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- PDB-6m20: Crystal structure of Plasmodium falciparum hexose transporter PfH... -

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Basic information

Entry
Database: PDB / ID: 6m20
TitleCrystal structure of Plasmodium falciparum hexose transporter PfHT1 bound with glucose
ComponentsHexose transporter 1
KeywordsTRANSPORT PROTEIN / MFS / hexose transporter / occluded state / Plasmodium falciparum
Function / homology
Function and homology information


hexose transmembrane transporter activity / plasma membrane
Similarity search - Function
Glucose transporter GLUT / Sugar/inositol transporter / Sugar transport proteins signature 2. / Sugar transport proteins signature 1. / MFS general substrate transporter like domains / Sugar transporter, conserved site / Major facilitator, sugar transporter-like / Sugar (and other) transporter / Growth Hormone; Chain: A; / Major facilitator superfamily domain ...Glucose transporter GLUT / Sugar/inositol transporter / Sugar transport proteins signature 2. / Sugar transport proteins signature 1. / MFS general substrate transporter like domains / Sugar transporter, conserved site / Major facilitator, sugar transporter-like / Sugar (and other) transporter / Growth Hormone; Chain: A; / Major facilitator superfamily domain / Major facilitator superfamily (MFS) profile. / MFS transporter superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
beta-D-glucopyranose / Hexose transporter 1
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsJiang, X. / Yuan, Y.Y. / Zhang, S. / Wang, N. / Yan, C.Y. / Yan, N.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31630017 China
National Natural Science Foundation of China (NSFC)81861138009 China
CitationJournal: Cell / Year: 2020
Title: Structural Basis for Blocking Sugar Uptake into the Malaria Parasite Plasmodium falciparum.
Authors: Jiang, X. / Yuan, Y. / Huang, J. / Zhang, S. / Luo, S. / Wang, N. / Pu, D. / Zhao, N. / Tang, Q. / Hirata, K. / Yang, X. / Jiao, Y. / Sakata-Kato, T. / Wu, J.W. / Yan, C. / Kato, N. / Yin, H. / Yan, N.
History
DepositionFeb 26, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 9, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 29, 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
Revision 1.3Oct 16, 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

Downloads & links

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Assembly

Deposited unit
A: Hexose transporter 1
B: Hexose transporter 1
C: Hexose transporter 1
D: Hexose transporter 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)230,57721
Polymers225,8734
Non-polymers4,70417
Water82946
1
A: Hexose transporter 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,8746
Polymers56,4681
Non-polymers1,4065
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Hexose transporter 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,2614
Polymers56,4681
Non-polymers7933
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Hexose transporter 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,8746
Polymers56,4681
Non-polymers1,4065
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Hexose transporter 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,5685
Polymers56,4681
Non-polymers1,0994
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)120.000, 68.300, 175.300
Angle α, β, γ (deg.)90.000, 103.300, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Hexose transporter 1 / PfHT1 / Putative sugar transporter


Mass: 56468.301 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Gene: ht1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O97467
#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.: 4 / Source method: isolated from a natural 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
#3: Sugar
ChemComp-BNG / nonyl beta-D-glucopyranoside / Beta-NONYLGLUCOSIDE / nonyl beta-D-glucoside / nonyl D-glucoside / nonyl glucoside


Type: D-saccharide / Mass: 306.395 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Formula: C15H30O6 / Comment: detergent*YM
IdentifierTypeProgram
b-nonylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / 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: 3.26 Å3/Da / Density % sol: 62.28 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.7
Details: 0.1 M NaCl, 0.1 M MES pH 5.7, 26% (w/v) PEG 400 and 2% (w/v) Benzamidine hydrochloride

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 29, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 84480 / % possible obs: 98.8 % / Redundancy: 3.43 % / CC1/2: 0.998 / Net I/σ(I): 7.89
Reflection shellResolution: 2.6→2.7 Å / Num. unique obs: 8948 / CC1/2: 0.666

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Processing

Software
NameVersionClassification
PHENIX1.8.3_1479refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZW9

4zw9


Resolution: 2.6→20 Å / FOM work R set: 0.7162 / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 33.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2656 4199 4.99 %
Rwork0.2446 79949 -
obs0.2457 84148 98.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 168.99 Å2 / Biso mean: 83.94 Å2 / Biso min: 34.85 Å2
Refinement stepCycle: final / Resolution: 2.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14937 0 321 46 15304
Biso mean--86.23 71.69 -
Num. residues----1908
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00415632
X-RAY DIFFRACTIONf_angle_d0.61421193
X-RAY DIFFRACTIONf_chiral_restr0.0282544
X-RAY DIFFRACTIONf_plane_restr0.0032519
X-RAY DIFFRACTIONf_dihedral_angle_d11.4975496
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.6-2.62950.40041350.4068243792
2.6295-2.66040.43431440.4039265398
2.6604-2.69270.44161390.3833261498
2.6927-2.72680.38771340.3738269399
2.7268-2.76250.44481200.3524266499
2.7625-2.80030.36711340.3505264999
2.8003-2.84020.33311310.3381266099
2.8402-2.88250.3721480.3182261899
2.8825-2.92740.36021450.3266267799
2.9274-2.97520.35621450.2988266999
2.9752-3.02630.32721390.2868262199
3.0263-3.08120.29741420.2893271099
3.0812-3.14020.28811510.2826258899
3.1402-3.20410.33661310.2716267599
3.2041-3.27340.2721340.2628265398
3.2734-3.34920.31051230.2576267399
3.3492-3.43260.25151550.254268799
3.4326-3.52490.25371380.2453264299
3.5249-3.6280.29991350.2527268999
3.628-3.74440.24481480.2558265699
3.7444-3.87730.27771450.2362268499
3.8773-4.03130.27521440.2368268599
4.0313-4.21320.22211510.2205265499
4.2132-4.4330.26811430.2195267399
4.433-4.70740.22461280.2108269899
4.7074-5.06540.26151560.2131269099
5.0654-5.56520.25381410.239270999
5.5652-6.34780.25911360.2481270699
6.3478-7.91430.21461490.2245271498
7.9143-200.19791350.1921280898

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