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- PDB-5oge: Crystal structure of a nucleotide sugar transporter -

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Basic information

Entry
Database: PDB / ID: 5oge
TitleCrystal structure of a nucleotide sugar transporter
ComponentsGDP-mannose transporter 1
KeywordsMEMBRANE PROTEIN / SLC35 / Golgi transporter
Function / homology
Function and homology information


GDP-mannose transmembrane transporter activity / GDP-mannose transmembrane transport / antiporter activity / carbohydrate transport / cytoplasmic vesicle membrane / Golgi membrane / endoplasmic reticulum membrane / Golgi apparatus / mitochondrion
Similarity search - Function
UAA transporter / UAA transporter family
Similarity search - Domain/homology
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / GDP-mannose transporter 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.22 Å
AuthorsNewstead, S. / Parker, J.L.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust102890/Z/13/Z United Kingdom
CitationJournal: Nature / Year: 2017
Title: Structural basis of nucleotide sugar transport across the Golgi membrane.
Authors: Parker, J.L. / Newstead, S.
History
DepositionJul 12, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 22, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.year
Revision 1.2Dec 6, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GDP-mannose transporter 1
B: GDP-mannose transporter 1
C: GDP-mannose transporter 1
D: GDP-mannose transporter 1
E: GDP-mannose transporter 1
F: GDP-mannose transporter 1
G: GDP-mannose transporter 1
H: GDP-mannose transporter 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)300,63520
Polymers296,3568
Non-polymers4,27812
Water0
1
A: GDP-mannose transporter 1
E: GDP-mannose transporter 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,8727
Polymers74,0892
Non-polymers1,7835
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1920 Å2
ΔGint-19 kcal/mol
Surface area31370 Å2
MethodPISA
2
B: GDP-mannose transporter 1
hetero molecules

G: GDP-mannose transporter 1


Theoretical massNumber of molelcules
Total (without water)74,8024
Polymers74,0892
Non-polymers7132
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area1480 Å2
ΔGint-16 kcal/mol
Surface area31850 Å2
MethodPISA
3
C: GDP-mannose transporter 1

H: GDP-mannose transporter 1


Theoretical massNumber of molelcules
Total (without water)74,0892
Polymers74,0892
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area1140 Å2
ΔGint-14 kcal/mol
Surface area31070 Å2
MethodPISA
4
D: GDP-mannose transporter 1
F: GDP-mannose transporter 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,8727
Polymers74,0892
Non-polymers1,7835
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2110 Å2
ΔGint-20 kcal/mol
Surface area32070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.570, 102.910, 181.410
Angle α, β, γ (deg.)89.92, 90.12, 90.06
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
GDP-mannose transporter 1 / GMT 1 / Low dye-binding protein 3 / Morphogenesis checkpoint-dependent protein 3 / Vanadate ...GMT 1 / Low dye-binding protein 3 / Morphogenesis checkpoint-dependent protein 3 / Vanadate resistance glycosylation protein 4


Mass: 37044.504 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Gene: VRG4, GOG5, LDB3, MCD3, VAN2, VIG4, YGL225W / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): BJ5460 / References: UniProt: P40107
#2: Chemical
ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C21H40O4

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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: 2.87 Å3/Da / Density % sol: 57.16 %
Crystal growTemperature: 277 K / Method: lipidic cubic phase / pH: 5
Details: 26 - 30 % (v/v) PEG 400, 0.1 M sodium citrate pH 5.0 and 75 mM sodium chloride or sodium acetate

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 2.7 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 30, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 2.7 Å / Relative weight: 1
ReflectionResolution: 3.22→45.35 Å / Num. obs: 48151 / % possible obs: 90.3 % / Redundancy: 8.4 % / Biso Wilson estimate: 112.71 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.162 / Rpim(I) all: 0.07 / Net I/σ(I): 8.9
Reflection shellResolution: 3.22→3.3 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.688 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 2345 / CC1/2: 0.564 / Rpim(I) all: 0.688 / % possible all: 60.1

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 3.22→45.35 Å / Cor.coef. Fo:Fc: 0.876 / Cor.coef. Fo:Fc free: 0.844 / Rfactor Rfree error: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.607
RfactorNum. reflection% reflectionSelection details
Rfree0.306 2328 4.83 %RANDOM
Rwork0.28 ---
obs0.281 48149 90.3 %-
Displacement parametersBiso mean: 97.43 Å2
Baniso -1Baniso -2Baniso -3
1-18.2152 Å22.9935 Å27.848 Å2
2---31.1612 Å27.6712 Å2
3---12.946 Å2
Refine analyzeLuzzati coordinate error obs: 0 Å
Refinement stepCycle: 1 / Resolution: 3.22→45.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18836 0 300 0 19136
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00919996HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0227519HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d6679SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes303HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2820HARMONIC5
X-RAY DIFFRACTIONt_it19996HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.05
X-RAY DIFFRACTIONt_other_torsion22.4
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion2675SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact23664SEMIHARMONIC4
LS refinement shellResolution: 3.22→3.3 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 153 6.54 %
Rwork0.271 2188 -
all0.275 2341 -
obs--60.16 %
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)
10.9259-0.1357-0.27380.45350.34692.0875-0.0291-0.02150.0158-0.11870.093-0.0282-0.1966-0.1428-0.0639-0.0986-0.0185-0.0525-0.1617-0.0333-0.1969-45.3088-49.095233.7087
20.8229-0.03530.20660.7155-0.69262.09-0.03030.0129-0.0505-0.13770.05290.06670.19560.0949-0.0226-0.1105-0.0002-0.0703-0.1295-0.0527-0.2132-41.4746-55.7349124.4102
30.75560.1741-0.40130.6-1.02621.7592-0.0115-0.0290.13950.10440.03260.0784-0.12890.1116-0.0211-0.1479-0.0226-0.0408-0.1028-0.0729-0.2047-41.4444-100.604359.5493
41.1354-0.0698-0.08440.78430.52861.7036-0.0278-0.0552-0.05060.17470.055-0.07660.127-0.1477-0.0272-0.0633-0.0457-0.0908-0.1828-0.0408-0.2227-45.393-106.8529150.1904
50.11150.06-0.20021.01070.1142.8037-0.0431-0.1438-0.05130.12060.0311-0.11640.07360.05440.012-0.2276-0.0215-0.0539-0.1123-0.0903-0.1463-25.1028-46.91975.9834
60.61120.14920.2870.63650.29292.237-0.01470.05160.0298-0.10560.01-0.1256-0.10140.06650.0046-0.1835-0.0252-0.0157-0.1238-0.0929-0.1702-25.2521-109.1237108.0626
70.54310.08130.12551.1381-0.31292.2982-0.0095-0.08760.03570.13920.03260.1099-0.0683-0.0497-0.0231-0.18010.0321-0.044-0.15260.0105-0.1911-16.4373-58.1685166.5592
80.7279-0.3122-0.26670.6905-0.28622.0324-0.02840.1241-0.0508-0.13580.0230.14020.0732-0.0710.0054-0.13570.005-0.0922-0.13890.0179-0.1781-16.3092-98.275917.3442
90.4020.2986-0.26320.00220.56860.55630.03380.14130.1479-0.1024-0.06970.0743-0.084-0.07370.03590.0127-0.02980.11-0.0091-0.15150.274-39.6829-74.1515102.2766
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }
5X-RAY DIFFRACTION5{ E|* }
6X-RAY DIFFRACTION6{ F|* }
7X-RAY DIFFRACTION7{ G|* }
8X-RAY DIFFRACTION8{ H|* }
9X-RAY DIFFRACTION9{ I|401-404, B|401-402, D|401-405, E|401 }

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