2IFG

Structure of the extracellular segment of human TRKA in complex with nerve growth factor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 0.331 
  • R-Value Work: 0.297 
  • R-Value Observed: 0.297 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Structural and mechanistic insights into nerve growth factor interactions with the TrkA and p75 receptors.

Wehrman, T.He, X.Raab, B.Dukipatti, A.Blau, H.Garcia, K.C.

(2007) Neuron 53: 25-38

  • DOI: 10.1016/j.neuron.2006.09.034
  • Primary Citation of Related Structures:  
    2IFG

  • PubMed Abstract: 
  • Nerve growth factor engages two structurally distinct transmembrane receptors, TrkA and p75, which have been proposed to create a "high-affinity" NGF binding site through formation of a ternary TrkA/NGF/p75 complex. To define a structural basis for the high-affinity site, we have determined the three-dimensional structure of a complete extracellular domain of TrkA complexed with NGF ...

    Nerve growth factor engages two structurally distinct transmembrane receptors, TrkA and p75, which have been proposed to create a "high-affinity" NGF binding site through formation of a ternary TrkA/NGF/p75 complex. To define a structural basis for the high-affinity site, we have determined the three-dimensional structure of a complete extracellular domain of TrkA complexed with NGF. The complex reveals a crab-shaped homodimeric TrkA structure, but a mechanism for p75 coordination is not obvious. We investigated the heterodimerization of membrane-bound TrkA and p75, on intact mammalian cells, using a beta-gal protein-protein interaction system. We find that NGF dimerizes TrkA and that p75 exists on the cell surface as a preformed oligomer that is not dissociated by NGF. We find no evidence for a direct TrkA/p75 interaction. We propose that TrkA and p75 likely communicate through convergence of downstream signaling pathways and/or shared adaptor molecules, rather than through direct extracellular interactions.


    Organizational Affiliation

    Baxter Laboratory for Genetic Pharmacology, Department of Microbiology and Immunology, The Stem Cell Institute, Stanford University School of Medicine, Stanford, CA 94305, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
High affinity nerve growth factor receptorA, B347Homo sapiensMutation(s): 0 
Gene Names: NTRK1TRKMTCTRKA
EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for P04629 (Homo sapiens)
Explore P04629 
Go to UniProtKB:  P04629
PHAROS:  P04629
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-nerve growth factorC [auth E], D [auth F]120Homo sapiensMutation(s): 0 
Gene Names: NGFBNGF
UniProt & NIH Common Fund Data Resources
Find proteins for P01138 (Homo sapiens)
Explore P01138 
Go to UniProtKB:  P01138
PHAROS:  P01138
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 3
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseE [auth C], K2N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G07375KG
GlyCosmos:  G07375KG
GlyGen:  G07375KG
Entity ID: 4
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseF [auth D], I, L, O3N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G52260VY
GlyCosmos:  G52260VY
GlyGen:  G52260VY
Entity ID: 5
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseG, H, J, M, N, P3N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G35926TG
GlyCosmos:  G35926TG
GlyGen:  G35926TG
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
NGF PDBBind:  2IFG Kd: 0.9 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 0.331 
  • R-Value Work: 0.297 
  • R-Value Observed: 0.297 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 110.215α = 90
b = 81.681β = 104.15
c = 115.748γ = 90
Software Package:
Software NamePurpose
MOLREPphasing
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

  • Deposited Date: 2006-09-20 
  • Released Date: 2007-02-13 
  • Deposition Author(s): He, X., Garcia, K.C.

Revision History  (Full details and data files)

  • Version 1.0: 2007-02-13
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary