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

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Basic information

Entry
Database: PDB / ID: 7pay
TitleStructure of the human heterotetrameric cis-prenyltransferase complex in complex with magnesium and GGsPP
Components(Dehydrodolichyl diphosphate synthase complex subunit ...) x 2
KeywordsTRANSFERASE / DHDDS / NgBR / hcit / cis-prenyltransferase / dolichol
Function / homology
Function and homology information


protein mannosylation / Defective DHDDS causes RP59 / dolichol biosynthetic process / dehydrodolichyl diphosphate synthase complex / Synthesis of Dolichyl-phosphate / dolichyl diphosphate biosynthetic process / regulation of intracellular cholesterol transport / ditrans,polycis-polyprenyl diphosphate synthase [(2E,6E)-farnesyl diphosphate specific] / dehydrodolichyl diphosphate synthase activity / polyprenol biosynthetic process ...protein mannosylation / Defective DHDDS causes RP59 / dolichol biosynthetic process / dehydrodolichyl diphosphate synthase complex / Synthesis of Dolichyl-phosphate / dolichyl diphosphate biosynthetic process / regulation of intracellular cholesterol transport / ditrans,polycis-polyprenyl diphosphate synthase [(2E,6E)-farnesyl diphosphate specific] / dehydrodolichyl diphosphate synthase activity / polyprenol biosynthetic process / polyprenyltransferase activity / vascular endothelial growth factor signaling pathway / protein glycosylation / positive regulation of blood vessel endothelial cell migration / lipid droplet / cholesterol homeostasis / positive regulation of nitric-oxide synthase activity / 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-GGS / 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: 2.4 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

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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)64,0005
Polymers63,4142
Non-polymers5873
Water1,44180
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)128,00110
Polymers126,8274
Non-polymers1,1746
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation1
Unit cell
Length a, b, c (Å)184.406, 184.406, 112.470
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, 83 molecules

#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: 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
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 80 / 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: 2.9 Å3/Da / Density % sol: 57.61 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 1 M LiSO4, 0.02 M Tris-HCl, 1.8% w/v PEG 8000

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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 14, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→46.1 Å / Num. obs: 28670 / % possible obs: 99.3 % / Redundancy: 2.9 % / CC1/2: 0.995 / Rrim(I) all: 0.116 / Net I/σ(I): 6.79
Reflection shellResolution: 2.4→2.55 Å / Num. unique obs: 8883 / CC1/2: 0.504 / Rrim(I) all: 0.983

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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: 2.4→46.1 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2443 2010 7.01 %
Rwork0.2019 --
obs0.2049 28656 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→46.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3973 0 35 80 4088
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044109
X-RAY DIFFRACTIONf_angle_d0.6915591
X-RAY DIFFRACTIONf_dihedral_angle_d6.2753286
X-RAY DIFFRACTIONf_chiral_restr0.043631
X-RAY DIFFRACTIONf_plane_restr0.004727
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.45990.35781450.30711838X-RAY DIFFRACTION99
2.4599-2.52640.31561420.28211897X-RAY DIFFRACTION100
2.5264-2.60080.2651380.25471904X-RAY DIFFRACTION100
2.6008-2.68470.30841440.23521876X-RAY DIFFRACTION100
2.6847-2.78060.26431430.23171885X-RAY DIFFRACTION100
2.7806-2.89190.28961440.23951916X-RAY DIFFRACTION100
2.8919-3.02350.28241410.23171880X-RAY DIFFRACTION100
3.0235-3.18290.25661400.23081909X-RAY DIFFRACTION100
3.1829-3.38230.24061440.20951894X-RAY DIFFRACTION100
3.3823-3.64330.27121480.2061913X-RAY DIFFRACTION100
3.6433-4.00980.22351430.18351913X-RAY DIFFRACTION100
4.0098-4.58950.21991400.1751908X-RAY DIFFRACTION100
4.5895-5.78060.2441440.18091923X-RAY DIFFRACTION100
5.7806-46.1020.20711540.18251990X-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)
18.8410.2237-0.53836.99810.33464.60760.07910.68270.4184-0.1788-0.0140.0746-0.79060.24110.02530.5122-0.04390.00460.56870.01140.32245.3642118.973837.1713
22.88520.534-0.73692.26950.022.4490.08890.29940.4440.0299-0.0996-0.3959-0.3778-0.05190.00840.495-0.0307-0.10190.49940.15510.683325.6371125.688732.1403
31.0039-0.5423-0.15141.3623-0.65141.2348-0.1039-0.13030.32690.5726-0.1328-0.3877-0.23040.27720.14350.6559-0.0951-0.2210.58520.0780.789633.0159116.882652.0633
44.5772-1.5929-2.11232.33821.50362.3586-0.32570.0743-0.07650.50540.0338-0.43441.3829-0.31350.15120.94720.0186-0.0880.72090.15510.745637.889487.769437.3389
51.0878-0.427-0.4492.804-0.32774.0036-0.1348-0.32640.02510.42020.052-0.74990.70380.72290.04690.69590.0491-0.24430.70770.14820.743240.936588.850748.1729
62.55171.83230.92771.43951.29293.52490.14810.17070.00440.6830.0265-1.23730.32711.0769-0.67070.7059-0.0521-0.37730.88440.16961.297649.7742114.590748.7363
71.1221-0.134-0.63323.99580.86052.37770.0860.2415-0.0322-0.0237-0.2013-0.30570.3048-0.01960.08570.4630.0148-0.1320.60540.13390.678832.586298.070536.891
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 22 )
2X-RAY DIFFRACTION2chain 'A' and (resid 23 through 157 )
3X-RAY DIFFRACTION3chain 'A' and (resid 158 through 328 )
4X-RAY DIFFRACTION4chain 'B' and (resid 80 through 113 )
5X-RAY DIFFRACTION5chain 'B' and (resid 114 through 196 )
6X-RAY DIFFRACTION6chain 'B' and (resid 197 through 239 )
7X-RAY DIFFRACTION7chain 'B' and (resid 240 through 293 )

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