Biological Assembly 1  

 3D View: Structure | Electron Density

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 1 assigned by authors and generated by PISA,PQS (software)

Macromolecule Content

• Total Structure Weight: 39.34 kDa 
• Atom Count: 2559 
• Residue Count: 311 
• Unique protein chains: 2

1M4U

Crystal structure of Bone Morphogenetic Protein-7 (BMP-7) in complex with the secreted antagonist Noggin

• DOI: 10.2210/pdb1M4U/pdb

• Classification: HORMONE/GROWTH FACTOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli, Cricetulus griseus
• Mutation(s): No 


• Deposited: 2002-07-03 Released: 2002-12-18 
• Deposition Author(s): Groppe, J., Greenwald, J., Wiater, E., Rodriguez-Leon, J., Economides, A.N., Kwiatkowski, W., Affolter, M., Vale, W.W., Izpisua-Belmonte, J.C., Choe, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.42 Å
• R-Value Free: 0.273 
• R-Value Work: 0.241 
• R-Value Observed: 0.242 

Literature

Structural Basis of BMP Signalling Inhibition by the Cystine Knot Protein Noggin

Groppe, J., Greenwald, J., Wiater, E., Rodriguez-Leon, J., Economides, A.N., Kwiatkowski, W., Affolter, M., Vale, W.W., Izpisua-Belmonte, J.C., Choe, S.

(2002) Nature 420: 636-642

• PubMed: 12478285 
• DOI: 10.1038/nature01245
• Primary Citation of Related Structures:  
  1M4U


• PubMed Abstract: 
  

The interplay between bone morphogenetic proteins (BMPs) and their antagonists governs developmental and cellular processes as diverse as establishment of the embryonic dorsal-ventral axis, induction of neural tissue, formation of joints in the skeletal system and neurogenesis in the adult brain. So far, the three-dimensional structures of BMP antagonists and the structural basis for inactivation have remained unknown. Here we report the crystal structure of the antagonist Noggin bound to BMP-7, which shows that Noggin inhibits BMP signalling by blocking the molecular interfaces of the binding epitopes for both type I and type II receptors. The BMP-7-binding affinity of site-specific variants of Noggin is correlated with alterations in bone formation and apoptosis in chick limb development, showing that Noggin functions by sequestering its ligand in an inactive complex. The scaffold of Noggin contains a cystine (the oxidized form of cysteine) knot topology similar to that of BMPs; thus, ligand and antagonist seem to have evolved from a common ancestral gene.

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Related Citations: 

• Three-dimensional structure of recombinant human osteogenic protein 1: Structural paradigm for the transforming growth factor beta superfamily
  Griffith, D.L., Keck, P.C., Sampath, T.K., Rueger, D.C., Carlson, W.D.
  (1996) Proc Natl Acad Sci U S A 93: 878

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Organizational Affiliation: 

Structural Biology, Salk Institute, 10010 North Torrey Pines Road, La Jolla, California 92037, USA.

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Noggin	A	206	Homo sapiens	Mutation(s): 0  Gene Names: NOG
Find proteins for Q13253 (Homo sapiens) Explore Q13253  Go to UniProtKB:  Q13253
NIH Common Fund Data Resources
PHAROS  Q13253 GTEx  ENSG00000183691

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bone Morphogenetic Protein-7	L	139	Homo sapiens	Mutation(s): 0  Gene Names: BMP7, OP1
Find proteins for P18075 (Homo sapiens) Explore P18075  Go to UniProtKB:  P18075
NIH Common Fund Data Resources
PHAROS  P18075 GTEx  ENSG00000101144

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Chain Length	2D Diagram
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B	2

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.42 Å
• R-Value Free: 0.273 
• R-Value Work: 0.241 
• R-Value Observed: 0.242 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.834	α = 90
b = 99.834	β = 90
c = 150.327	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
TRUNCATE	data reduction
MLPHARE	phasing
REFMAC	refinement
HKL-2000	data reduction
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2002-07-03 
• Released Date: 2002-12-18 
Deposition Author(s): Groppe, J., Greenwald, J., Wiater, E., Rodriguez-Leon, J., Economides, A.N., Kwiatkowski, W., Affolter, M., Vale, W.W., Izpisua-Belmonte, J.C., Choe, S.

Revision History 

• Version 1.0: 2002-12-18
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary