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- PDB-6z1n: Structure of the human heterotetrameric cis-prenyltransferase complex -

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Basic information

Entry
Database: PDB / ID: 6z1n
TitleStructure of the human heterotetrameric cis-prenyltransferase complex
Components(Dehydrodolichyl diphosphate synthase complex subunit ...) x 2
KeywordsTRANSFERASE / dolichol / cis-prenyltransferase / NgBR / DHDDS / Nogo-B receptor
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 / positive regulation of nitric-oxide synthase activity / 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
FARNESYL DIPHOSPHATE / PHOSPHATE ION / 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: 2.3 Å
AuthorsLisnyansky Bar-El, M. / Haitin, Y. / Giladi, M.
Funding support Israel, 5items
OrganizationGrant numberCountry
Israel Science Foundation1721/16 Israel
Israel Science Foundation1775/12 Israel
Other privateICRF-01214 Israel
Other privateICRF-19202 Israel
German-Israeli Foundation for Research and DevelopmentI2425418.13-2016 Israel
CitationJournal: Nat Commun / Year: 2020
Title: Structural basis of heterotetrameric assembly and disease mutations in the human cis-prenyltransferase complex.
Authors: Bar-El, M.L. / Vankova, P. / Yeheskel, A. / Simhaev, L. / Engel, H. / Man, P. / Haitin, Y. / Giladi, M.
History
DepositionMay 14, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 21, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 28, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)63,9155
Polymers63,4142
Non-polymers5023
Water2,198122
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)127,83010
Polymers126,8274
Non-polymers1,0036
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_566x-y+2/3,-y+4/3,-z+4/31
Buried area12430 Å2
ΔGint-95 kcal/mol
Surface area45160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)184.074, 184.074, 112.593
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-557-

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, 125 molecules

#3: Chemical ChemComp-FPP / FARNESYL DIPHOSPHATE


Mass: 382.326 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H28O7P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4 / 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.: 122 / 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: 2.91 Å3/Da / Density % sol: 57.8 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop
Details: 0.1 M NaCl, 0.1 M NaP pH 7.0, 33% w/v PEG 300, 760 mM FPP

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Feb 24, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.3→46.019 Å / Num. obs: 32476 / % possible obs: 100 % / Redundancy: 21.1 % / CC1/2: 0.999 / Rrim(I) all: 0.17 / Net I/σ(I): 16.32
Reflection shellResolution: 2.3→2.44 Å / Mean I/σ(I) obs: 1.56 / Num. unique obs: 5182 / CC1/2: 0.677 / Rrim(I) all: 1.978 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
XDSdata scaling
MrBUMPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1x09

1x09


Resolution: 2.3→45.983 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.45 / Phase error: 24.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2229 1633 5.03 %
Rwork0.1888 --
obs0.1905 32473 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→45.983 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4061 0 30 122 4213
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054193
X-RAY DIFFRACTIONf_angle_d0.7015693
X-RAY DIFFRACTIONf_dihedral_angle_d6.8723416
X-RAY DIFFRACTIONf_chiral_restr0.041635
X-RAY DIFFRACTIONf_plane_restr0.004738
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3004-2.36810.36561370.29192536X-RAY DIFFRACTION100
2.3681-2.44460.31991300.2552561X-RAY DIFFRACTION100
2.4446-2.53190.30451340.23632546X-RAY DIFFRACTION100
2.5319-2.63330.27271370.21822562X-RAY DIFFRACTION100
2.6333-2.75310.2751360.21812540X-RAY DIFFRACTION100
2.7531-2.89830.26771330.22182565X-RAY DIFFRACTION100
2.8983-3.07980.30151390.22372543X-RAY DIFFRACTION100
3.0798-3.31750.26931370.21052587X-RAY DIFFRACTION100
3.3175-3.65130.20911320.19152563X-RAY DIFFRACTION100
3.6513-4.17930.17511370.15692588X-RAY DIFFRACTION100
4.1793-5.26430.18151390.1482592X-RAY DIFFRACTION100
5.2643-45.9830.18631420.17982657X-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)
12.96942.8026-1.58768.1889-3.22864.91020.13620.2920.7044-0.2626-0.01370.2691-0.16940.2581-0.16380.33580.06360.04810.5237-0.00210.53755.8531119.933836.4353
24.1440.0406-1.81791.01010.40142.99010.23570.25420.5267-0.04360.058-0.1699-0.3773-0.1335-0.29390.36890.01160.03980.320.04850.397625.6529125.677132.1587
31.296-0.07780.64070.7022-0.22012.1865-0.0753-0.08450.14770.13470.0522-0.0563-0.0875-0.00150.01780.35230.0139-0.02850.3935-0.05840.41430.6267113.789748.7707
41.86530.0288-0.10244.8031-5.72598.5414-0.3458-0.09730.15310.26770.3076-0.0445-0.2385-0.69070.16810.6565-0.0555-0.10870.448-0.11290.507439.8387123.809467.5903
58.4666-4.69822.70038.2723-4.21932.242-0.2067-0.0521-0.1816-0.49840.015-0.46551.65760.08840.52920.87230.0315-0.00650.525-0.0520.510643.572979.4930.1059
62.0298-0.6415-0.02372.24540.47383.12150.0049-0.24410.01540.21580.0951-0.11020.17940.0245-0.01280.3550.047-0.07480.3443-0.03220.318236.407291.623345.0442
78.6228-4.2792-0.32365.85093.45894.1747-0.8275-0.8075-0.1840.6380.47370.46991.10571.00020.04420.65550.0952-0.09820.58120.11690.415842.236181.990450.3242
81.6067-1.64980.08373.0318-0.47630.1063-0.0161-0.04160.37930.0259-0.1061-0.44110.03430.20250.09630.47820.055-0.06090.6181-0.03040.463347.2904102.486951.8942
91.51870.60990.52383.66830.78062.0041-0.04650.01710.01920.04480.1728-0.5044-0.03370.2904-0.1610.3360.0108-0.04780.4693-0.06230.434339.8026105.271843.5437
101.15521.8835-1.16057.1983-2.14441.1771-0.2051-0.03320.2808-0.73960.1620.64470.2896-0.3648-0.00730.51460.0328-0.09590.472-0.07660.387434.599396.04829.1055
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -2 through 22 )
2X-RAY DIFFRACTION2chain 'A' and (resid 23 through 157 )
3X-RAY DIFFRACTION3chain 'A' and (resid 158 through 282 )
4X-RAY DIFFRACTION4chain 'A' and (resid 283 through 326 )
5X-RAY DIFFRACTION5chain 'B' and (resid 79 through 93 )
6X-RAY DIFFRACTION6chain 'B' and (resid 94 through 144 )
7X-RAY DIFFRACTION7chain 'B' and (resid 145 through 176 )
8X-RAY DIFFRACTION8chain 'B' and (resid 177 through 212 )
9X-RAY DIFFRACTION9chain 'B' and (resid 213 through 273 )
10X-RAY DIFFRACTION10chain 'B' and (resid 274 through 293 )

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