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- PDB-7dj1: Crystal structure of the G26C mutant of LeuT -

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Basic information

Entry
Database: PDB / ID: 7dj1
TitleCrystal structure of the G26C mutant of LeuT
ComponentsNa(+):neurotransmitter symporter (Snf family)
KeywordsTRANSPORT PROTEIN / Neurotransmitter transporter / NSS / SLC6
Function / homologynitrogen compound transport / Sodium:neurotransmitter symporter / Sodium:neurotransmitter symporter superfamily / Sodium:neurotransmitter symporter family / Sodium:neurotransmitter symporter family profile. / sodium ion transmembrane transport / plasma membrane / LEUCINE / Na(+):neurotransmitter symporter (Snf family)
Function and homology information
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.528 Å
AuthorsFan, J. / Xiao, Y. / Sun, Z. / Zhou, X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31770783 China
CitationJournal: J.Biol.Chem. / Year: 2021
Title: Crystal structures of LeuT reveal conformational dynamics in the outward-facing states.
Authors: Fan, J. / Xiao, Y. / Quick, M. / Yang, Y. / Sun, Z. / Javitch, J.A. / Zhou, X.
History
DepositionNov 19, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 7, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 21, 2021Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jul 21, 2021Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Nov 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Na(+):neurotransmitter symporter (Snf family)
B: Na(+):neurotransmitter symporter (Snf family)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,3528
Polymers114,9982
Non-polymers3546
Water0
1
A: Na(+):neurotransmitter symporter (Snf family)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,6764
Polymers57,4991
Non-polymers1773
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Na(+):neurotransmitter symporter (Snf family)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,6764
Polymers57,4991
Non-polymers1773
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.853, 94.115, 94.248
Angle α, β, γ (deg.)90.000, 95.930, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21(chain B and (resid 5 through 467 or resid 480 through 702))

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain AA5 - 507
211(chain B and (resid 5 through 467 or resid 480 through 702))B5 - 467
221(chain B and (resid 5 through 467 or resid 480 through 702))B480 - 702

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Components

#1: Protein Na(+):neurotransmitter symporter (Snf family) / LeuT


Mass: 57498.781 Da / Num. of mol.: 2 / Mutation: G26C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: O67854
#2: Chemical ChemComp-LEU / LEUCINE / Leucine


Type: L-peptide linking / Mass: 131.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
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: 3.14 Å3/Da / Density % sol: 60.83 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M choline chloride, 0.1 M Tris-HCI pH 7.5, 14% (w/v) PEG 2000 MME, 15% (v/v) glycerol and 1 mM L-Leu

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 25, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 3.528→47.058 Å / Num. obs: 17501 / % possible obs: 98.8 % / Redundancy: 3.4 % / CC1/2: 0.996 / Rmerge(I) obs: 0.145 / Rpim(I) all: 0.092 / Rrim(I) all: 0.172 / Net I/σ(I): 6.6
Reflection shell

Num. unique obs: 891 / Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
3.528-3.5893.50.75831510.8030.4670.8931.898.7
9.551-47.0583.10.03327910.9990.0220.042297.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XDSdata reduction
Aimless0.7.4data scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2A65

2a65


Resolution: 3.528→46.872 Å / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 31.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2715 924 5.32 %
Rwork0.2474 16444 -
obs0.2486 17368 98.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 147.37 Å2 / Biso min: 54.42 Å2
Refinement stepCycle: final / Resolution: 3.528→46.872 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7766 0 22 0 7788
Biso mean--73.93 --
Num. residues----978
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4584X-RAY DIFFRACTION3.044TORSIONAL
12B4584X-RAY DIFFRACTION3.044TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.528-3.71380.32621540.3199230298
3.7138-3.94640.30411470.3028231298
3.9464-4.25090.26931410.2798231298
4.2509-4.67840.24261030.2328237799
4.6784-5.35450.27471160.222238899
5.3545-6.74290.28941280.2519238098
6.7429-46.8720.24241350.2142237397
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)
11.48150.4447-1.00661.2302-0.12631.44710.1248-0.7052-0.71720.6978-0.1069-0.92980.38640.0366-0.00720.93250.0137-0.03280.7940.31260.962555.101413.545145.7248
23.80261.41170.17710.7876-0.40032.644-0.1435-0.32510.36760.02610.22390.2624-0.16880.17070.01790.55080.03320.01560.5518-0.04230.632160.333628.147630.3307
32.1842-0.68940.13131.404-2.05082.95330.1433-1.00330.32010.3415-0.05380.2767-0.30040.1741-0.10070.63520.0553-0.09251.1072-0.22640.758463.288128.217247.4801
42.5769-1.00890.53621.0103-0.08521.1699-0.1236-0.6217-0.39840.20080.08050.01910.223-0.173-0.00220.5646-0.00990.01530.64680.10090.592748.410816.711839.1778
52.63330.3457-0.20311.37890.1190.9317-0.0260.9038-0.4757-0.0643-0.01560.39150.2193-0.0145-0.0320.8113-0.01190.0961.0352-0.27080.681419.484116.22572.3136
62.8528-0.78070.04890.6010.02832.406-0.207-0.0568-0.0970.01850.32940.1483-0.0586-0.1909-0.10660.5304-0.054-0.04930.58730.06910.709914.433628.714219.4533
73.2825-0.0834-0.35970.94671.18542.00260.07520.92190.2318-0.33850.0649-0.2143-0.038-0.3125-0.14150.7329-0.121-0.13550.99870.15470.796711.353430.99692.5072
83.2559-0.24480.41771.1028-0.35291.15-0.07150.6894-0.2132-0.06230.1226-0.35170.2590.1907-0.10020.6154-0.05220.00710.7048-0.12610.713426.415818.70029.1118
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 87 )A5 - 87
2X-RAY DIFFRACTION2chain 'A' and (resid 88 through 214 )A88 - 214
3X-RAY DIFFRACTION3chain 'A' and (resid 215 through 336 )A215 - 336
4X-RAY DIFFRACTION4chain 'A' and (resid 337 through 601 )A337 - 601
5X-RAY DIFFRACTION5chain 'B' and (resid 5 through 87 )B5 - 87
6X-RAY DIFFRACTION6chain 'B' and (resid 88 through 214 )B88 - 214
7X-RAY DIFFRACTION7chain 'B' and (resid 215 through 336 )B215 - 336
8X-RAY DIFFRACTION8chain 'B' and (resid 337 through 601 )B337 - 601

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