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- PDB-6qsk: Crystal structure of a nucleotide sugar transporter with bound nu... -

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Basic information

Entry
Database: PDB / ID: 6qsk
TitleCrystal structure of a nucleotide sugar transporter with bound nucleotide monophosphate.
ComponentsGDP-mannose transporter 1
KeywordsMEMBRANE PROTEIN / Golgi transporter / SLC35 / GDP-mannose transport / glycosylation
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
GUANOSINE-5'-MONOPHOSPHATE / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / GDP-mannose transporter 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288C (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.394 Å
AuthorsNewstead, S. / Parker, J.L.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust102890/Z/13/A United Kingdom
CitationJournal: Nat Commun / Year: 2019
Title: Structural basis for substrate specificity and regulation of nucleotide sugar transporters in the lipid bilayer.
Authors: Parker, J.L. / Corey, R.A. / Stansfeld, P.J. / Newstead, S.
History
DepositionFeb 21, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 2, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 8, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
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 / refine
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine.pdbx_diffrn_id

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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)298,18214
Polymers296,3568
Non-polymers1,8266
Water18010
1
A: GDP-mannose transporter 1
E: GDP-mannose transporter 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,1655
Polymers74,0892
Non-polymers1,0763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2530 Å2
ΔGint-21 kcal/mol
Surface area29900 Å2
MethodPISA
2
B: GDP-mannose transporter 1

G: 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 area1120 Å2
ΔGint-14 kcal/mol
Surface area30750 Å2
MethodPISA
3
C: GDP-mannose transporter 1
hetero molecules

H: GDP-mannose transporter 1


Theoretical massNumber of molelcules
Total (without water)74,4523
Polymers74,0892
Non-polymers3631
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area1770 Å2
ΔGint-16 kcal/mol
Surface area30250 Å2
MethodPISA
4
D: GDP-mannose transporter 1
F: GDP-mannose transporter 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,4754
Polymers74,0892
Non-polymers3862
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1950 Å2
ΔGint-30 kcal/mol
Surface area30280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.705, 102.716, 181.253
Angle α, β, γ (deg.)89.93, 90.08, 90.19
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 S288C (yeast) / Gene: VRG4, GOG5, LDB3, MCD3, VAN2, VIG4, YGL225W / Production host: Saccharomyces cerevisiae (brewer's yeast) / 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.: 2 / Source method: obtained synthetically / Formula: C21H40O4
#3: Chemical ChemComp-5GP / GUANOSINE-5'-MONOPHOSPHATE / Guanosine monophosphate


Mass: 363.221 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H14N5O8P
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: H2O

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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. GMP was soaked in at 20mM overnight.

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Data collection

DiffractionMean temperature: 83 K / Ambient temp details: 277 / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 30, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 3.39→49.43 Å / Num. obs: 44054 / % possible obs: 96.7 % / Redundancy: 2 % / Biso Wilson estimate: 68.12 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.09 / Rrim(I) all: 0.135 / Net I/σ(I): 5.4
Reflection shellResolution: 3.39→3.52 Å / Redundancy: 2 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 4492 / CC1/2: 0.523 / Rpim(I) all: 0.61 / Rrim(I) all: 0.92 / % possible all: 92.3

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Processing

Software
NameVersionClassification
PHENIX(dev_3360: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5OGE

5oge


Resolution: 3.394→49.428 Å / SU ML: 0.63 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 36.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3196 2129 4.84 %
Rwork0.2527 --
obs0.2559 43971 96.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.394→49.428 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18492 0 123 10 18625
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01219017
X-RAY DIFFRACTIONf_angle_d1.38125795
X-RAY DIFFRACTIONf_dihedral_angle_d3.20411137
X-RAY DIFFRACTIONf_chiral_restr0.073119
X-RAY DIFFRACTIONf_plane_restr0.0093124
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3942-3.47310.39171570.31552562X-RAY DIFFRACTION90
3.4731-3.560.34221170.30942832X-RAY DIFFRACTION96
3.56-3.65620.35361750.29572745X-RAY DIFFRACTION97
3.6562-3.76380.35551130.28072836X-RAY DIFFRACTION97
3.7638-3.88520.37441400.27672809X-RAY DIFFRACTION97
3.8852-4.0240.34351430.28642806X-RAY DIFFRACTION98
4.024-4.1850.42661440.29572859X-RAY DIFFRACTION97
4.185-4.37540.37851590.27792744X-RAY DIFFRACTION97
4.3754-4.60590.32821330.23592865X-RAY DIFFRACTION97
4.6059-4.89420.31311680.2342792X-RAY DIFFRACTION98
4.8942-5.27170.25871300.23692773X-RAY DIFFRACTION97
5.2717-5.80150.33711700.25212851X-RAY DIFFRACTION98
5.8015-6.63930.34431380.27052819X-RAY DIFFRACTION98
6.6393-8.35820.34721090.22422792X-RAY DIFFRACTION96
8.3582-49.43320.20511330.20722757X-RAY DIFFRACTION94

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