3TJQ | pdb_00003tjq

N-domain of HtrA1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.270 (Depositor), 0.266 (DCC) 
  • R-Value Work: 
    0.217 (Depositor), 0.218 (DCC) 
  • R-Value Observed: 
    0.222 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 3TJQ

This is version 1.3 of the entry. See complete history

Literature

Structural and Functional Analysis of HtrA1 and Its Subdomains.

Eigenbrot, C.Ultsch, M.Lipari, M.T.Moran, P.Lin, S.J.Ganesan, R.Quan, C.Tom, J.Sandoval, W.van Lookeren Campagne, M.Kirchhofer, D.

(2012) Structure 20: 1040-1050

  • DOI: https://doi.org/10.1016/j.str.2012.03.021
  • Primary Citation Related Structures: 
    3TJN, 3TJO, 3TJQ

  • PubMed Abstract: 

    The homotrimeric human serine protease HtrA1 is homologous to bacterial HtrA proteases regarding the trypsin-like catalytic and PDZ domains but differs by the presence of an N-terminal domain with IGFBP and Kazal homology. The crystal structures and SAXS analysis presented herein reveal the rare tandem of IGFBP- and Kazal-like modules, a protease active site that adopts a competent conformation in the absence of substrate or inhibitor and a model for the intact protein in solution. Highly sensitive enzymatic assays and binding studies demonstrate that the N-terminal tandem has no apparent effect on protease activity, and in accordance with the structure-based predictions, neither the IGFBP- nor Kazal-like module retains the function of their prototype proteins. Our structures of the unliganded HtrA1 active site suggest two-state equilibrium and a "conformational selection" model, in which substrate binds to the active conformer.


  • Organizational Affiliation
    • Department of Structural Biology, Genentech, Inc., South San Francisco, CA 94080, USA.

Macromolecule Content 

  • Total Structure Weight: 15.58 kDa 
  • Atom Count: 831 
  • Modeled Residue Count: 106 
  • Deposited Residue Count: 140 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Serine protease HTRA1140Homo sapiensMutation(s): 0 
Gene Names: HTRAHTRA1PRSS11
EC: 3.4.21
UniProt & NIH Common Fund Data Resources
Find proteins for Q92743 (Homo sapiens)
Explore Q92743 
Go to UniProtKB:  Q92743
PHAROS:  Q92743
GTEx:  ENSG00000166033 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ92743
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PT

Query on PT



Download:Ideal Coordinates CCD File
B [auth A],
F [auth A]
PLATINUM (II) ION
Pt
HRGDZIGMBDGFTC-UHFFFAOYSA-N
GOL

Query on GOL



Download:Ideal Coordinates CCD File
J [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
SCN

Query on SCN



Download:Ideal Coordinates CCD File
I [auth A],
L [auth A],
M [auth A],
N [auth A]
THIOCYANATE ION
C N S
ZMZDMBWJUHKJPS-UHFFFAOYSA-M
CL

Query on CL



Download:Ideal Coordinates CCD File
C [auth A]
D [auth A]
E [auth A]
G [auth A]
H [auth A]
C [auth A],
D [auth A],
E [auth A],
G [auth A],
H [auth A],
K [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.270 (Depositor), 0.266 (DCC) 
  • R-Value Work:  0.217 (Depositor), 0.218 (DCC) 
  • R-Value Observed: 0.222 (Depositor) 
Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.085α = 90
b = 72.085β = 90
c = 41.289γ = 120
Software Package:
Software NamePurpose
BOSdata collection
PHENIXmodel building
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-05-16
    Type: Initial release
  • Version 1.1: 2012-06-13
    Changes: Database references
  • Version 1.2: 2012-06-27
    Changes: Database references
  • Version 1.3: 2024-10-09
    Changes: Data collection, Database references, Derived calculations, Structure summary