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- PDB-5xpd: Sugar transporter of AtSWEET13 in inward-facing state with a subs... -

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Basic information

Entry
Database: PDB / ID: 5xpd
TitleSugar transporter of AtSWEET13 in inward-facing state with a substrate analog
Componentssugar transporter
KeywordsTRANSPORT PROTEIN / SWEETs sugar transporter complex
Function / homology
Function and homology information


sucrose transmembrane transporter activity / sucrose transport / seed growth / gibberellic acid transmembrane transport / gibberellin transmembrane transporter activity / sugar transmembrane transporter activity / callose deposition in cell wall / anther dehiscence / pollen development / plasma membrane => GO:0005886 ...sucrose transmembrane transporter activity / sucrose transport / seed growth / gibberellic acid transmembrane transport / gibberellin transmembrane transporter activity / sugar transmembrane transporter activity / callose deposition in cell wall / anther dehiscence / pollen development / plasma membrane => GO:0005886 / carbohydrate transport / membrane => GO:0016020 / plasma membrane
Similarity search - Function
SWEET sugar transporter / Sugar efflux transporter for intercellular exchange / Rubrerythrin, domain 2 - #10 / Rubrerythrin, domain 2 / Single Sheet / Mainly Beta
Similarity search - Domain/homology
2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE / Bidirectional sugar transporter SWEET13
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.788 Å
AuthorsHan, L. / Zhang, X.J.
Funding support China, 3items
OrganizationGrant numberCountry
the Ministry of Science and Technology2014CB910104 to XCZ China
the Chinese Academy of SciencesXDB080203 to XCZ China
National Natural Science Foundation of China31470745 to XCZ China
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Molecular mechanism of substrate recognition and transport by the AtSWEET13 sugar transporter
Authors: Han, L. / Zhu, Y.P. / Liu, M. / Zhou, Y. / Lu, G.Y. / Lan, L. / Wang, X.P. / Zhao, Y.F. / Zhang, X.C.
History
DepositionJun 1, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 13, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation_author.name
Revision 1.2Nov 22, 2023Group: 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

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Assembly

Deposited unit
A: sugar transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,3142
Polymers33,0071
Non-polymers3071
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area620 Å2
ΔGint-2 kcal/mol
Surface area15000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.780, 42.831, 116.553
Angle α, β, γ (deg.)90.00, 93.85, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein sugar transporter /


Mass: 33006.668 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9FGQ2*PLUS
#2: Chemical ChemComp-DCM / 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE / Deoxycytidine monophosphate


Mass: 307.197 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N3O7P

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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: 2.86 Å3/Da / Density % sol: 56.98 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 5.9
Details: 100mM MES (pH 5.9), 38% (w/v) PEG 600, 100mM KH2PO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9778 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 9, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9778 Å / Relative weight: 1
ReflectionResolution: 2.788→50 Å / Num. obs: 9248 / % possible obs: 96.3 % / Redundancy: 2.3 % / Rmerge(I) obs: 0.148 / Net I/σ(I): 5.8

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Processing

Software
NameVersionClassification
PHENIXdev_1819refinement
HKL-2000data processing
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CTG and 1FHH

5ctg

1fhh


Resolution: 2.788→36.684 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.26
RfactorNum. reflection% reflection
Rfree0.2821 940 10.19 %
Rwork0.2474 --
obs0.2513 9229 96.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.788→36.684 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2104 0 20 0 2124
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052180
X-RAY DIFFRACTIONf_angle_d0.9622968
X-RAY DIFFRACTIONf_dihedral_angle_d12.981755
X-RAY DIFFRACTIONf_chiral_restr0.033347
X-RAY DIFFRACTIONf_plane_restr0.005359
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7877-2.93460.36091330.3251136X-RAY DIFFRACTION93
2.9346-3.11840.31331310.29841184X-RAY DIFFRACTION97
3.1184-3.3590.33961280.27371186X-RAY DIFFRACTION97
3.359-3.69680.28361370.24261188X-RAY DIFFRACTION99
3.6968-4.2310.28631390.2321195X-RAY DIFFRACTION98
4.231-5.32810.24731300.22641200X-RAY DIFFRACTION97
5.3281-36.68740.26021420.2351200X-RAY DIFFRACTION95

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