Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 114.59 kDa 
• Atom Count: 7955 
• Modelled Residue Count: 931 
• Deposited Residue Count: 958 
• Unique protein chains: 1

3C6G

Crystal structure of CYP2R1 in complex with vitamin D3

• DOI: 10.2210/pdb3C6G/pdb
• Entry: 3C6G supersedes: 2OJD

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-02-04 Released: 2008-02-19 
• Deposition Author(s): Strushkevich, N.V., Min, J., Loppnau, P., Tempel, W., Arrowsmith, C.H., Edwards, A.M., Sundstrom, M., Weigelt, J., Bochkarev, A., Plotnikov, A.N., Park, H., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.231 
• R-Value Work: 0.193 
• R-Value Observed: 0.195 

Literature

Structural analysis of CYP2R1 in complex with vitamin D3.

Strushkevich, N., Usanov, S.A., Plotnikov, A.N., Jones, G., Park, H.W.

(2008) J Mol Biol 380: 95-106

• PubMed: 18511070 
• DOI: 10.1016/j.jmb.2008.03.065
• Primary Citation of Related Structures:  
  3C6G


• PubMed Abstract: 
  

The activation of vitamin D to its hormonal form is mediated by cytochrome P450 enzymes. CYP2R1 catalyzes the initial step converting vitamin D into 25-hydroxyvitamin D. A CYP2R1 gene mutation causes an inherited form of rickets due to 25-hydroxylase deficiency. To understand the narrow substrate specificity of CYP2R1 we obtained the hemeprotein in a highly purified state, confirmed the enzyme as a vitamin D 25-hydroxylase, and solved the crystal structure of CYP2R1 in complex with vitamin D3. The CYP2R1 structure adopts a closed conformation with the substrate access channel being covered by the ordered B'-helix and slightly opened to the surface, which defines the substrate entrance point. The active site is lined by conserved, mostly hydrophobic residues. Vitamin D3 is bound in an elongated conformation with the aliphatic side-chain pointing toward the heme. The structure reveals the secosteroid binding mode in an extended active site and allows rationalization of the molecular basis of the inherited rickets associated with CYP2R1.

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Organizational Affiliation: 

Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome P450 2R1	A, B	479	Homo sapiens	Mutation(s): 0  Gene Names: CYP2R1 EC: 1.14.14 (PDB Primary Data), 1.14.14.24 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q6VVX0 (Homo sapiens) Explore Q6VVX0  Go to UniProtKB:  Q6VVX0
PHAROS:  Q6VVX0 GTEx:  ENSG00000186104

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
Cycloheptakis-(1-4)-(alpha-D-glucopyranose)	C, D	7		N/A
Glycosylation Resources
GlyTouCan:  G01435GL GlyCosmos:  G01435GL

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	H [auth A], N [auth B]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
VD3	I [auth A], O [auth B]	(1S,3Z)-3-[(2E)-2-[(1R,3AR,7AS)-7A-METHYL-1-[(2R)-6-METHYLHEPTAN-2-YL]-2,3,3A,5,6,7-HEXAHYDRO-1H-INDEN-4-YLIDENE]ETHYLI DENE]-4-METHYLIDENE-CYCLOHEXAN-1-OL C27 H44 O QYSXJUFSXHHAJI-RWDMXNMGSA-N
UNX	E [auth A], F [auth A], G [auth A], J [auth B], K [auth B], L [auth B], M [auth B]	UNKNOWN ATOM OR ION X

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900012	C, D	beta-cyclodextrin	Oligosaccharide /  Drug delivery		Ligand Interaction

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.231 
• R-Value Work: 0.193 
• R-Value Observed: 0.195 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 137.68	α = 90
b = 163.051	β = 90
c = 152.755	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2008-02-04 
• Released Date: 2008-02-19 
Deposition Author(s): Strushkevich, N.V., Min, J., Loppnau, P., Tempel, W., Arrowsmith, C.H., Edwards, A.M., Sundstrom, M., Weigelt, J., Bochkarev, A., Plotnikov, A.N., Park, H., Structural Genomics Consortium (SGC)
• This entry supersedes: 2OJD

Revision History  

• Version 1.0: 2008-02-19
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary