9R08 | pdb_00009r08

Structure of the human heterotetrameric cis-prenyltransferase complex harboring NgBR-S249A in complex with magnesium, FsPP and IPP

• PDB DOI: https://doi.org/10.2210/pdb9R08/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2025-04-24 Released: 2025-10-29 
• Deposition Author(s): Giladi, M., Haitin, Y.
• Funding Organization(s): Israel Science Foundation, United States - Israel Binational Science Foundation (BSF), Other private

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.241 (Depositor), 0.241 (DCC) 
• R-Value Work: 
  0.196 (Depositor), 0.197 (DCC) 
• R-Value Observed: 
  0.198 (Depositor) 

Starting Model: experimental

Literature

Structural mechanisms of allosteric network regulation in the human cis-prenyltransferase complex

Giladi, M., Haitin, Y.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

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

Biological Assembly Evidence: mass spectrometry

Macromolecule Content 

• Total Structure Weight: 64.64 kDa 
• Atom Count: 4,197 
• Modeled Residue Count: 529 
• Deposited Residue Count: 562 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dehydrodolichyl diphosphate synthase complex subunit DHDDS	A	340	Homo sapiens	Mutation(s): 0  Gene Names: DHDDS, HDS EC: 2.5.1.87
UniProt & NIH Common Fund Data Resources
Find proteins for Q86SQ9 (Homo sapiens) Explore Q86SQ9  Go to UniProtKB:  Q86SQ9
PHAROS:  Q86SQ9 GTEx:  ENSG00000117682

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Dehydrodolichyl diphosphate synthase complex subunit NUS1	B	222	Homo sapiens	Mutation(s): 1  Gene Names: NUS1, C6orf68, NGBR EC: 2.5.1.87
UniProt & NIH Common Fund Data Resources
Find proteins for Q96E22 (Homo sapiens) Explore Q96E22  Go to UniProtKB:  Q96E22
PHAROS:  Q96E22 GTEx:  ENSG00000153989

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FPS (Subject of Investigation/LOI)	D [auth A]	S-[(2E,6E)-3,7,11-TRIMETHYLDODECA-2,6,10-TRIENYL] TRIHYDROGEN THIODIPHOSPHATE C15 H28 O6 P2 S MYMLCRQRXFRQGP-YFVJMOTDSA-N
IPE (Subject of Investigation/LOI)	C [auth A]	3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE C5 H12 O7 P2 NUHSROFQTUXZQQ-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)	E [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.241 (Depositor), 0.241 (DCC) 
• R-Value Work:  0.196 (Depositor), 0.197 (DCC) 
• R-Value Observed: 0.198 (Depositor) 

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 184.399	α = 90
b = 184.399	β = 90
c = 112.575	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-10-29 
Deposition Author(s): Giladi, M., Haitin, Y.

---

Funding Organization	Location	Grant Number
Israel Science Foundation	Israel	1653/21
United States - Israel Binational Science Foundation (BSF)	United States	2023190
Other private		Israel Cancer Research Fund 1289067

Revision History  

• Version 1.0: 2025-10-29
  Type: Initial release