1GMO

CRYSTAL STRUCTURES OF NK1-HEPARIN COMPLEXES REVEAL THE BASIS FOR NK1 ACTIVITY AND ENABLE ENGINEERING OF POTENT AGONISTS OF THE MET RECEPTOR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.254 
  • R-Value Observed: 0.254 

Starting Models: experimental
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This is version 3.2 of the entry. See complete history


Literature

Crystal Structures of Nk1-Heparin Complexes Reveal the Basis for Nk1 Activity and Enable Engineering of Potent Agonists of the met Receptor

Lietha, D.Chirgadze, D.Y.Mulloy, B.Blundell, T.L.Gherardi, E.

(2001) EMBO J 20: 5543

  • DOI: https://doi.org/10.1093/emboj/20.20.5543
  • Primary Citation of Related Structures:  
    1GMN, 1GMO

  • PubMed Abstract: 

    NK1 is a splice variant of the polypeptide growth factor HGF/SF, which consists of the N-terminal (N) and first kringle (K) domain and requires heparan sulfate or soluble heparin for activity. We describe two X-ray crystal structures of NK1-heparin complexes that define a heparin-binding site in the N domain, in which a major role is played by R73, with further contributions from main chain atoms of T61, K63 and G79 and the side chains of K60, T61, R76, K62 and K58. Mutagenesis experiments demonstrate that heparin binding to this site is essential for dimerization in solution and biological activity of NK1. Heparin also comes into contact with a patch of positively charged residues (K132, R134, K170 and R181) in the K domain. Mutation of these residues yields NK1 variants with increased biological activity. Thus, we uncover a complex role for heparan sulfate in which binding to the primary site in the N domain is essential for biological activity whereas binding to the K domain reduces activity. We exploit the interaction between heparin and the K domain site in order to engineer NK1 as a potent receptor agonist and suggest that dual (positive and negative) control may be a general mechanism of heparan sulfate-dependent regulation of growth factor activity.


  • Organizational Affiliation

    Growth Factors Group, MRC Centre, Hills Road, Cambridge CB2 2QH, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HEPATOCYTE GROWTH FACTOR
A, B, C, D, E
A, B, C, D, E, F, G, H
183Homo sapiensMutation(s): 2 
UniProt & NIH Common Fund Data Resources
Find proteins for P14210 (Homo sapiens)
Explore P14210 
Go to UniProtKB:  P14210
PHAROS:  P14210
GTEx:  ENSG00000019991 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP14210
Sequence Annotations
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid
I
6N/A
Glycosylation Resources
GlyTouCan:  G82873VJ
GlyCosmos:  G82873VJ
Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid
J
7N/A
Glycosylation Resources
GlyTouCan:  G07892WL
GlyCosmos:  G07892WL
Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid
K
8N/A
Glycosylation Resources
GlyTouCan:  G22032RS
GlyCosmos:  G22032RS
Entity ID: 5
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose
L
9N/A
Glycosylation Resources
GlyTouCan:  G10608JX
GlyCosmos:  G10608JX
Entity ID: 6
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose
M, N
6N/A
Glycosylation Resources
GlyTouCan:  G30141AL
GlyCosmos:  G30141AL
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
EPE
Query on EPE

Download Ideal Coordinates CCD File 
AA [auth F]
BA [auth G]
DA [auth H]
P [auth A]
R [auth B]
AA [auth F],
BA [auth G],
DA [auth H],
P [auth A],
R [auth B],
T [auth C],
V [auth D],
X [auth E]
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
CA [auth H]
O [auth A]
Q [auth B]
S [auth C]
U [auth D]
CA [auth H],
O [auth A],
Q [auth B],
S [auth C],
U [auth D],
W [auth E],
Y [auth F],
Z [auth F]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.254 
  • R-Value Observed: 0.254 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 179.7α = 90
b = 174.1β = 90
c = 59.9γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-10-02
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2017-07-12
    Changes: Advisory, Atomic model, Derived calculations
  • Version 3.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
  • Version 3.1: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
  • Version 3.2: 2024-11-06
    Changes: Structure summary