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- PDB-8bb6: Crystal structure of Arabidopsis thaliana sucrose transporter SUC1 -

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Basic information

Entry
Database: PDB / ID: 8bb6
TitleCrystal structure of Arabidopsis thaliana sucrose transporter SUC1
ComponentsSucrose transport protein SUC1
KeywordsMEMBRANE PROTEIN / plant sucrose/proton symporter / Major Facilitator Superfamily
Function / homology
Function and homology information


sucrose:proton symporter activity / pollen germination / sucrose metabolic process / plasmodesma / response to nematode / vacuole / mitochondrion / plasma membrane
Similarity search - Function
Sucrose/H+ symporter, plant / MFS general substrate transporter like domains / Growth Hormone; Chain: A; / Major facilitator superfamily / Major Facilitator Superfamily / MFS transporter superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Sucrose transport protein SUC1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.68 Å
AuthorsBavnhoej, L. / Pedersen, B.P.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)101000936European Union
CitationJournal: Nat.Plants / Year: 2023
Title: Structure and sucrose binding mechanism of the plant SUC1 sucrose transporter.
Authors: Bavnhoj, L. / Driller, J.H. / Zuzic, L. / Stange, A.D. / Schiott, B. / Pedersen, B.P.
History
DepositionOct 12, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 31, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 28, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2May 1, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sucrose transport protein SUC1
B: Sucrose transport protein SUC1


Theoretical massNumber of molelcules
Total (without water)110,9712
Polymers110,9712
Non-polymers00
Water61334
1
A: Sucrose transport protein SUC1


Theoretical massNumber of molelcules
Total (without water)55,4861
Polymers55,4861
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Sucrose transport protein SUC1


Theoretical massNumber of molelcules
Total (without water)55,4861
Polymers55,4861
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.776, 65.622, 82.813
Angle α, β, γ (deg.)89.960, 101.740, 94.720
Int Tables number1
Space group name H-MP1
Symmetry operation#1: x,y,z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 27 through 242 or resid 244...
21(chain B and (resid 27 through 242 or resid 244...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROLEULEU(chain A and (resid 27 through 242 or resid 244...AA27 - 24228 - 243
12TYRTYRASPASP(chain A and (resid 27 through 242 or resid 244...AA244 - 247245 - 248
13GLNGLNPROPRO(chain A and (resid 27 through 242 or resid 244...AA249 - 254250 - 255
14ASNASNALAALA(chain A and (resid 27 through 242 or resid 244...AA256 - 257257 - 258
15LYSLYSPHEPHE(chain A and (resid 27 through 242 or resid 244...AA262 - 276263 - 277
16VALVALPROPRO(chain A and (resid 27 through 242 or resid 244...AA278 - 500279 - 501
21PROPROLEULEU(chain B and (resid 27 through 242 or resid 244...BB27 - 24228 - 243
22TYRTYRASPASP(chain B and (resid 27 through 242 or resid 244...BB244 - 247245 - 248
23GLNGLNPROPRO(chain B and (resid 27 through 242 or resid 244...BB249 - 254250 - 255
24ASNASNALAALA(chain B and (resid 27 through 242 or resid 244...BB256 - 257257 - 258
25LYSLYSPHEPHE(chain B and (resid 27 through 242 or resid 244...BB262 - 276263 - 277
26VALVALPROPRO(chain B and (resid 27 through 242 or resid 244...BB278 - 500279 - 501

NCS oper: (Code: givenMatrix: (-0.915373106874, 0.0103079958826, -0.402474620856), (0.0042826378681, -0.99936632701, -0.0353355833586), (-0.402583822607, -0.0340688957744, 0.914748914247)Vector: -7. ...NCS oper: (Code: given
Matrix: (-0.915373106874, 0.0103079958826, -0.402474620856), (0.0042826378681, -0.99936632701, -0.0353355833586), (-0.402583822607, -0.0340688957744, 0.914748914247)
Vector: -7.99249196073, 61.7545306039, 41.6878972808)

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Components

#1: Protein Sucrose transport protein SUC1 / Sucrose permease 1 / Sucrose-proton symporter 1


Mass: 55485.676 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: SUC1, At1g71880, F17M19.3 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q39232
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / Source method: isolated from a natural source / Formula: H2O
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: 56.2 %
Crystal growTemperature: 292 K / Method: lipidic cubic phase / pH: 6.3
Details: 43.5% PEG 400, 0.25 M Ammonium dihydrogen phosphate, 0.15 M BIS-TRIS propane

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 10, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.68→57.35 Å / Num. obs: 33404 / % possible obs: 98.6 % / Redundancy: 3.3 % / Biso Wilson estimate: 34.39 Å2 / Rpim(I) all: 0.171 / Rrim(I) all: 0.314 / Net I/σ(I): 4.7 / Num. measured all: 110948
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) all% possible all
2.68-2.733.40.8538515861.0731.98595.1
7.27-57.363.219.5541216970.0470.08599.7

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
xia23.3.2data scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
DIALS3.3.2data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: RoseTTAFold predicted model

Resolution: 2.68→34.74 Å / SU ML: 0.48 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 33.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.293 2003 6.02 %
Rwork0.2696 31272 -
obs0.2711 33275 98.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 144.19 Å2 / Biso mean: 48.3563 Å2 / Biso min: 29.91 Å2
Refinement stepCycle: final / Resolution: 2.68→34.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7188 0 0 34 7222
Biso mean---43.85 -
Num. residues----952
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2794X-RAY DIFFRACTION5.859TORSIONAL
12B2794X-RAY DIFFRACTION5.859TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.68-2.750.42971420.34452125226795
2.75-2.820.36771370.3322222235998
2.82-2.90.32471480.312205235398
2.9-30.3271390.30962265240498
3-3.10.33931440.30672243238798
3.11-3.230.30991490.28652209235898
3.23-3.380.32761400.27982235237598
3.38-3.550.36141340.28382244237899
3.55-3.780.30631480.26622260240899
3.78-4.070.25571390.2432261240099
4.07-4.480.2611460.24332219236599
4.48-5.120.29531460.25652255240199
5.12-6.450.25961460.27792282242899
6.45-34.740.2351450.23432247239299
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)
10.8042-0.08950.09950.66160.10251.3903-0.0982-0.01710.06890.15250.0855-0.19650.04880.2251-0.00010.4140.0447-0.0060.45270.03390.41889.707932.372830.8284
20.13380.03640.10360.18070.51942.1736-0.4469-0.1634-0.1383-0.4167-0.2307-0.8301-0.22181.5203-0.04421.26770.15010.14110.85030.20481.011920.66618.364520.5168
30.5498-0.09810.07231.9171-0.10082.1509-0.0553-0.0889-0.0833-0.01930.11450.1692-0.2232-0.1406-0.00010.37290.01930.01130.3952-0.00730.3908-4.694134.973813.1031
41.3406-0.01630.18480.07750.15960.7327-0.3606-0.20620.1559-0.4260.43680.272-0.3704-0.22680.01890.52110.12110.02310.5121-0.05310.3317-4.414339.5223-11.7816
51.02420.24950.03720.7364-0.30531.17370.01850.1294-0.07280.23110.07130.29260.1184-0.1241-00.43250.02940.01110.4444-0.01710.4633-13.001528.5606-16.6457
60.25710.23370.08290.22010.08810.1763-0.06080.30270.2759-0.558-0.07480.1086-0.8522-0.46460.00031.12620.20210.0250.603-0.00830.7265-17.83554.6139-29.3967
70.788-0.6615-0.79741.2360.45061.6377-0.1165-0.0766-0.0082-0.0820.0667-0.13730.26910.20460.00010.40980.0079-0.06390.41130.0090.4038.382927.7812-26.5181
80.30880.1831-0.59680.0305-0.16930.88110.20310.03410.0298-0.1195-0.2658-0.1536-0.0725-0.1527-00.3653-0.0039-0.02470.45540.00110.39572.491234.6133-35.853
90.7497-0.17970.12420.17360.06970.92820.1658-0.0363-0.20180.0196-0.21890.40560.15470.2944-00.5-0.03170.01010.366-0.02570.37694.479828.43476.7142
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 25 through 244 )B25 - 244
2X-RAY DIFFRACTION2chain 'B' and (resid 245 through 280 )B245 - 280
3X-RAY DIFFRACTION3chain 'B' and (resid 281 through 440 )B281 - 440
4X-RAY DIFFRACTION4chain 'A' and (resid 25 through 52 )A25 - 52
5X-RAY DIFFRACTION5chain 'A' and (resid 53 through 244 )A53 - 244
6X-RAY DIFFRACTION6chain 'A' and (resid 245 through 280 )A245 - 280
7X-RAY DIFFRACTION7chain 'A' and (resid 281 through 440 )A281 - 440
8X-RAY DIFFRACTION8chain 'A' and (resid 441 through 500 )A441 - 500
9X-RAY DIFFRACTION9chain 'B' and (resid 441 through 500 )B441 - 500

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