Mus musculus
• Expression System: Escherichia coli
• Mutation(s): No 
• Membrane Protein: Yes  OPM


• Deposited: 2010-07-16 Released: 2011-02-23 
• Deposition Author(s): Truebestein, L., Tennstaedt, A., Hauske, P., Krojer, T., Kaiser, M., Clausen, T., Ehrmann, M.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free: 0.249 
• R-Value Work: 0.200 
• R-Value Observed: 0.202 

Starting Model: experimental

Literature

Substrate-induced remodeling of the active site regulates human HTRA1 activity.

Truebestein, L., Tennstaedt, A., Monig, T., Krojer, T., Canellas, F., Kaiser, M., Clausen, T., Ehrmann, M.

(2011) Nat Struct Mol Biol 18: 386-388

• PubMed: 21297635 
• DOI: https://doi.org/10.1038/nsmb.2013
• Primary Citation of Related Structures:  
  3NUM, 3NWU, 3NZI


• PubMed Abstract: 
  

  Crystal structures of active and inactive conformations of the human serine protease HTRA1 reveal that substrate binding to the active site is sufficient to stimulate proteolytic activity. HTRA1 attaches to liposomes, digests misfolded proteins into defined fragments and undergoes substrate-mediated oligomer conversion. In contrast to those of other serine proteases, the PDZ domain of HTRA1 is dispensable for activation or lipid attachment, indicative of different underlying mechanistic features.

---

Organizational Affiliation: 

Centre for Medical Biotechnology, Faculty of Biology, University Duisburg-Essen, Essen, Germany.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Hetero 6-mer - A3B3 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 6-mer - A3B1C1D1 

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

Macromolecule Content

• Total Structure Weight: 37.54 kDa 
• Atom Count: 1,632 
• Modelled Residue Count: 216 
• Deposited Residue Count: 341 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine protease HTRA1	A	334	Homo sapiens	Mutation(s): 0  Gene Names: HTRA1, HTRA, PRSS11 EC: 3.4.21 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q92743 (Homo sapiens) Explore Q92743  Go to UniProtKB:  Q92743
PHAROS:  Q92743 GTEx:  ENSG00000166033

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Citrate synthase	B	7	N/A	Mutation(s): 0  EC: 2.3.3.1 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q9CZU6 (Mus musculus) Explore Q9CZU6  Go to UniProtKB:  Q9CZU6
IMPC:  MGI:88529

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
B2V	B	PEPTIDE-LIKE	C4 H12 B N O2		VAL

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free: 0.249 
• R-Value Work: 0.200 
• R-Value Observed: 0.202 
• Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.965	α = 90
b = 105.965	β = 90
c = 118.336	γ = 120

Software Package:

Software Name	Purpose
PHASER	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-02-23 
Deposition Author(s): Truebestein, L., Tennstaedt, A., Hauske, P., Krojer, T., Kaiser, M., Clausen, T., Ehrmann, M.

Revision History  

• Version 1.0: 2011-02-23
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2018-04-18
  Changes: Data collection
• Version 1.3: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2023-11-22
  Changes: Data collection