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- PDB-6w2l: Crystal structure of human dehydrodolichyl diphosphate synthase (... -

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Basic information

Entry
Database: PDB / ID: 6w2l
TitleCrystal structure of human dehydrodolichyl diphosphate synthase (NgBR/DHDDS) in complex with Mg and IPP
Components
  • Dehydrodolichyl diphosphate synthase complex subunit DHDDS
  • Dehydrodolichyl diphosphate synthase complex subunit NUS1
KeywordsTRANSFERASE / cis-prenyltransferase / dehydrodolichyl diphosphate synthase
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. / Decaprenyl diphosphate synthase-like / Putative undecaprenyl diphosphate synthase / Decaprenyl diphosphate synthase-like superfamily
Similarity search - Domain/homology
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: 2.306 Å
AuthorsEdani, B.H. / Ha, Y. / Sessa, W.C.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)2P01 HLHL107205-06A1 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)5R35 HL139945-03 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Structural elucidation of thecis-prenyltransferase NgBR/DHDDS complex reveals insights in regulation of protein glycosylation.
Authors: Edani, B.H. / Grabinska, K.A. / Zhang, R. / Park, E.J. / Siciliano, B. / Surmacz, L. / Ha, Y. / Sessa, W.C.
History
DepositionMar 6, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 2, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Sep 9, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Oct 18, 2023Group: 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

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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)63,0585
Polymers62,5422
Non-polymers5163
Water1,928107
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5310 Å2
ΔGint-37 kcal/mol
Surface area23510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)185.670, 185.670, 113.351
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32

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Components

#1: Protein Dehydrodolichyl diphosphate synthase complex subunit DHDDS / Cis-isoprenyltransferase / Cis-IPTase / Cis-prenyltransferase subunit hCIT / Epididymis tissue protein Li 189m


Mass: 38455.242 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DHDDS, HDS / Plasmid: pRSF-Duet1
Details (production host): Bacterial expression, coexpression
Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2
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: 24086.416 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NUS1, C6orf68, NGBR / Plasmid: pRSF-Duet1
Details (production host): Bacterial expression, coexpression
Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2
References: UniProt: Q96E22, ditrans,polycis-polyprenyl diphosphate synthase [(2E,6E)-farnesyl diphosphate specific]
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-IPE / 3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE / ISOPENTENYL PYROPHOSPHATE


Mass: 246.092 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H12O7P2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.09 Å3/Da / Density % sol: 60.21 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 2.5 mM MgCl2, 3.3 mM IPP, 0.1 M Bicine, 10% v/v 2-propanol, 22% PEG 1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 20, 2019
RadiationMonochromator: Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.306→40 Å / Num. obs: 31367 / % possible obs: 99.2 % / Redundancy: 12.8 % / Rmerge(I) obs: 0.108 / Rpim(I) all: 0.032 / Rrim(I) all: 0.113 / Χ2: 1.001 / Net I/av σ(I): 29.6 / Net I/σ(I): 7.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.5-2.598.70.87724010.8260.2910.9270.58594.3
2.59-2.6910.80.78325090.8880.2380.820.61798.5
2.69-2.8213.30.68525530.950.1920.7110.603100
2.82-2.9614.40.53825580.9660.1460.5580.64100
2.96-3.1513.90.36125740.9830.10.3750.71100
3.15-3.3913.20.20925630.990.0590.2170.86499.9
3.39-3.7314.90.14525700.9950.0390.151.059100
3.73-4.2713.90.09825650.9960.0280.1021.229100
4.27-5.3812.20.07126020.9970.0220.0741.42499.4
5.38-4012.70.0726580.9970.0220.0742.08599.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
DENZOdata reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1X06, 6JCN

1x06

6jcn


Resolution: 2.306→37.916 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.948 / SU B: 11.973 / SU ML: 0.262 / Cross valid method: FREE R-VALUE / ESU R: 0.276 / ESU R Free: 0.224
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.255 1611 5.136 %
Rwork0.2123 29756 -
all0.214 --
obs-31367 94.939 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 72.717 Å2
Baniso -1Baniso -2Baniso -3
1--1.743 Å2-0.871 Å20 Å2
2---1.743 Å20 Å2
3---5.654 Å2
Refinement stepCycle: LAST / Resolution: 2.306→37.916 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3900 0 29 107 4036
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0124003
X-RAY DIFFRACTIONr_angle_refined_deg1.1331.6315443
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0885518
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.65922190
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.36915598
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5421524
X-RAY DIFFRACTIONr_chiral_restr0.0920.2539
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023053
X-RAY DIFFRACTIONr_nbd_refined0.2190.21846
X-RAY DIFFRACTIONr_nbtor_refined0.3060.22673
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1580.2160
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2120.225
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1310.23
X-RAY DIFFRACTIONr_mcbond_it4.637.8822087
X-RAY DIFFRACTIONr_mcangle_it6.96611.8022600
X-RAY DIFFRACTIONr_scbond_it5.3537.7711916
X-RAY DIFFRACTIONr_scangle_it7.91111.5532843
X-RAY DIFFRACTIONr_lrange_it10.999104.6576006
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.306-2.3660.39970.3921688X-RAY DIFFRACTION72.9763
2.366-2.4310.35810.3681794X-RAY DIFFRACTION80.1282
2.431-2.5010.3641170.3661869X-RAY DIFFRACTION86.423
2.501-2.5780.3731080.3431990X-RAY DIFFRACTION93.4105
2.578-2.6620.4361350.3121962X-RAY DIFFRACTION97.7622
2.662-2.7560.3041110.3041979X-RAY DIFFRACTION99.6187
2.756-2.860.3511020.2691928X-RAY DIFFRACTION100
2.86-2.9760.2811020.2451856X-RAY DIFFRACTION99.949
2.976-3.1090.361860.2511779X-RAY DIFFRACTION100
3.109-3.260.3181000.2481688X-RAY DIFFRACTION99.9441
3.26-3.4360.321770.2241630X-RAY DIFFRACTION100
3.436-3.6440.218890.1881527X-RAY DIFFRACTION100
3.644-3.8960.237720.1811428X-RAY DIFFRACTION100
3.896-4.2070.223730.1831373X-RAY DIFFRACTION100
4.207-4.6080.214590.1741222X-RAY DIFFRACTION99.6887
4.608-5.150.165440.1591152X-RAY DIFFRACTION99.2531
5.15-5.9440.266530.222992X-RAY DIFFRACTION99.9044
5.944-7.2720.312450.221857X-RAY DIFFRACTION99.8893
7.272-10.2530.186390.16663X-RAY DIFFRACTION99.7159
10.253-37.910.206210.209379X-RAY DIFFRACTION97.561

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