1SGF | pdb_00001sgf

CRYSTAL STRUCTURE OF 7S NGF: A COMPLEX OF NERVE GROWTH FACTOR WITH FOUR BINDING PROTEINS (SERINE PROTEINASES)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.15 Å
  • R-Value Free: 
    0.282 (Depositor) 
  • R-Value Work: 
    0.246 (Depositor), 0.230 (DCC) 
  • R-Value Observed: 
    0.246 (Depositor) 

Starting Models: experimental
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Ligand Structure Quality Assessment 

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Literature

Structure of mouse 7S NGF: a complex of nerve growth factor with four binding proteins.

Bax, B.Blundell, T.L.Murray-Rust, J.McDonald, N.Q.

(1997) Structure 5: 1275-1285

  • DOI: https://doi.org/10.1016/s0969-2126(97)00280-3
  • Primary Citation of Related Structures:  
    1SGF

  • PubMed Abstract: 

    Nerve growth factor (NGF) is a neurotrophic factor that promotes the differentiation and survival of certain populations of neurons in the central and peripheral nervous systems. 7S NGF is an alpha 2 beta 2 gamma 2 complex in which the beta-NGF dimer (the active neurotrophin) is associated with two alpha-NGF and two gamma-NGF subunits, which belong to the glandular kallikrein family of serine proteinases. The gamma-NGF subunit is an active serine proteinase capable of processing the precursor form of beta-NGF, whereas alpha-NGF is an inactive serine proteinase. The structure of 7S NGF could be used as a starting point to design inhibitors that prevent NGF binding to its receptors, as a potential treatment of neurodegenerative diseases. The crystal structure of 7S NGF shows that the two gamma-NGF subunits make extensive interactions with each other around the twofold axis of the complex and have the C-terminal residues of the beta-NGF subunits bound within their active sites. The 'activation domain' of each of the alpha-NGF subunits is in an inactive (zymogen-like) conformation and makes extensive interactions with the beta-NGF dimer. The two zinc ions that stabilize the complex are located at the relatively small interfaces between the alpha-NGF and gamma-NGF subunits. The structure of 7S NGF shows how the twofold axis of the central beta-NGF dimer organizes the symmetry of this multisubunit growth factor complex. The extensive surface of beta-NGF buried within the 7S complex explains the lack of neurotrophic activity observed for 7S NGF. The regions of the beta-NGF dimer that contact the alpha-NGF subunits overlap with those known to engage NGF receptors. Two disulphide-linked loops on alpha-NGF make multiple interactions with beta-NGF and suggest that it might be possible to design peptides that inhibit the binding of beta-NGF to its receptors.


  • Organizational Affiliation

    Department of Crystallography, Birkbeck College, London, UK. b.bax@cryst.bbk.ac.uk


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NERVE GROWTH FACTORA,
D [auth X]
240Mus musculusMutation(s): 0 
EC: 3.4.21.35
UniProt
Find proteins for P00757 (Mus musculus)
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Go to UniProtKB:  P00757
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00757
Glycosylation
Glycosylation Sites: 1Go to GlyGen: P00757-1
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
NERVE GROWTH FACTORB,
E [auth Y]
118Mus musculusMutation(s): 0 
EC: 3.4.21.35
UniProt
Find proteins for P01139 (Mus musculus)
Explore P01139 
Go to UniProtKB:  P01139
Entity Groups  
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UniProt GroupP01139
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
NERVE GROWTH FACTORC [auth G],
F [auth Z]
237Mus musculusMutation(s): 0 
EC: 3.4.21.35
UniProt
Find proteins for P00756 (Mus musculus)
Explore P00756 
Go to UniProtKB:  P00756
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00756
Glycosylation
Glycosylation Sites: 1Go to GlyGen: P00756-1
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseG [auth C],
H [auth D]
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.15 Å
  • R-Value Free:  0.282 (Depositor) 
  • R-Value Work:  0.246 (Depositor), 0.230 (DCC) 
  • R-Value Observed: 0.246 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 95.68α = 90
b = 96.59β = 90
c = 147γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
ROTAVATA/AGROVATAdata reduction
TFFCmodel building
X-PLORmodel building
X-PLORrefinement
CCP4data scaling
ROTAVATAdata scaling
TFFCphasing
X-PLORphasing

Structure Validation

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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted NAGClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1998-05-27
    Type: Initial release
  • Version 1.1: 2008-03-24
    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, Non-polymer description, Refinement description, Structure summary
  • Version 2.1: 2023-08-09
    Changes: Database references, Refinement description, Structure summary
  • Version 2.2: 2024-11-13
    Changes: Data collection, Structure summary