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- PDB-5ogk: Crystal structure of a nucleotide sugar transporter with bound nu... -

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Basic information

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


GDP-fucose transmembrane transporter activity / GDP-mannose transmembrane transporter activity / GDP-mannose transmembrane transport / antiporter activity / 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'-DIPHOSPHATE-ALPHA-D-MANNOSE / (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 / MOLECULAR REPLACEMENT / Resolution: 3.6 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 13, 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
Revision 1.3Oct 3, 2018Group: Data collection / Category: reflns / reflns_shell
Item: _reflns.pdbx_Rpim_I_all / _reflns_shell.pdbx_Rpim_I_all
Revision 1.4Jan 17, 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: 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)301,02419
Polymers296,3568
Non-polymers4,66811
Water00
1
A: GDP-mannose transporter 1
B: GDP-mannose transporter 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,4075
Polymers74,0892
Non-polymers1,3183
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2780 Å2
ΔGint-30 kcal/mol
Surface area29430 Å2
MethodPISA
2
C: GDP-mannose transporter 1
E: GDP-mannose transporter 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,7646
Polymers74,0892
Non-polymers1,6754
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3030 Å2
ΔGint-30 kcal/mol
Surface area29610 Å2
MethodPISA
3
D: GDP-mannose transporter 1
hetero molecules

F: GDP-mannose transporter 1


Theoretical massNumber of molelcules
Total (without water)75,0514
Polymers74,0892
Non-polymers9622
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_554x,y,z-11
Buried area2010 Å2
ΔGint-21 kcal/mol
Surface area29800 Å2
MethodPISA
4
G: GDP-mannose transporter 1
hetero molecules

H: 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_556x,y,z+11
Buried area1580 Å2
ΔGint-16 kcal/mol
Surface area29840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.319, 101.694, 180.192
Angle α, β, γ (deg.)89.86, 90.07, 90.11
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)
Strain: ATCC 204508 / S288c / Gene: VRG4, GOG5, LDB3, MCD3, VAN2, VIG4, YGL225W / Production host: Saccharomyces (fungus) / Strain (production host): BJ5460 / References: UniProt: P40107
#2: Chemical ChemComp-GDD / GUANOSINE-5'-DIPHOSPHATE-ALPHA-D-MANNOSE


Mass: 605.341 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C16H25N5O16P2
#3: Chemical
ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 8 / 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: 2.8 Å3/Da / Density % sol: 56.11 % / Description: 30 x 5 uM
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. GDP-mannose was soaked in at 20mM overnight.

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Data collection

DiffractionMean temperature: 83 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: May 26, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.6→45.3 Å / Num. obs: 36110 / % possible obs: 96.8 % / Redundancy: 1.8 % / CC1/2: 0.98 / Rpim(I) all: 0.2 / Net I/σ(I): 3.8
Reflection shellResolution: 3.6→3.76 Å / Redundancy: 1.8 % / Mean I/σ(I) obs: 0.6 / Num. unique obs: 4518 / CC1/2: 0.3 / Rpim(I) all: 1.11 / % possible all: 97.2

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5OGE

5oge


Resolution: 3.6→44.328 Å / SU ML: 0.58 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 35.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3127 1950 5.41 %
Rwork0.2566 --
obs0.2597 36015 96.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.6→44.328 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18492 0 317 0 18809
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00319426
X-RAY DIFFRACTIONf_angle_d0.65226323
X-RAY DIFFRACTIONf_dihedral_angle_d11.15211418
X-RAY DIFFRACTIONf_chiral_restr0.0393195
X-RAY DIFFRACTIONf_plane_restr0.0033178
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.6-3.690.33991400.32132442X-RAY DIFFRACTION97
3.69-3.78970.40631440.31612488X-RAY DIFFRACTION97
3.7897-3.90120.38571050.3182425X-RAY DIFFRACTION98
3.9012-4.0270.34681510.29622459X-RAY DIFFRACTION97
4.027-4.17080.37461830.2982434X-RAY DIFFRACTION97
4.1708-4.33770.41991050.28082449X-RAY DIFFRACTION97
4.3377-4.53490.321570.282476X-RAY DIFFRACTION96
4.5349-4.77380.34641230.24962319X-RAY DIFFRACTION96
4.7738-5.07250.3731150.25772546X-RAY DIFFRACTION97
5.0725-5.46350.37221440.27912391X-RAY DIFFRACTION96
5.4635-6.01210.34271620.29342404X-RAY DIFFRACTION98
6.0121-6.87920.3071290.26882487X-RAY DIFFRACTION97
6.8792-8.65650.22441550.20012405X-RAY DIFFRACTION97
8.6565-44.33110.19741370.17742340X-RAY DIFFRACTION92

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