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- PDB-7pb0: Structure of the human heterotetrameric cis-prenyltransferase com... -

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Basic information

Entry
Database: PDB / ID: 7pb0
TitleStructure of the human heterotetrameric cis-prenyltransferase complex in complex with magnesium, GGsPP and IsPP
Components(Dehydrodolichyl diphosphate synthase complex subunit ...) x 2
KeywordsTRANSFERASE / DHDDS / NgBR / hcit / 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. / Undecaprenyl pyrophosphate synthetase / Decaprenyl diphosphate synthase-like / Decaprenyl diphosphate synthase-like / Putative undecaprenyl diphosphate synthase / Decaprenyl diphosphate synthase-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-GGS / Chem-ISY / 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: 2.301 Å
AuthorsGiladi, M. / Lisnyansky Bar-El, M. / Haitin, Y.
Funding support Israel, 7items
OrganizationGrant numberCountry
Other privateICRF-19202 Israel
Israel Science Foundation1721/16 Israel
Other privateRecanati Foundation for Medical Research Israel
German-Israeli Foundation for Research and DevelopmentI2425418.13/2016 Israel
Other governmentICORE-1775/12 Israel
Other privateTel Aviv Sourasky Medical Center Orion Project Israel
Other privateICA-20200037 Israel
CitationJournal: Sci Adv / Year: 2022
Title: Structural basis for long-chain isoprenoid synthesis by cis -prenyltransferases.
Authors: Giladi, M. / Lisnyansky Bar-El, M. / Vankova, P. / Ferofontov, A. / Melvin, E. / Alkaderi, S. / Kavan, D. / Redko, B. / Haimov, E. / Wiener, R. / Man, P. / Haitin, Y.
History
DepositionJul 30, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 1, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)64,1675
Polymers63,4142
Non-polymers7533
Water2,342130
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)128,33310
Polymers126,8274
Non-polymers1,5066
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_566x-y+2/3,-y+4/3,-z+4/31
Buried area10270 Å2
ΔGint-65 kcal/mol
Surface area43610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)185.119, 185.119, 113.062
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-553-

HOH

21A-584-

HOH

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Components

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Dehydrodolichyl diphosphate synthase complex subunit ... , 2 types, 2 molecules AB

#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: 24211.598 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]

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Non-polymers , 4 types, 133 molecules

#3: Chemical ChemComp-ISY / 3-methylbut-3-enylsulfanyl(phosphonooxy)phosphinic acid / Isopentyl S-Thiolodiphosphate


Mass: 262.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12O6P2S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GGS / phosphonooxy-[(10E)-3,7,11,15-tetramethylhexadeca-2,6,10,14-tetraenyl]sulfanyl-phosphinic acid


Mass: 466.509 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H36O6P2S / 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
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 58.16 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1 M KCl, 0.1 M MES, 36% w/v PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 13, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→46.2 Å / Num. obs: 32739 / % possible obs: 99.3 % / Redundancy: 4.4 % / CC1/2: 0.995 / Rrim(I) all: 0.14 / Net I/σ(I): 8.23
Reflection shellResolution: 2.3→2.44 Å / Mean I/σ(I) obs: 1.4 / Num. unique obs: 5106 / CC1/2: 0.547 / Rrim(I) all: 1.112

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6Z1N

6z1n


Resolution: 2.301→46.198 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.41 / Phase error: 25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2375 2013 6.15 %
Rwork0.1906 --
obs0.1934 32737 99.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.301→46.198 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3942 0 44 130 4116
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044061
X-RAY DIFFRACTIONf_angle_d0.6915522
X-RAY DIFFRACTIONf_dihedral_angle_d6.5572415
X-RAY DIFFRACTIONf_chiral_restr0.042628
X-RAY DIFFRACTIONf_plane_restr0.003713
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3012-2.35870.34211340.28632054X-RAY DIFFRACTION93
2.3587-2.42250.3071410.27552172X-RAY DIFFRACTION100
2.4225-2.49380.31491450.25492185X-RAY DIFFRACTION100
2.4938-2.57430.31341450.24792203X-RAY DIFFRACTION100
2.5743-2.66630.28741440.23422176X-RAY DIFFRACTION100
2.6663-2.7730.25881480.21952192X-RAY DIFFRACTION100
2.773-2.89920.29931510.2192201X-RAY DIFFRACTION100
2.8992-3.0520.27431410.21372196X-RAY DIFFRACTION100
3.052-3.24320.26961520.21172208X-RAY DIFFRACTION100
3.2432-3.49350.25741380.19642191X-RAY DIFFRACTION100
3.4935-3.84490.22861400.17142215X-RAY DIFFRACTION100
3.8449-4.40090.18191510.15182206X-RAY DIFFRACTION99
4.4009-5.54320.20391440.15372230X-RAY DIFFRACTION100
5.5432-46.1980.19141390.17392295X-RAY DIFFRACTION99
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)
16.58650.1272-1.30382.4769-4.37527.9313-0.2350.3390.751-0.06620.2605-0.0139-0.5624-0.20160.08470.32050.0161-0.03120.35650.01950.40762.4182115.384238.4453
22.98170.2159-1.34431.6470.2753.23550.15360.42940.6484-0.1614-0.04-0.2342-0.3663-0.1392-0.09110.32860.0055-0.00920.34690.15280.423125.1507124.65830.7115
31.4291-0.01350.41941.617-0.53391.80580.0054-0.00410.42610.2147-0.145-0.3615-0.28740.14180.10650.3184-0.0571-0.06880.3230.05620.447232.0436121.45543.1234
44.1725-0.34344.9810.3149-0.22936.9253-0.0129-0.162-0.0660.22850.0815-0.00110.1742-0.1646-0.1080.3476-0.00070.00090.37080.03750.307826.8719108.919955.9293
52.2923-2.04711.31815.5536-4.533.6657-0.48330.00290.60850.2483-0.238-0.2525-0.5049-0.16940.77690.6447-0.061-0.19440.2924-0.04020.560540.2505124.617767.4899
64.1656-2.2042-1.40735.20182.51832.6206-0.1416-0.0157-0.18930.0928-0.1405-0.10.79970.10490.33680.45620.0170.03860.40940.11230.373138.121989.104337.0092
71.725-0.64470.67652.4296-0.23283.48130.1357-0.2364-0.03110.04590.0975-0.24620.60630.0996-0.17080.40650.027-0.0610.4090.07390.292339.74487.676947.4273
80.7023-0.24360.99731.35020.39581.94-0.13480.19290.58290.3279-0.0404-0.9642-0.11980.49380.07990.3282-0.0663-0.07890.55510.11410.637149.4567108.990950.6311
90.5889-0.7138-0.12243.151-0.4271.96820.00410.16050.032-0.1153-0.0301-0.0520.20020.02950.06070.2576-0.0011-0.0390.40970.05690.306234.599999.176337.9032
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 7 through 22 )
2X-RAY DIFFRACTION2chain 'A' and (resid 23 through 128 )
3X-RAY DIFFRACTION3chain 'A' and (resid 129 through 236 )
4X-RAY DIFFRACTION4chain 'A' and (resid 237 through 282 )
5X-RAY DIFFRACTION5chain 'A' and (resid 283 through 327 )
6X-RAY DIFFRACTION6chain 'B' and (resid 80 through 113 )
7X-RAY DIFFRACTION7chain 'B' and (resid 114 through 176 )
8X-RAY DIFFRACTION8chain 'B' and (resid 177 through 229 )
9X-RAY DIFFRACTION9chain 'B' and (resid 230 through 293 )

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