3KQ4

Structure of Intrinsic Factor-Cobalamin bound to its receptor Cubilin

• PDB DOI:  https://doi.org/10.2210/pdb3KQ4/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Homo sapiens
• Expression System: Komagataella pastoris, Cricetulus griseus
• Mutation(s): No 


• Deposited: 2009-11-17 Released: 2010-03-09 
• Deposition Author(s): Andersen, C.B.F., Madsen, M., Moestrup, S.K., Andersen, G.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.30 Å
• R-Value Free: 0.242 
• R-Value Work: 0.211 
• R-Value Observed: 0.211 

Literature

Structural basis for receptor recognition of vitamin-B(12)-intrinsic factor complexes.

Andersen, C.B., Madsen, M., Storm, T., Moestrup, S.K., Andersen, G.R.

(2010) Nature 464: 445-448

• PubMed: 20237569 
• DOI: https://doi.org/10.1038/nature08874
• Primary Citation of Related Structures:  
  3KQ4


• PubMed Abstract: 
  

Cobalamin (Cbl, vitamin B(12)) is a bacterial organic compound and an essential coenzyme in mammals, which take it up from the diet. This occurs by the combined action of the gastric intrinsic factor (IF) and the ileal endocytic cubam receptor formed by the 460-kilodalton (kDa) protein cubilin and the 45-kDa transmembrane protein amnionless. Loss of function of any of these proteins ultimately leads to Cbl deficiency in man. Here we present the crystal structure of the complex between IF-Cbl and the cubilin IF-Cbl-binding-region (CUB(5-8)) determined at 3.3 A resolution. The structure provides insight into how several CUB (for 'complement C1r/C1s, Uegf, Bmp1') domains collectively function as modular ligand-binding regions, and how two distant CUB domains embrace the Cbl molecule by binding the two IF domains in a Ca(2+)-dependent manner. This dual-point model provides a probable explanation of how Cbl indirectly induces ligand-receptor coupling. Finally, the comparison of Ca(2+)-binding CUB domains and the low-density lipoprotein (LDL) receptor-type A modules suggests that the electrostatic pairing of a basic ligand arginine/lysine residue with Ca(2+)-coordinating acidic aspartates/glutamates is a common theme of Ca(2+)-dependent ligand-receptor interactions.

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Organizational Affiliation: 

Department of Medical Biochemistry, Aarhus University, 8000 Aarhus C, Denmark.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 299.19 kDa 
• Atom Count: 20,793 
• Modelled Residue Count: 2,526 
• Deposited Residue Count: 2,550 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Gastric intrinsic factor	A, C, E	393	Homo sapiens	Mutation(s): 0  Gene Names: GIF, IFMH, CBLIF
UniProt & NIH Common Fund Data Resources
Find proteins for P27352 (Homo sapiens) Explore P27352  Go to UniProtKB:  P27352
PHAROS:  P27352

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cubilin	B, D, F	457	Homo sapiens	Mutation(s): 0  Gene Names: CUBN, IFCR
UniProt & NIH Common Fund Data Resources
Find proteins for O60494 (Homo sapiens) Explore O60494  Go to UniProtKB:  O60494
PHAROS:  O60494

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	G, H, J, K, M, N	5		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G22768VO GlyCosmos:  G22768VO GlyGen:  G22768VO

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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
B12	CA [auth C], OA [auth E], Q [auth A]	COBALAMIN C62 H89 Co N13 O14 P LKVIQTCSMMVGFU-DWSMJLPVSA-N
NAG	BA [auth C], DA [auth D], EA [auth D], FA [auth D], GA [auth D], HA [auth D], IA [auth D], NA [auth E], P [auth A], PA [auth F], QA [auth F], R [auth B], RA [auth F], S [auth B], SA [auth F], T [auth B], TA [auth F], U [auth B], UA [auth F], V [auth B], W [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
CA	AA [auth B], JA [auth D], KA [auth D], LA [auth D], MA [auth D], VA [auth F], WA [auth F], X [auth B], XA [auth F], Y [auth B], YA [auth F], Z [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.30 Å
• R-Value Free: 0.242 
• R-Value Work: 0.211 
• R-Value Observed: 0.211 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 117.684	α = 90
b = 204.179	β = 90
c = 410.023	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-03-09 
Deposition Author(s): Andersen, C.B.F., Madsen, M., Moestrup, S.K., Andersen, G.R.

Revision History  

• Version 1.0: 2010-03-09
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2012-10-24
  Changes: Non-polymer description
• Version 1.3: 2018-03-07
  Changes: Advisory, Data collection
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary