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- PDB-7pb1: Structure of the human heterotetrameric cis-prenyltransferase com... -

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Basic information

Entry
Database: PDB / ID: 7pb1
TitleStructure of the human heterotetrameric cis-prenyltransferase complex in complex with magnesium, GGPP 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
GERANYLGERANYL DIPHOSPHATE / 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: 2.59 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)64,1505
Polymers63,4142
Non-polymers7373
Water362
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)128,30110
Polymers126,8274
Non-polymers1,4746
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation1
Unit cell
Length a, b, c (Å)183.470, 183.470, 112.290
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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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, 5 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GRG / GERANYLGERANYL DIPHOSPHATE


Mass: 450.443 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C20H36O7P2 / Feature type: SUBJECT OF INVESTIGATION
#5: 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
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 2.89 Å3/Da / Density % sol: 57.4 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.6
Details: 0.07 M MES, 25% w/v PEG 400, 1.5 mM MgCl2, 4.5% v/v ethanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 8, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.57→45.867 Å / Num. obs: 20716 / % possible obs: 89.7 % / Redundancy: 6 % / CC1/2: 0.995 / Rrim(I) all: 0.2 / Net I/σ(I): 8.61
Reflection shellResolution: 2.57→2.64 Å / Num. unique obs: 989 / CC1/2: 0.139 / Rrim(I) all: 2.598

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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: 2.59→45.86 Å / SU ML: 0.52 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 34.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.249 1034 5.01 %
Rwork0.2052 --
obs0.2075 20634 91.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.59→45.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3646 0 44 2 3692
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043771
X-RAY DIFFRACTIONf_angle_d0.6895143
X-RAY DIFFRACTIONf_dihedral_angle_d19.6031268
X-RAY DIFFRACTIONf_chiral_restr0.041593
X-RAY DIFFRACTIONf_plane_restr0.004663
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5901-2.72670.44271180.38972363X-RAY DIFFRACTION78
2.7267-2.89750.41541340.32642435X-RAY DIFFRACTION80
2.8975-3.12110.36591300.29482474X-RAY DIFFRACTION81
3.1211-3.43510.29921570.2493035X-RAY DIFFRACTION100
3.4351-3.9320.26121670.20653060X-RAY DIFFRACTION100
3.932-4.95290.2231630.17113087X-RAY DIFFRACTION100
4.9529-45.860.19581650.17723146X-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)
16.61713.86640.34523.3306-2.59867.7308-0.10470.31550.75950.2693-0.120.74270.1090.14840.27920.64780.08010.08650.82610.14420.7962.3222114.338.9497
22.61220.4742-0.95422.73450.51112.87270.16690.21350.4903-0.30970.0627-0.17-0.23690.0156-0.23550.5103-0.0310.00370.48920.10730.572224.3819121.666529.3968
37.65053.2042-3.57578.992-1.55738.9680.1395-0.46910.71910.55280.1162-0.1619-0.21690.0691-0.31950.4876-0.1108-0.08740.4075-0.14240.725526.2985132.007138.3599
45.67882.0999-2.32037.4726-2.94694.60520.44230.06190.77150.2305-0.2809-0.5389-0.8768-0.2111-0.19950.6336-0.0769-0.05960.6013-0.11890.80227.8225131.287838.9852
53.36220.43421.01797.77386.23178.8248-0.2634-0.42130.3950.45550.842-0.9983-0.89340.4676-0.49770.6574-0.0528-0.29380.72440.02170.931343.6429122.660248.0769
63.3099-0.59682.52173.86810.45014.5213-0.6976-0.67350.49880.2321-0.3035-0.5992-0.8287-0.42040.86340.7526-0.1335-0.16180.7179-0.05990.953936.2167121.511253.7535
72.9019-0.51230.45392.79110.1755.0536-0.04150.30970.18210.17870.1267-0.08650.2542-0.2099-0.06120.411-0.0587-0.03080.51780.02330.53725.7206110.544636.0269
85.2368-0.17515.88241.6061-0.41318.45680.3058-0.0559-0.43720.51710.03560.0260.440.1295-0.40350.6177-0.0515-0.05810.64020.06990.543426.9781108.140355.5938
91.9201-1.04560.22822.5513-2.75793.1986-0.5458-0.31530.09931.5972-0.1859-0.2186-1.4994-0.11140.88951.2474-0.1652-0.10710.6245-0.0590.601339.6948124.22666.3861
103.3795-1.9984-1.19845.49211.63567.0995-0.2492-0.4569-0.08830.90320.2119-0.63441.05330.69360.04920.63330.0598-0.12210.59390.01540.525239.012389.198643.6773
112.1691.78430.71123.87071.78692.11260.0427-0.18550.62810.81260.3053-0.71830.22320.4631-0.36220.57930.0674-0.22070.7321-0.10270.878644.7954110.728647.3468
122.9894-0.20840.43883.4256-0.7543.6158-0.1680.35790.1656-0.15360.1334-0.05370.45940.17090.09520.48480.0248-0.05870.533-0.01760.613733.272397.632735.9621
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 106 )
3X-RAY DIFFRACTION3chain 'A' and (resid 107 through 128 )
4X-RAY DIFFRACTION4chain 'A' and (resid 129 through 157 )
5X-RAY DIFFRACTION5chain 'A' and (resid 158 through 174 )
6X-RAY DIFFRACTION6chain 'A' and (resid 175 through 201 )
7X-RAY DIFFRACTION7chain 'A' and (resid 202 through 236 )
8X-RAY DIFFRACTION8chain 'A' and (resid 237 through 284 )
9X-RAY DIFFRACTION9chain 'A' and (resid 285 through 326 )
10X-RAY DIFFRACTION10chain 'B' and (resid 82 through 196 )
11X-RAY DIFFRACTION11chain 'B' and (resid 197 through 249 )
12X-RAY DIFFRACTION12chain 'B' and (resid 250 through 293 )

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