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 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 2.1 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: https://doi.org/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. 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)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
High affinity nerve growth factor receptor
A, B
347Homo sapiensMutation(s): 0 
Gene Names: NTRK1TRK
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
GTEx:  ENSG00000198400 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04629
Glycosylation
Glycosylation Sites: 6Go to GlyGen: P04629-1
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-nerve growth factorC [auth E],
D [auth F]
120Homo sapiensMutation(s): 0 
Gene Names: NGFB
UniProt & NIH Common Fund Data Resources
Find proteins for P01138 (Homo sapiens)
Explore P01138 
Go to UniProtKB:  P01138
PHAROS:  P01138
GTEx:  ENSG00000134259 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01138
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

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Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseE [auth C],
K
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G07375KG
GlyCosmos:  G07375KG
GlyGen:  G07375KG
Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D 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,
O
3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G52260VY
GlyCosmos:  G52260VY
GlyGen:  G52260VY
Entity ID: 5
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
G, H, J, M, N
G, H, J, M, N, P
3N-Glycosylation
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

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Entry History 

Deposition Data

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
  • Version 2.1: 2023-08-30
    Changes: Data collection, Database references, Refinement description, Structure summary