9NJW | pdb_00009njw

Structure of ancestral-reconstructed cytochrome P450 11A1 (CYP11A1) in complex with cholesterol

• PDB DOI: https://doi.org/10.2210/pdb9NJW/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2025-02-28 Released: 2025-10-22 
• Deposition Author(s): Chagas, B.C., Wang, P.C., Brixius-Anderko, S.
• Funding Organization(s): Not funded

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.260 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.227 (Depositor), 0.227 (DCC) 
• R-Value Observed: 
  0.230 (Depositor) 

Starting Model: experimental

Literature

How evolution shaped the structure of steroidogenic cytochrome P450 11A.

Chagas, B.C.A., Brixius, B., Wang, P.C., Pirhadi, S., Aziz, O., Koes, D.R., Gillam, E.M.J., Bernhardt, R., Brixius-Anderko, S.

(2025) J Inorg Biochem 274: 113105-113105

• PubMed: 41075759 
• DOI: https://doi.org/10.1016/j.jinorgbio.2025.113105
• Primary Citation of Related Structures:  
  9NJW, 9ONH


• PubMed Abstract: 
  

  The cytochrome P450 enzyme 11A1 (CYP11A1) is the most important player in steroid hormone biosynthesis, catalysing the first and rate-limiting step, the side-chain cleavage of cholesterol to pregnenolone, which provides the precursor for all major steroid hormones. A resurrected ancestral isoform of CYP11A (CYP11A_N1) exhibits different substrate specificities to extant vertebrate CYP11A1 forms which implies an evolutionary change in structural features. Hence, we solved the structure of the resurrected ancestral CYP11A_N1 isoform and identified the major structural changes between ancestral and extant CYP11A isoforms that lead to different catalytic properties for cholesterol metabolism. Our work presents the first structure of an ancestral mitochondrial cytochrome P450 and highlights how structural changes shaped the evolution of steroid hormone biosynthesis.

---

Organizational Affiliation: 
• University of Pittsburgh School of Pharmacy, Pittsburgh, USA.
University of Pittsburgh School of Medicine, Pittsburgh, USA.
School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Australia.
Saarland University, Saarbruecken, Germany.
University of Pittsburgh School of Pharmacy, Pittsburgh, USA. Electronic address: [e-mail].

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 57.35 kDa 
• Atom Count: 3,871 
• Modeled Residue Count: 460 
• Deposited Residue Count: 484 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome P450, CYP11A1	A	484	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM (Subject of Investigation/LOI)	B [auth A]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
CLR (Subject of Investigation/LOI)	C [auth A]	CHOLESTEROL C27 H46 O HVYWMOMLDIMFJA-DPAQBDIFSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.260 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.227 (Depositor), 0.227 (DCC) 
• R-Value Observed: 0.230 (Depositor) 

Space Group: I 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 155.894	α = 90
b = 155.894	β = 90
c = 155.894	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
autoXDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-10-22 
Deposition Author(s): Chagas, B.C., Wang, P.C., Brixius-Anderko, S.

---

Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-10-22
  Type: Initial release