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- PDB-7aar: sugar/H+ symporter STP10 in inward open conformation -

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Basic information

Entry
Database: PDB / ID: 7aar
Titlesugar/H+ symporter STP10 in inward open conformation
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
Octyl Glucose Neopentyl Glycol / beta-D-glucopyranose / Sugar transport protein 10
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.64 Å
AuthorsBavnhoej, L. / Paulsen, P.A. / Pedersen, B.P.
Funding support Denmark, 3items
OrganizationGrant numberCountry
European Research Council (ERC)637372 Denmark
Danish Council for Independent ResearchDFF-4002-00052 Denmark
The Carlsberg FoundationCF17-0180 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 1.1Oct 13, 2021Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name / _diffrn_source.pdbx_synchrotron_site
Revision 1.2Oct 27, 2021Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Nov 3, 2021Group: Data collection / Database references / Category: citation_author / pdbx_database_proc / Item: _citation_author.identifier_ORCID
Revision 1.4Jan 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
Revision 1.5Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)57,5965
Polymers56,2431
Non-polymers1,3534
Water1629
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area570 Å2
ΔGint-9 kcal/mol
Surface area19680 Å2
Unit cell
Length a, b, c (Å)83.917, 99.005, 184.515
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 56242.812 Da / Num. of mol.: 1 / Mutation: E162Q, D344N
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): DSY-5 / References: UniProt: Q9LT15
#2: Chemical ChemComp-37X / Octyl Glucose Neopentyl Glycol


Mass: 568.695 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C27H52O12
#3: 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
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 3.4 Å3/Da / Density % sol: 63.86 %
Crystal growTemperature: 292.15 K / Method: vapor diffusion, sitting drop / pH: 9 / Details: 0.3M NaCl, 0.1M MgCl2, 0.1M Bicine, 36-43% PEG400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 2, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.64→92.27 Å / Num. obs: 23016 / % possible obs: 99.9 % / Redundancy: 6.6 % / CC1/2: 0.987 / Rmerge(I) obs: 0.123 / Rpim(I) all: 0.052 / Rrim(I) all: 0.134 / Net I/σ(I): 6.6 / Num. measured all: 152793 / Scaling rejects: 545
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.64-2.716.81.29717290.7980.5351.405100
11.81-92.275.30.0532890.8940.030.06292.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XDSdata processing
Aimless0.7.4data scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
DIALS1.12data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6H7D

6h7d


Resolution: 2.64→19.856 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 36.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2779 1092 4.85 %
Rwork0.2466 21401 -
obs0.2481 22493 98.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 184.29 Å2 / Biso mean: 85.8728 Å2 / Biso min: 55.29 Å2
Refinement stepCycle: final / Resolution: 2.64→19.856 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3760 0 91 9 3860
Biso mean--92.33 72.35 -
Num. residues----485
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.64-2.75940.40971650.3799260097
2.7594-2.90450.38151260.3291261698
2.9045-3.08590.28221630.284264098
3.0859-3.32310.32331160.2619262898
3.3231-3.65560.29061470.2363266999
3.6556-4.18030.26131240.2104272299
4.1803-5.25060.25211250.22482771100
5.2506-19.8560.24971260.2465275596
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)
10.845-0.915-0.76591.91190.21271.1548-0.0177-0.30290.28530.18320.0026-0.1494-0.37220.4398-0.00040.7697-0.05220.02730.7821-0.04030.81232.26860.799-27.547
21.323-0.19760.08660.7883-0.48792.748-0.0087-0.1753-0.02620.10950.13780.2377-0.2682-0.4487-00.78640.04960.02320.6509-0.03630.8219-13.05960.084-24.186
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 16:81 )A16 - 81
2X-RAY DIFFRACTION2( CHAIN A AND ( RESID 82:500 OR RESID 601:604 OR RESID 701:709 ) )A82 - 500
3X-RAY DIFFRACTION2( CHAIN A AND ( RESID 82:500 OR RESID 601:604 OR RESID 701:709 ) )A601 - 604
4X-RAY DIFFRACTION2( CHAIN A AND ( RESID 82:500 OR RESID 601:604 OR RESID 701:709 ) )A701 - 709

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