1KF9

PHAGE DISPLAY DERIVED VARIANT OF HUMAN GROWTH HORMONE COMPLEXED WITH TWO COPIES OF THE EXTRACELLULAR DOMAIN OF ITS RECEPTOR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.326 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.234 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure of a Phage Display Derived Variant of Human Growth Hormone Complexed to Two Copies of the Extracellular Domain of its Receptor: Evidence for Strong Structural Coupling between Receptor Binding Sites

Schiffer, C.A.Ultsch, M.Walsh, S.Somers, W.De Vos, A.M.Kossiakoff, A.A.

(2002) J Mol Biol 316: 277-289

  • DOI: 10.1006/jmbi.2001.5348
  • Primary Citation of Related Structures:  
    1KF9

  • PubMed Abstract: 
  • The structure of the ternary complex between the phage display- optimized, high-affinity Site 1 variant of human growth hormone (hGH) and two copies of the extracellular domain (ECD) of the hGH receptor (hGHR) has been determined at 2.6 A resolution. There are widespread and significant structural differences compared to the wild-type ternary hGH hGHR complex ...

    The structure of the ternary complex between the phage display- optimized, high-affinity Site 1 variant of human growth hormone (hGH) and two copies of the extracellular domain (ECD) of the hGH receptor (hGHR) has been determined at 2.6 A resolution. There are widespread and significant structural differences compared to the wild-type ternary hGH hGHR complex. The hGH variant (hGH(v)) contains 15 Site 1 mutations and binds>10(2) tighter to the hGHR ECD (hGH(R1)) at Site 1. It is biologically active and specific to hGHR. The hGH(v) Site 1 interface is somewhat smaller and 20% more hydrophobic compared to the wild-type (wt) counterpart. Of the ten hormone-receptor H-bonds in the site, only one is the same as in the wt complex. Additionally, several regions of hGH(v) structure move up to 9A in forming the interface. The contacts between the C-terminal domains of two receptor ECDs (hGH(R1)- hGH(R2)) are conserved; however, the large changes in Site 1 appear to cause global changes in the domains of hGH(R1) that affect the hGH(v)-hGH(R2) interface indirectly. This coupling is manifested by large changes in the conformation of groups participating in the Site 2 interaction and results in a structure for the site that is reorganized extensively. The hGH(v)- hGH(R2) interface contains seven H-bonds, only one of which is found in the wt complex. Several groups on hGH(v) and hGH(R2) undergo conformational changes of up to 8 A. Asp116 of hGH(v) plays a central role in the reorganization of Site 2 by forming two new H-bonds to the side-chains of Trp104(R2) and Trp169(R2), which are the key binding determinants of the receptor. The fact that a different binding solution is possible for Site 2, where there were no mutations or binding selection pressures, indicates that the structural elements found in these molecules possess an inherent functional plasticity that enables them to bind to a wide variety of binding surfaces.


    Organizational Affiliation

    Department of Protein Engineering, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PHAGE DISPLAY DERIVED VARIANT HUMAN GROWTH HORMONEA, D191Homo sapiensMutation(s): 0 
Gene Names: GH1
UniProt & NIH Common Fund Data Resources
Find proteins for P01241 (Homo sapiens)
Explore P01241 
Go to UniProtKB:  P01241
PHAROS:  P01241
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
EXTRACELLULAR DOMAIN HUMAN GROWTH HORMONE RECEPTOR (1-238)B, C, E, F238Homo sapiensMutation(s): 0 
Gene Names: GHR
UniProt & NIH Common Fund Data Resources
Find proteins for P10912 (Homo sapiens)
Explore P10912 
Go to UniProtKB:  P10912
PHAROS:  P10912
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.326 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.234 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.289α = 90
b = 111.937β = 90.06
c = 95.29γ = 90
Software Package:
Software NamePurpose
SCALEdata collection
MARSCALEdata reduction
X-PLORmodel building
X-PLORrefinement
SCALEdata reduction
MARSCALEdata scaling
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-11-20
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance