6QM3

Crystal structure of a calcium- and sodium-bound mouse Olfactomedin-1 disulfide-linked dimer of the Olfactomedin domain and part of coiled coil

• PDB DOI: https://doi.org/10.2210/pdb6QM3/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Mus musculus
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2019-02-01 Released: 2019-09-11 
• Deposition Author(s): Pronker, M.F., van den Hoek, H.G., Janssen, B.J.C.
• Funding Organization(s): Netherlands Organisation for Scientific Research

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.216 
• R-Value Work: 0.179 
• R-Value Observed: 0.181 

Literature

Design and structural characterisation of olfactomedin-1 variants as tools for functional studies.

Pronker, M.F., van den Hoek, H., Janssen, B.J.C.

(2019) BMC Mol Cell Biol 20: 50-50

• PubMed: 31726976 
• DOI: https://doi.org/10.1186/s12860-019-0232-1
• Primary Citation of Related Structures:  
  6QHJ, 6QM3


• PubMed Abstract: 
  

  Olfactomedin-1 (Olfm1; also known as Noelin or Pancortin) is a highly-expressed secreted brain and retina protein and its four isoforms have different roles in nervous system development and function. Structural studies showed that the long Olfm1 isoform BMZ forms a disulfide-linked tetramer with a V-shaped architecture. The tips of the Olfm1 "V" each consist of two C-terminal β-propeller domains that enclose a calcium binding site. Functional characterisation of Olfm1 may be aided by new biochemical tools derived from these core structural elements.

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Organizational Affiliation: 

MRC Laboratory of Molecular Biology, Division of Neurobiology, Francis Crick Avenue, Cambridge, CB2 0QH, UK. [e-mail].

Biological Assembly 1  

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

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

Biological Assembly Evidence: assay for oligomerization

Macromolecule Content

• Total Structure Weight: 65.75 kDa 
• Atom Count: 4,553 
• Modelled Residue Count: 534 
• Deposited Residue Count: 554 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Noelin	A, B	277	Mus musculus	Mutation(s): 0  Gene Names: Olfm1, Noe1, Noel, Noel1
UniProt
Find proteins for O88998 (Mus musculus) Explore O88998  Go to UniProtKB:  O88998

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	C [auth A], D [auth A], E [auth A], F [auth A], L [auth B], M [auth B], N [auth B], O [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
CAC	G [auth A]	CACODYLATE ION C2 H6 As O2 OGGXGZAMXPVRFZ-UHFFFAOYSA-M
ACT	J [auth A], K [auth A], R [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
CA	H [auth A], P [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
NA	I [auth A], Q [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.216 
• R-Value Work: 0.179 
• R-Value Observed: 0.181 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 160.705	α = 90
b = 46.971	β = 117.435
c = 104.952	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
PHENIX	refinement
Aimless	data scaling
PHASER	phasing
Coot	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-09-11 
Deposition Author(s): Pronker, M.F., van den Hoek, H.G., Janssen, B.J.C.

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Funding Organization	Location	Grant Number
Netherlands Organisation for Scientific Research	Netherlands	723.012.002

Revision History  

• Version 1.0: 2019-09-11
  Type: Initial release
  
• Version 1.1: 2019-11-20
  Changes: Database references
• Version 1.2: 2019-11-27
  Changes: Database references
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Database references, Derived calculations, Structure summary
• Version 1.4: 2024-01-24
  Changes: Data collection, Database references, Refinement description, Structure summary