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- PDB-6h7d: Crystal Structure of A. thaliana Sugar Transport Protein 10 in co... -

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Basic information

Entry
Database: PDB / ID: 6h7d
TitleCrystal Structure of A. thaliana Sugar Transport Protein 10 in complex with glucose in the outward occluded state
ComponentsSugar transport protein 10
KeywordsMEMBRANE PROTEIN / alpha-helical protein / sugar transport / protoin/sugar symporter / MAjor Facilitator
Function / homology
Function and homology information


mannose transmembrane transporter activity / : / hexose:proton symporter activity / galactose transmembrane transporter activity / hexose transmembrane transport / cellular response to glucose stimulus / plasma membrane
Similarity search - Function
Sugar transport protein STP/MST-like, plant / Sugar transport protein STP/Polyol transporter PLT, plant / Sugar/inositol transporter / Sugar transport proteins signature 2. / Sugar transport proteins signature 1. / Major facilitator, sugar transporter-like / Sugar (and other) transporter / Sugar transporter, conserved site / Major facilitator superfamily domain / Major facilitator superfamily (MFS) profile. / MFS transporter superfamily
Similarity search - Domain/homology
beta-D-glucopyranose / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / PHOSPHATE ION / Sugar transport protein 10
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsPedersen, B.P. / Paulsen, P.A. / Custodio, T.F.
Funding support Denmark, 2items
OrganizationGrant numberCountry
Danish Council for Independent ResearchDFF-4002-0052 Denmark
European Research CouncilStG-637372 Denmark
CitationJournal: Nat Commun / Year: 2019
Title: Crystal structure of the plant symporter STP10 illuminates sugar uptake mechanism in monosaccharide transporter superfamily.
Authors: Paulsen, P.A. / Custodio, T.F. / Pedersen, B.P.
History
DepositionJul 31, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 6, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2019Group: Data collection / Category: chem_comp / reflns_shell / Item: _chem_comp.type / _reflns_shell.percent_possible_all
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.pdbx_synonyms ..._chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Oct 9, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _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: Sugar transport protein 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,3219
Polymers56,9371
Non-polymers2,3848
Water61334
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1480 Å2
ΔGint-6 kcal/mol
Surface area18600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.680, 92.460, 66.800
Angle α, β, γ (deg.)90.000, 109.370, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Sugar transport protein 10 / Hexose transporter 10


Mass: 56936.637 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: STP10, At3g19940, MPN9.19 / Plasmid: p423_GAL1 / Production host: Saccharomyces cerevisiae (brewer's yeast) / Variant (production host): DSY-5 / References: UniProt: Q9LT15
#2: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 41 molecules

#3: Chemical ChemComp-P33 / 3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL / HEPTAETHYLENE GLYCOL / PEG330


Mass: 326.383 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H30O8 / Comment: precipitant*YM
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Chemical
ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C21H40O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.81 Å3/Da / Density % sol: 56.17 % / Description: 70x10x30 um
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 4.5
Details: 0.1M NaCitrate pH 4.5, 0.01 M Ammonium dihydrogen phosphate, 5% DMSO, 30% PEG400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 4, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.4→63.018 Å / Num. obs: 23248 / % possible obs: 99.8 % / Redundancy: 6.591 % / Biso Wilson estimate: 41.32 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.282 / Rrim(I) all: 0.306 / Χ2: 0.989 / Net I/σ(I): 4.9 / Num. measured all: 153232 / Scaling rejects: 34
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.4-2.56.6462.1550.8926560.3482.34399.8
2.5-2.66.661.7181.1322770.4971.86799.8
2.6-2.76.6641.4171.419560.5681.539100
2.7-2.86.6491.0181.9916770.7261.10699.6
2.8-2.96.5550.8982.214730.7590.975100
2.9-36.5110.7682.5712670.7830.83699.8
3-3.26.4880.6013.1620810.8610.65499.7
3.2-3.46.6060.444.3416190.9220.47899.8
3.4-3.66.760.3035.9512820.9710.328100
3.6-3.86.720.2317.5210350.9820.2599.6
3.8-46.5930.1868.768480.9870.20199.5
4-56.6110.14211.0924530.9910.154100
5-66.5830.14311.0611020.9880.15599.4
6-86.3790.11812.138680.9940.12999.9
8-95.9530.08914.261920.9950.09799
9-105.9290.09915.591260.9960.108100
10-156.2460.08916.362320.9970.09698.3
15-205.9830.07617.07580.9920.08496.7
20-63.0184.8260.08314.59460.9990.09697.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSJan 26, 2018data reduction
XSCALEJan 26, 2018data scaling
PHASER2.8.1phasing
PHENIX1.13rc1refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→63.018 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 30.59
RfactorNum. reflection% reflection
Rfree0.2682 1161 5 %
Rwork0.2025 --
obs0.2057 23216 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 163.34 Å2 / Biso mean: 54.437 Å2 / Biso min: 23.76 Å2
Refinement stepCycle: final / Resolution: 2.4→63.018 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3771 0 164 34 3969
Biso mean--68.7 46.43 -
Num. residues----487
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4-2.50920.36511450.317127342879100
2.5092-2.64150.35291490.274127322881100
2.6415-2.8070.3171360.253227622898100
2.807-3.02370.3411530.236227592912100
3.0237-3.3280.30651450.218527412886100
3.328-3.80950.23261420.187127522894100
3.8095-4.79930.24891430.165327822925100
4.7993-63.04020.21651480.17512793294199
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)
10.91110.03450.02781.9717-0.26651.0631-0.0456-0.1487-0.10560.16340.0545-0.05040.1325-0.0266-0.00390.68390.02590.09660.266-0.00720.3556-21.9167-17.87970.7933
21.89691.1938-0.0612.29090.81061.7925-0.17060.4545-0.0395-0.64450.2089-0.14790.12140.1779-0.05021.0469-0.00150.13560.42440.03930.3867-16.21-7.3278-28.5862
31.69080.11180.12082.4483-0.05940.7652-0.0045-0.13210.05210.16890.0256-0.0226-0.30370.0096-0.03150.47110.00470.03160.2133-0.01610.2462-19.08851.7251.3504
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth seq-ID
1X-RAY DIFFRACTION1resid 21 through 225 OR resid 601 OR resid 602 OR resid 603 OR resid 606 OR resid 6070
2X-RAY DIFFRACTION2resid 226 through 280 OR resid 472 through 5070
3X-RAY DIFFRACTION3resid 281 through 471 OR resid 600 OR resid 604 OR resid 6050

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