9CQH

CRYSTAL STRUCTURE OF APO CLEAVED N-TERNMINAL HIS-TAG GAGA-DOG HSP47(36-418) IN A C 2 CRYSTAL FORM


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.235 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Improving the diffraction quality of heat-shock protein 47 crystals.

Kish, K.Cobell, S.Szapiel, N.Yan, C.Newitt, J.A.Tredup, J.Rodrigo, I.Tomasco, E.Gao, M.Marsilio, F.Haugner, J.Lipovsek, D.Deng, B.Bousquet, P.Zhang, Y.Schmidt, H.Sheriff, S.

(2024) Acta Crystallogr F Struct Biol Commun 80: 302-313

  • DOI: https://doi.org/10.1107/S2053230X24009233
  • Primary Citation of Related Structures:  
    9CQE, 9CQF, 9CQG, 9CQH, 9CQI, 9CQJ

  • PubMed Abstract: 

    Heat-shock protein 47 (HSP47) is a potential target for inhibitors that ameliorate fibrosis by reducing collagen assembly. In an effort to develop a structure-based drug-design system, it was not possible to replicate a previous literature result (PDB entry 4au4) for apo dog HSP47; instead, crystal forms were obtained in which pairs of dog HSP47 molecules interacted through a noncleavable C-terminal His-tag to build up tetramers, all of which had multiple molecules of HSP47 in the asymmetric unit and none of which diffracted as well as the literature precedent. To overcome these difficulties, a two-pronged approach was followed: (i) the His-tag was moved from the C-terminus to the N-terminus and was made cleavable, and (ii) Adnectin (derived from the tenth domain of human fibronectin type III) crystallization chaperones were developed. Both approaches provided well diffracting crystals, but the latter approach yielded crystal forms with only one or two HSP47 complexes per asymmetric unit, which made model building less onerous.


  • Organizational Affiliation

    Molecular Structure & Design, Bristol Myers Squibb Research & Development, PO Box 4000, Princeton, NJ 08543-4000, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Serpin H1
A, B, C, D, E
A, B, C, D, E, F, G
387Canis lupus familiarisMutation(s): 0 
Gene Names: SERPINH1
UniProt
Find proteins for A0A8I3NIH9 (Canis lupus familiaris)
Explore A0A8I3NIH9 
Go to UniProtKB:  A0A8I3NIH9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A8I3NIH9
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
H [auth A]
I [auth A]
J [auth A]
K [auth A]
L [auth B]
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth B],
N [auth C],
P [auth E],
Q [auth E]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
M [auth B],
O [auth D]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.235 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 180.037α = 90
b = 115.493β = 106.8
c = 187.534γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
autoPROCdata processing
XDSdata reduction
Aimlessdata scaling
STARANISOdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Released Date: 2024-10-30 
  • Deposition Author(s): Sheriff, S.

Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-10-30
    Type: Initial release
  • Version 1.1: 2024-11-13
    Changes: Database references
  • Version 1.2: 2024-11-20
    Changes: Database references