1BMO | pdb_00001bmo

BM-40, FS/EC DOMAIN PAIR

• PDB DOI: https://doi.org/10.2210/pdb1BMO/pdb

• Classification: EXTRACELLULAR MODULE
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 1997-03-25 Released: 1997-10-15 
• Deposition Author(s): Hohenester, E., Maurer, P., Timpl, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 
  0.322 (Depositor), 0.320 (DCC) 
• R-Value Work: 
  0.262 (Depositor), 0.266 (DCC) 
• R-Value Observed: 
  0.262 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of a pair of follistatin-like and EF-hand calcium-binding domains in BM-40.

Hohenester, E., Maurer, P., Timpl, R.

(1997) EMBO J 16: 3778-3786

• PubMed: 9233787 
• DOI: https://doi.org/10.1093/emboj/16.13.3778
• Primary Citation Related Structures: 
  1BMO


• PubMed Abstract: 
  

  BM-40 (also known as SPARC or osteonectin) is an anti-adhesive secreted glycoprotein involved in tissue remodelling. Apart from an acidic N-terminal segment, BM-40 consists of a follistatin-like (FS) domain and an EF-hand calcium-binding (EC) domain. Here we report the crystal structure at 3.1 A resolution of the FS-EC domain pair of human BM-40. The two distinct domains interact through a small interface that involves the EF-hand pair of the EC domain. Residues implicated in cell binding, inhibition of cell spreading and disassembly of focal adhesions cluster on one face of BM-40, opposite the binding epitope for collagens and the N-linked carbohydrate. The elongated FS domain is structurally related to serine protease inhibitors of the Kazal family. Notable differences are an insertion into the inhibitory loop in BM-40 and a protruding N-terminal beta-hairpin with striking similarities to epidermal growth factor. This hairpin is likely to act as a rigid spacer in proteins containing tandemly repeated FS domains, such as follistatin and agrin, and forms the heparin-binding site in follistatin.

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Organizational Affiliation: 
• Department of Crystallography, Birkbeck College, London, UK.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 55.23 kDa 
• Atom Count: 3,854 
• Modeled Residue Count: 466 
• Deposited Residue Count: 466 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BM-40	A, B	233	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P09486 (Homo sapiens) Explore P09486  Go to UniProtKB:  P09486
PHAROS:  P09486 GTEx:  ENSG00000113140
Glycosylation
Glycosylation Sites: 1		Go to GlyGen: P09486-1

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C, D	2		N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	E [auth A], F [auth A], G [auth B], H [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free:  0.322 (Depositor), 0.320 (DCC) 
• R-Value Work:  0.262 (Depositor), 0.266 (DCC) 
• R-Value Observed: 0.262 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.77	α = 90
b = 56.35	β = 104.38
c = 111.6	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
CCP4	data reduction
Agrovata	data reduction
TRUNCATE	data reduction
MAMA	model building
X-PLOR	model building
X-PLOR	refinement
CCP4	data scaling
TRUNCATE	data scaling
SCALA	data scaling
MAMA	phasing
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1997-10-15 
Deposition Author(s): Hohenester, E., Maurer, P., Timpl, R.

Revision History  

• Version 1.0: 1997-10-15
  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, Refinement description, Structure summary
• Version 2.1: 2021-03-31
  Changes: Source and taxonomy, Structure summary
• Version 2.2: 2023-08-09
  Changes: Advisory, Database references, Refinement description
• Version 2.3: 2024-10-30
  Changes: Data collection, Structure summary