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

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Basic information

Entry
Database: PDB / ID: 7pax
TitleStructure of the human heterotetrameric cis-prenyltransferase complex in complex with magnesium, FsPP and IPP
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-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 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)64,0825
Polymers63,4142
Non-polymers6693
Water1,42379
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)128,16510
Polymers126,8274
Non-polymers1,3386
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_566x-y+2/3,-y+4/3,-z+4/31
Buried area13360 Å2
ΔGint-83 kcal/mol
Surface area44090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)183.987, 183.987, 112.537
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-543-

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, 82 molecules

#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
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / 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: 57.44 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1 M NaCl, 0.1 M MES, 33% w/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: 0.9762 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: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2→46 Å / Num. obs: 47371 / % possible obs: 96.3 % / Redundancy: 20.9 % / CC1/2: 1 / Rrim(I) all: 0.066 / Net I/σ(I): 22.94
Reflection shellResolution: 2→2.12 Å / Mean I/σ(I) obs: 1.23 / Num. unique obs: 7888 / CC1/2: 0.696 / Rrim(I) all: 2.005

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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→41.134 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 26.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2325 2018 4.26 %
Rwork0.2047 --
obs0.2059 47359 96.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→41.134 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4032 0 39 79 4150
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044200
X-RAY DIFFRACTIONf_angle_d0.7745714
X-RAY DIFFRACTIONf_dihedral_angle_d19.8521497
X-RAY DIFFRACTIONf_chiral_restr0.046641
X-RAY DIFFRACTIONf_plane_restr0.004741
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0001-2.05010.36421470.31433314X-RAY DIFFRACTION100
2.0501-2.10550.33961490.29583323X-RAY DIFFRACTION100
2.1055-2.16750.30721490.26823368X-RAY DIFFRACTION100
2.1675-2.23740.28961390.25623129X-RAY DIFFRACTION100
2.2374-2.31740.241950.23592051X-RAY DIFFRACTION99
2.3174-2.41020.29051480.23413353X-RAY DIFFRACTION100
2.4102-2.51980.25661500.22853354X-RAY DIFFRACTION100
2.5198-2.65270.25441500.2313362X-RAY DIFFRACTION100
2.6527-2.81880.26961430.23193345X-RAY DIFFRACTION100
2.8188-3.03640.28881510.2523361X-RAY DIFFRACTION100
3.0364-3.34180.27221470.23423363X-RAY DIFFRACTION100
3.3418-3.82510.23121430.19883235X-RAY DIFFRACTION96
3.8251-4.8180.19571470.16363303X-RAY DIFFRACTION97
4.818-41.1340.1961600.18493480X-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)
13.91525.1685-4.55999.7196-4.70945.87580.25040.45350.8226-0.1362-0.0166-0.0342-0.61540.3866-0.51510.41660.01230.03760.54850.04740.52985.269118.327136.882
21.3554-0.30480.0991.5863-0.04571.65640.07870.1260.45980.0566-0.1071-0.466-0.34990.15640.0340.3662-0.0613-0.03310.40130.10830.602428.5227122.412237.0268
34.7697-0.52394.56841.1442-0.48455.99350.0842-0.2192-0.51880.4150.27920.0736-0.0366-0.0641-0.38220.46430.01110.00370.45970.02670.40326.5661108.215255.5584
41.4586-1.10331.12711.032-2.04667.3684-0.3494-0.15510.33340.39230.08920.1069-0.4994-0.50550.42960.8165-0.1082-0.24050.4428-0.05010.78439.9123.762867.312
57.0002-2.884-3.63913.4315.08337.9348-0.2525-0.2575-0.46690.5184-0.0102-0.05421.1565-0.16180.15430.57140.0368-0.02650.56250.19790.581637.90887.344837.4427
61.9743-1.73360.55916.13211.48722.66220.1332-0.1019-0.0370.3082-0.177-0.40940.41740.0964-0.02580.50540.0272-0.08330.56690.06790.432237.450690.735846.9972
77.8242-3.1194-0.92023.06033.14574.3559-0.5796-0.4307-0.34480.54550.46620.33370.89510.69390.14790.84560.1204-0.10140.6760.1760.517542.381581.097949.0007
80.80891.1695-0.232.97550.62341.5329-0.03820.10220.56230.4323-0.071-1.4188-0.04830.55940.08460.4939-0.0447-0.23510.76360.08580.983949.2553108.476950.2699
90.6241-0.9857-0.70744.6459-0.88573.52380.11670.14740.1493-0.0288-0.1855-0.24770.16850.22310.06950.30260.0042-0.05340.50910.05690.468634.160798.488337.362
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 22 )
2X-RAY DIFFRACTION2chain 'A' and (resid 23 through 236 )
3X-RAY DIFFRACTION3chain 'A' and (resid 237 through 282 )
4X-RAY DIFFRACTION4chain 'A' and (resid 283 through 327 )
5X-RAY DIFFRACTION5chain 'B' and (resid 78 through 113 )
6X-RAY DIFFRACTION6chain 'B' and (resid 114 through 144 )
7X-RAY DIFFRACTION7chain 'B' and (resid 145 through 176 )
8X-RAY DIFFRACTION8chain 'B' and (resid 177 through 230 )
9X-RAY DIFFRACTION9chain 'B' and (resid 231 through 293 )

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