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- PDB-7aaq: sugar/H+ symporter STP10 in outward occluded conformation -

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Basic information

Entry
Database: PDB / ID: 7aaq
Titlesugar/H+ symporter STP10 in outward occluded conformation
ComponentsSugar transport protein 10
KeywordsMEMBRANE PROTEIN / ALPHA-HELICAL PROTEIN / SUGAR TRANSPORT / PROTOIN/SUGAR SYMPORTER / MAJOR FACILITATOR
Function / homology
Function and homology information


hexose:proton symporter activity / mannose transmembrane transporter activity / D-glucose: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
ACETATE ION / beta-D-glucopyranose / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / Sugar transport protein 10
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.81 Å
AuthorsBavnhoej, L. / Paulsen, P.A. / Pedersen, B.P.
Funding support Denmark, 3items
OrganizationGrant numberCountry
European Research Council (ERC)637372 Denmark
The Carlsberg FoundationCF17-0180 Denmark
Danish Council for Independent ResearchDFF-4002-00052 Denmark
CitationJournal: Nat.Plants / Year: 2021
Title: Molecular mechanism of sugar transport in plants unveiled by structures of glucose/H + symporter STP10.
Authors: Bavnhoj, L. / Paulsen, P.A. / Flores-Canales, J.C. / Schiott, B. / Pedersen, B.P.
History
DepositionSep 4, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 18, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 3, 2021Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / diffrn / diffrn_detector / diffrn_radiation / diffrn_radiation_wavelength / diffrn_source / pdbx_database_proc
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 / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / diffrn_source / pdbx_initial_refinement_model
Item: _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sugar transport protein 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,4289
Polymers56,2451
Non-polymers2,1838
Water2,828157
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1910 Å2
ΔGint3 kcal/mol
Surface area18530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.496, 92.780, 119.788
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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: 56244.781 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) / Strain (production host): DSY5 / References: UniProt: Q9LT15
#2: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / 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, 164 molecules

#3: Chemical
ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H40O4
#4: Chemical ChemComp-XPE / 3,6,9,12,15,18,21,24,27-NONAOXANONACOSANE-1,29-DIOL / DECAETHYLENE GLYCOL / Polyethylene glycol


Mass: 458.541 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H42O11 / Comment: precipitant*YM
#5: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 157 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.94 Å3/Da / Density % sol: 58.1 %
Crystal growTemperature: 292.15 K / Method: lipidic cubic phase / pH: 4
Details: 0.1-0.15M Ammonium Acetate, 0.1M Sodium Citrate and 36-40% PEG400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97942 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 20, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97942 Å / Relative weight: 1
ReflectionResolution: 1.81→59.9 Å / Num. obs: 61268 / % possible obs: 100 % / Redundancy: 11 % / CC1/2: 0.998 / Rmerge(I) obs: 0.168 / Rpim(I) all: 0.053 / Rrim(I) all: 0.176 / Net I/σ(I): 7.7 / Num. measured all: 665695 / Scaling rejects: 1006
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.81-1.8412.5014758029640.6510.7882.491.198.7
4.91-59.9322.20.047741133170.9990.0150.0525.2100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.17.1refinement
DIALS1-14-4data reduction
Aimless0.7.4data scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6H7D

6h7d


Resolution: 1.81→46.39 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 24.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.212 3030 4.96 %
Rwork0.1874 58054 -
obs0.1887 61268 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 120.64 Å2 / Biso mean: 37.451 Å2 / Biso min: 19.99 Å2
Refinement stepCycle: final / Resolution: 1.81→46.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3771 0 151 157 4079
Biso mean--55.13 43.21 -
Num. residues----487
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 22

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.81-1.840.43461340.36992536267098
1.84-1.870.36141160.341426112727100
1.87-1.90.2691200.308126302750100
1.9-1.930.32791300.289126312761100
1.93-1.970.29881420.269625872729100
1.97-2.010.30831430.242625852728100
2.01-2.060.2411520.229526052757100
2.06-2.10.25881320.207226032735100
2.1-2.160.25321310.191526322763100
2.16-2.210.21221330.176926332766100
2.21-2.280.20291450.167125922737100
2.28-2.350.20961360.159226322768100
2.35-2.440.2031530.156126212774100
2.44-2.530.17691200.158426372757100
2.54-2.650.18631460.158226302776100
2.65-2.790.19031460.158326432789100
2.79-2.960.18241480.15926492797100
2.96-3.190.20271290.176426712800100
3.19-3.510.181370.178426752812100
3.51-4.020.2261500.1726762826100
4.02-5.070.19121380.189927332871100
5.07-46.390.18751490.179428422991100
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)
10.77260.2176-0.78561.3343-0.11184.46110.0668-0.22310.11390.28090.0350.0862-0.13090.2398-0.13250.254-0.02170.01550.2557-0.01490.297426.6778106.393839.1928
20.71920.4475-0.21992.03230.6745.1953-0.04840.06860.1019-0.25430.00410.2089-0.3368-0.16650.05310.21340.0587-0.03550.1771-0.00010.309519.053113.325526.6873
30.7589-0.1544-0.11631.84090.74043.1340.00350.00170.0005-0.07730.0184-0.0889-0.1560.237-0.04180.1601-0.04090.00940.21290.02060.273128.1993105.379225.6559
40.64990.18080.00061.46040.23751.9474-0.0640.13130.0537-0.3360.05740.0022-0.17340.02160.03010.21680.00910.02520.2085-0.00380.245523.588103.792316.5103
51.07470.2164-0.97491.8236-0.59634.5511-0.0964-0.1408-0.01820.0282-0.0095-0.09370.39770.36290.10010.2130.07140.02240.24720.00630.316730.26886.70830.651
64.19720.1970.58214.06830.57254.6756-0.0182-0.8036-0.34030.86620.0637-0.06250.3797-0.2034-0.0920.39130.06170.02070.35220.04110.329.694183.563843.2735
70.49680.0634-0.28241.334-0.43872.4328-0.01-0.04550.0068-0.0058-0.00650.11250.0686-0.02910.01610.162-0.0170.00970.2312-0.01050.286316.776992.492327.0992
82.46360.55681.43642.4387-0.4952.87580.10550.1663-0.1258-0.47790.05350.1540.3434-0.0739-0.14560.442-0.0318-0.02080.2872-0.03060.297416.402588.36834.0995
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 21 through 81 )A21 - 81
2X-RAY DIFFRACTION2chain 'A' and (resid 82 through 134 )A82 - 134
3X-RAY DIFFRACTION3chain 'A' and (resid 135 through 196 )A135 - 196
4X-RAY DIFFRACTION4chain 'A' and (resid 197 through 316 )A197 - 316
5X-RAY DIFFRACTION5chain 'A' and (resid 317 through 373 )A317 - 373
6X-RAY DIFFRACTION6chain 'A' and (resid 374 through 403 )A374 - 403
7X-RAY DIFFRACTION7chain 'A' and (resid 404 through 473 )A404 - 473
8X-RAY DIFFRACTION8chain 'A' and (resid 474 through 507 )A474 - 507

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