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- PDB-9r0k: Structure of the human heterotetrameric cis-prenyltransferase com... -

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Basic information

Entry
Database: PDB / ID: 9r0k
TitleStructure of the human heterotetrameric cis-prenyltransferase complex in its apo form
Components
  • Dehydrodolichyl diphosphate synthase complex subunit DHDDS
  • Dehydrodolichyl diphosphate synthase complex subunit NUS1
KeywordsTRANSFERASE / cis-prenyltransferase / dolichol
Function / homology
Function and homology information


dolichyl diphosphate biosynthetic process / : / Defective DHDDS causes RP59 / : / dehydrodolichyl diphosphate synthase complex / Synthesis of dolichyl-phosphate / regulation of intracellular cholesterol transport / ditrans,polycis-polyprenyl diphosphate synthase [(2E,6E)-farnesyl diphosphate specific] / ditrans,polycis-polyprenyl diphosphate synthase [(2E,6E)-farnesyl diphosphate specific] activity / polyprenol biosynthetic process ...dolichyl diphosphate biosynthetic process / : / Defective DHDDS causes RP59 / : / dehydrodolichyl diphosphate synthase complex / Synthesis of dolichyl-phosphate / regulation of intracellular cholesterol transport / ditrans,polycis-polyprenyl diphosphate synthase [(2E,6E)-farnesyl diphosphate specific] / ditrans,polycis-polyprenyl diphosphate synthase [(2E,6E)-farnesyl diphosphate specific] activity / polyprenol biosynthetic process / positive regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / positive regulation of cell migration involved in sprouting angiogenesis / vascular endothelial growth factor signaling pathway / : / cholesterol homeostasis / angiogenesis / cell differentiation / endoplasmic reticulum membrane / endoplasmic reticulum / metal ion binding
Similarity search - Function
Dehydrodolichyl diphosphate synthase complex subunit Nus1 / Di-trans-poly-cis-decaprenylcistransferase-like, conserved site / Undecaprenyl pyrophosphate synthase family signature. / Decaprenyl diphosphate synthase-like / Putative undecaprenyl diphosphate synthase / Decaprenyl diphosphate synthase-like superfamily
Similarity search - Domain/homology
GLYCINE / Dehydrodolichyl diphosphate synthase complex subunit DHDDS / Dehydrodolichyl diphosphate synthase complex subunit NUS1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.89 Å
AuthorsGiladi, M. / Haitin, Y.
Funding support Israel, United States, 3items
OrganizationGrant numberCountry
Israel Science Foundation1653/21 Israel
United States - Israel Binational Science Foundation (BSF)2023190 United States
Other privateIsrael Cancer Research Fund 1289067 Israel
CitationJournal: To Be Published
Title: Structural mechanisms of allosteric network regulation in the human cis-prenyltransferase complex
Authors: Giladi, M. / Haitin, Y.
History
DepositionApr 24, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 29, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dehydrodolichyl diphosphate synthase complex subunit DHDDS
B: Dehydrodolichyl diphosphate synthase complex subunit NUS1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,0663
Polymers63,9912
Non-polymers751
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2940 Å2
ΔGint-26 kcal/mol
Surface area23580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)183.346, 183.346, 112.356
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein Dehydrodolichyl diphosphate synthase complex subunit DHDDS / Cis-isoprenyltransferase / Cis-IPTase / Cis-prenyltransferase subunit hCIT / Epididymis tissue protein Li 189m


Mass: 39201.965 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DHDDS, HDS / Production host: Escherichia coli (E. coli)
References: UniProt: Q86SQ9, ditrans,polycis-polyprenyl diphosphate synthase [(2E,6E)-farnesyl diphosphate specific]
#2: Protein Dehydrodolichyl diphosphate synthase complex subunit NUS1 / Cis-prenyltransferase subunit NgBR / Nogo-B receptor / NgBR / Nuclear undecaprenyl pyrophosphate ...Cis-prenyltransferase subunit NgBR / Nogo-B receptor / NgBR / Nuclear undecaprenyl pyrophosphate synthase 1 homolog


Mass: 24789.227 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NUS1, C6orf68, NGBR / Production host: Escherichia coli (E. coli)
References: UniProt: Q96E22, ditrans,polycis-polyprenyl diphosphate synthase [(2E,6E)-farnesyl diphosphate specific]
#3: Chemical ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H5NO2
Has ligand of interestN
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.89 Å3/Da / Density % sol: 57.37 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 9.5
Details: 0.1 M LiCl, 0.05 M Glycine pH 9.5, 40% (v/v) PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Aug 6, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.89→45.858 Å / Num. obs: 16334 / % possible obs: 100 % / Redundancy: 20.6 % / Rrim(I) all: 0.055 / Net I/σ(I): 35.95
Reflection shellResolution: 2.89→3.06 Å / Num. unique obs: 2603 / Rrim(I) all: 1.388

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
PDB_EXTRACTdata extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.89→41.013 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.47 / Phase error: 37.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3021 812 4.98 %
Rwork0.2649 --
obs0.2668 16319 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.89→41.013 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3423 0 4 0 3427
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043508
X-RAY DIFFRACTIONf_angle_d0.6524815
X-RAY DIFFRACTIONf_dihedral_angle_d3.0682331
X-RAY DIFFRACTIONf_chiral_restr0.044562
X-RAY DIFFRACTIONf_plane_restr0.005646
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8903-3.07130.36991350.37422552X-RAY DIFFRACTION100
3.0713-3.30830.40831380.34572583X-RAY DIFFRACTION100
3.3083-3.64110.33331310.31722544X-RAY DIFFRACTION100
3.6411-4.16750.31551300.28512585X-RAY DIFFRACTION100
4.1675-5.24890.30671360.25372588X-RAY DIFFRACTION100
5.2489-41.0130.2711420.23412655X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.12941.0932-0.89571.0119-0.4150.19310.20740.3519-0.8118-0.2706-0.02940.2550.3177-0.3194-0.1390.94850.1275-0.10351.03540.00581.720115.16528.6723-42.0806
23.9215.5937-4.46757.8727-4.33227.1680.31410.7743-1.1352-0.90230.53580.3687-0.1935-0.4682-1.00760.88840.08860.01220.8439-0.03061.442723.506515.3843-44.4919
33.86353.26890.2864.8226-1.05632.14221.86470.3610.7398-1.657-0.9044-1.2862-2.42411.0947-0.56741.4080.21620.30161.02170.441.606930.226124.5776-50.5748
42.23451.44-1.98499.00911.48668.6621-0.1556-0.69051.5974-0.29290.0288-1.635-1.6855-0.2991-0.44940.86090.0966-0.09210.7721-0.09441.750926.175326.4526-37.8599
51.4286-1.8153-0.80515.0743-0.14762.25110.13970.08160.1099-0.0317-0.0873-0.371-0.3083-0.2254-0.04740.66250.0121-0.09850.72130.01591.358228.597712.4155-33.069
61.3651.63773.918-0.24662.22832.6894-0.38731.57210.9531.4343-0.0477-0.11840.18911.0637-0.02741.6382-0.0636-0.49341.1219-0.09241.517233.57182.1885-10.4753
7-1.611-1.87753.62832.6816-9.18048.6161.27160.1702-0.17530.37811.37052.0069-0.0061-0.617-1.45791.9670.0556-0.36910.9322-0.23341.190137.960618.4369-8.7196
83.5625-0.6428-1.09939.3159-2.31783.2864-0.17460.158-0.511-0.7321-0.4942-1.02480.58390.35360.64710.875-0.0481-0.01720.7591-0.11941.148637.7063-17.7259-33.7088
95.5082-0.7406-0.55015.057-1.4070.79730.31-0.06960.87730.3487-0.236-0.94220.18880.4322-0.23720.9480.0333-0.41331.032-0.1061.126545.8259-6.6599-24.0873
103.4704-4.7954-2.49677.72812.06617.85230.1860.2307-0.00430.52350.1045-1.2438-0.05810.0786-0.28950.46870.034-0.13780.663-0.00850.923134.1614-9.1362-36.3781
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 8 through 46 )
2X-RAY DIFFRACTION2chain 'A' and (resid 47 through 86 )
3X-RAY DIFFRACTION3chain 'A' and (resid 87 through 104 )
4X-RAY DIFFRACTION4chain 'A' and (resid 105 through 128 )
5X-RAY DIFFRACTION5chain 'A' and (resid 129 through 250 )
6X-RAY DIFFRACTION6chain 'A' and (resid 251 through 285 )
7X-RAY DIFFRACTION7chain 'A' and (resid 286 through 327 )
8X-RAY DIFFRACTION8chain 'B' and (resid 79 through 141 )
9X-RAY DIFFRACTION9chain 'B' and (resid 142 through 229 )
10X-RAY DIFFRACTION10chain 'B' and (resid 230 through 289 )

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