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- PDB-9r0e: Structure of the human heterotetrameric cis-prenyltransferase com... -

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Basic information

Entry
Database: PDB / ID: 9r0e
TitleStructure of the human heterotetrameric cis-prenyltransferase complex harboring NgBR-S249T in complex with magnesium, FsPP and IPP
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
Chem-FPS / 3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE / 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: 2.82 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
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)63,6645
Polymers62,9952
Non-polymers6693
Water00
1
A: Dehydrodolichyl diphosphate synthase complex subunit DHDDS
B: Dehydrodolichyl diphosphate synthase complex subunit NUS1
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)127,32810
Polymers125,9904
Non-polymers1,3386
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_566x-y+2/3,-y+4/3,-z+4/31
Unit cell
Length a, b, c (Å)184.658, 184.658, 112.732
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Space group name HallR32"
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x-y,-y,-z
#5: -x,-x+y,-z
#6: y,x,-z
#7: x+1/3,y+2/3,z+2/3
#8: -y+1/3,x-y+2/3,z+2/3
#9: -x+y+1/3,-x+2/3,z+2/3
#10: x-y+1/3,-y+2/3,-z+2/3
#11: -x+1/3,-x+y+2/3,-z+2/3
#12: y+1/3,x+2/3,-z+2/3
#13: x+2/3,y+1/3,z+1/3
#14: -y+2/3,x-y+1/3,z+1/3
#15: -x+y+2/3,-x+1/3,z+1/3
#16: x-y+2/3,-y+1/3,-z+1/3
#17: -x+2/3,-x+y+1/3,-z+1/3
#18: y+2/3,x+1/3,-z+1/3

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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: 23793.230 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-IPE / 3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE / ISOPENTENYL PYROPHOSPHATE


Mass: 246.092 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12O7P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-FPS / S-[(2E,6E)-3,7,11-TRIMETHYLDODECA-2,6,10-TRIENYL] TRIHYDROGEN THIODIPHOSPHATE / FARNESYL THIOPYROPHOSPHATE


Mass: 398.392 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H28O6P2S / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
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: 2.94 Å3/Da / Density % sol: 58.1 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Hepes pH 8, 30% Pentaerythritol ethoxylate, 4% PVP K15, 30% (w/v) 1,6-Hexanediol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Nov 19, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.82→46.164 Å / Num. obs: 17888 / % possible obs: 99.9 % / Redundancy: 10.4 % / Biso Wilson estimate: 89.76 Å2 / Rrim(I) all: 0.192 / Net I/σ(I): 9.2
Reflection shellResolution: 2.82→2.99 Å / Num. unique obs: 2849 / Rrim(I) all: 2.983

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.82→46.16 Å / SU ML: 0.5743 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 34.606
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2899 887 5.06 %
Rwork0.2399 16634 -
obs0.2425 17521 97.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 90.17 Å2
Refinement stepCycle: LAST / Resolution: 2.82→46.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3854 0 39 0 3893
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053970
X-RAY DIFFRACTIONf_angle_d0.68425404
X-RAY DIFFRACTIONf_chiral_restr0.0415606
X-RAY DIFFRACTIONf_plane_restr0.0057705
X-RAY DIFFRACTIONf_dihedral_angle_d18.12921363
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.82-30.53471300.56222451X-RAY DIFFRACTION87.91
3-3.230.33681490.33542829X-RAY DIFFRACTION99.93
3.23-3.550.33561550.30862795X-RAY DIFFRACTION99.93
3.55-4.070.30271510.23392810X-RAY DIFFRACTION100
4.07-5.120.26191470.19872849X-RAY DIFFRACTION99.97
5.12-46.160.25261550.20272900X-RAY DIFFRACTION99.9
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)
15.722735929853.37073719405-4.517658388276.81965374173-4.980555899254.626033340330.3464114353740.9385353871011.49206657268-0.24803235119-0.1535064351720.000432131148181-1.386735788440.992184794693-0.02892888646180.7886857923380.01845775722620.03687585865991.074251092670.1646453617720.8914373551956.46413913247119.54712698336.2447183585
22.73298060814-0.586357165274-0.4029328281823.49442744548-0.5271057086292.544543223660.02813319485440.07079464486140.7083383993920.142394171724-0.117562006862-0.745536444251-0.4865468147650.3039256521240.06730374636740.393835364886-0.0777496732319-0.07391092404250.4144176005880.1045447554830.70614963467228.5803378502122.71301917937.0671795928
33.475034181420.3901738833341.775061447411.23220338868-1.438292175053.46034160160.155870412401-0.3040510068730.04122623311510.847877467931-0.233970137146-0.211256749238-0.335095724140.3224672951120.01587350825170.8514013523720.0145568360396-0.1184814156510.5964828199-0.03844300793840.57314507461432.5773514614116.06547256159.7276698201
43.36984010949-1.73362974275-0.6491377618496.847049319992.452366105477.58953040959-0.062418272623-0.17901141286-0.1770087547960.62725720977-0.214519351289-0.6072563408461.58991113662-0.1437284268450.05612286179890.8869357085990.0258246936866-0.08037358674840.8498736351660.1653612406420.79272247883837.457545035688.23955872239.0958131013
52.60402444076-1.79065564299-0.809596381796.084627856822.238432914535.52611788422-0.0739464913161-0.954537225339-0.2373717710181.525369331750.502096268063-0.7001432321221.791121410640.67535831839-0.05591263762541.050231743630.106455065859-0.2020124549240.9022433803110.1555922771240.75661552766639.765911902989.862369081950.1840154875
61.117902638281.92873259087-0.1246304668966.743758052222.185673739463.339251100370.3621124009650.0264184822255-0.1590386252530.9733263237650.0239236487662-2.776749454460.4247142653350.577988195418-0.3793180603220.837569073877-0.0548894545969-0.4140046252451.028973453980.09751059779211.2773269646548.0285322007108.58448288250.9462052665
70.1286022363960.755872015981-0.1160179464096.979472869832.097954532662.632540233170.6568972127250.22919699605-0.4348768352460.55475744438-0.1454155802-1.323696636640.4080715752121.23863315228-0.4123321102740.7845086125970.00902235382192-0.1699753575710.9817381369890.1654275484560.82169781646440.1283636038103.98711283542.3893336607
81.91329501189-0.572461730988-0.8792378065895.739928902461.346852488023.872454562450.1044301977140.3912320959370.241892578538-0.08279789349-0.137208639684-0.5141158999320.312131142610.191211914425-0.04081900897260.4596257470350.0125851574385-0.1228328484290.5931556826860.1140044308040.63749943790233.557662331198.331572359835.9585020453
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 0 through 22 )AA0 - 221 - 23
22chain 'A' and (resid 23 through 236 )AA23 - 23624 - 237
33chain 'A' and (resid 237 through 327 )AA237 - 327238 - 328
44chain 'B' and (resid 82 through 127 )BB82 - 1271 - 46
55chain 'B' and (resid 128 through 157 )BB128 - 15747 - 76
66chain 'B' and (resid 158 through 222 )BB158 - 22277 - 121
77chain 'B' and (resid 223 through 249 )BB223 - 249122 - 148
88chain 'B' and (resid 250 through 293 )BB250 - 293149 - 192

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