1SGF

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

PDB DOI: https://doi.org/10.2210/pdb1SGF/pdb

Classification: GROWTH FACTOR
Organism(s): Mus musculus
Mutation(s): No

Deposited: 1997-08-08 Released: 1998-05-27
Deposition Author(s): Bax, B.D.V., Blundell, T.L., Murray-Rust, J., Mcdonald, N.Q.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.15 Å
R-Value Free: 0.282
R-Value Work: 0.246
R-Value Observed: 0.246

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

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

PubMed: 9351801 Search on PubMed
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.

Organizational Affiliation

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

Macromolecule Content

Total Structure Weight: 134.41 kDa
Atom Count: 8,549
Modelled Residue Count: 1,089
Deposited Residue Count: 1,190
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NERVE GROWTH FACTOR	A, D [auth X]	240	Mus musculus	Mutation(s): 0 EC: 3.4.21.35
UniProt
Find proteins for P00757 (Mus musculus) Explore P00757 Go to UniProtKB: P00757
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00757
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
NERVE GROWTH FACTOR	B, E [auth Y]	118	Mus musculus	Mutation(s): 0 EC: 3.4.21.35
UniProt
Find proteins for P01139 (Mus musculus) Explore P01139 Go to UniProtKB: P01139
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P01139
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
NERVE GROWTH FACTOR	C [auth G], F [auth Z]	237	Mus musculus	Mutation(s): 0 EC: 3.4.21.35
UniProt
Find proteins for P00756 (Mus musculus) Explore P00756 Go to UniProtKB: P00756
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00756
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	G [auth C], H [auth D]	2		N-Glycosylation	Interactions Focus chain G [auth C] Focus chain H [auth D] Interactions & Density Focus chain G [auth C] Focus chain H [auth D]
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain K [auth X] MOL2 format, chain I [auth A] MOL2 format, chain K [auth X]	I [auth A], K [auth X]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain I [auth A] Focus chain K [auth X] Interactions & Density Focus chain I [auth A] Focus chain K [auth X]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain L [auth X] MOL2 format, chain J [auth A] MOL2 format, chain L [auth X]	J [auth A], L [auth X]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain L [auth X] Interactions & Density Focus chain J [auth A] Focus chain L [auth X]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.15 Å
R-Value Free: 0.282
R-Value Work: 0.246
R-Value Observed: 0.246
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.68	α = 90
b = 96.59	β = 90
c = 147	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
ROTAVATA/AGROVATA	data reduction
TFFC	model building
X-PLOR	model building
X-PLOR	refinement
CCP4	data scaling
ROTAVATA	data scaling
TFFC	phasing
X-PLOR	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 1998-05-27

Deposition Author(s):

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