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- PDB-7dix: Crystal structure of LeuT in lipidic cubic phase at pH 5 -

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Basic information

Entry
Database: PDB / ID: 7dix
TitleCrystal structure of LeuT in lipidic cubic phase at pH 5
ComponentsNa(+):neurotransmitter symporter (Snf family)
KeywordsTRANSPORT PROTEIN / Neurotransmitter transporter / NSS / SLC6
Function / homologySodium:neurotransmitter symporter / Sodium:neurotransmitter symporter superfamily / Sodium:neurotransmitter symporter family / Sodium:neurotransmitter symporter family profile. / sodium ion transmembrane transport / membrane / SELENOMETHIONINE / Na(+):neurotransmitter symporter (Snf family)
Function and homology information
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.49 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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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)115,3677
Polymers114,9052
Non-polymers4615
Water1086
1
A: Na(+):neurotransmitter symporter (Snf family)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,6954
Polymers57,4531
Non-polymers2423
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Na(+):neurotransmitter symporter (Snf family)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,6723
Polymers57,4531
Non-polymers2192
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.162, 115.070, 80.819
Angle α, β, γ (deg.)90.000, 102.890, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 5 through 43 or resid 45...
21(chain B and (resid 5 through 43 or resid 45...

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
11ARGARGPHEPHE(chain A and (resid 5 through 43 or resid 45...AA5 - 435 - 43
12ILEILELYSLYS(chain A and (resid 5 through 43 or resid 45...AA45 - 9145 - 91
13LEULEUPROPRO(chain A and (resid 5 through 43 or resid 45...AA93 - 13193 - 131
14THRTHRMSEMSE(chain A and (resid 5 through 43 or resid 45...AA - C135 - 601135
15HOHHOHHOHHOH(chain A and (resid 5 through 43 or resid 45...AH701
21ARGARGPHEPHE(chain B and (resid 5 through 43 or resid 45...BB5 - 435 - 43
22ILEILELYSLYS(chain B and (resid 5 through 43 or resid 45...BB45 - 9145 - 91
23LEULEUMETMET(chain B and (resid 5 through 43 or resid 45...BB93 - 47693 - 476
24THRTHRMSEMSE(chain B and (resid 5 through 43 or resid 45...BB - F482 - 601482
25HOHHOHHOHHOH(chain B and (resid 5 through 43 or resid 45...BI702

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Components

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


Mass: 57452.680 Da / Num. of mol.: 2
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-MSE / SELENOMETHIONINE / Selenomethionine


Type: L-peptide linking / Mass: 196.106 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H11NO2Se / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O
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: 2.93 Å3/Da / Density % sol: 57.96 %
Crystal growTemperature: 293.15 K / Method: lipidic cubic phase / pH: 5
Details: 0.1 M NaCl, 0.1 M Na+-HEPES pH 7.0, 32% (v/v) PEG 350 MME, 10 mM TCEP-HCl unbuffered and 1 mM L-SeMet (the final solution at pH ~5.0)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.49→46.463 Å / Num. obs: 16453 / % possible obs: 97.2 % / Redundancy: 3 % / Biso Wilson estimate: 73.46 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.15 / Rpim(I) all: 0.1 / Rrim(I) all: 0.18 / Net I/σ(I): 7.3 / Num. measured all: 48779
Reflection shell

Num. unique obs: 817 / Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
3.49-3.5530.64724750.7630.4260.777298.6
9.447-46.4632.90.02924090.9990.020.0352293.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.4data scaling
PHASERphasing
PHENIX1.13_2998refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2A65 and 3TT1

2a65

3tt1


Resolution: 3.49→41.66 Å / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 27.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2502 801 4.88 %
Rwork0.2212 15597 -
obs0.2226 16398 96.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 138.42 Å2 / Biso mean: 61.4363 Å2 / Biso min: 29.64 Å2
Refinement stepCycle: final / Resolution: 3.49→41.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7872 0 21 6 7899
Biso mean--53.81 47.48 -
Num. residues----992
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4387X-RAY DIFFRACTION6.153TORSIONAL
12B4387X-RAY DIFFRACTION6.153TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.49-3.70810.33851410.2728261898
3.7081-3.99420.23761480.258257798
3.9942-4.39580.28091330.2378262797
4.3958-5.03090.23881170.209260197
5.0309-6.33490.27291400.2295258997
6.3349-41.660.18851220.1722258594
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)
11.01690.5704-0.70330.3612-0.51710.8282-0.1419-0.15640.20130.1737-0.22880.0345-0.04120.1789-00.38930.0264-0.00410.4682-0.01040.432526.7038-26.701834.9458
20.1060.20160.04250.36820.08970.0152-0.08220.0710.04060.0898-0.04730.0015-0.1151-0.1546-00.4314-0.0382-0.05050.459-0.00040.470121.8043-20.469922.6822
30.1428-0.0017-0.07980.0262-0.04920.15110.1986-0.0496-0.7748-0.0048-0.15040.1677-0.0115-0.2670.00030.4728-0.0213-0.08660.5590.11390.62487.5476-51.191636.1606
41.24190.2868-0.39610.8369-1.01061.2128-0.09060.1130.10470.01660.07170.22210.00240.0538-0.00020.35050.06180.0220.3805-0.05720.41889.4633-29.722433.9625
50.252-0.0204-0.27760.5650.43180.5902-0.3690.1131-0.1066-0.33830.3299-0.87760.22-0.34270.00010.49040.00770.12030.6164-0.04420.736133.092-41.32837.9511
60.3190.17040.1450.1467-0.10560.56420.0452-0.12280.1170.04-0.00290.195-0.1450.056-00.4435-0.034-0.01930.43040.00390.501619.4769-30.138735.7543
70.31280.0031-0.7185-0.0018-0.00541.6144-0.1166-0.0262-0.052-0.20450.0337-0.0117-0.092-0.1175-00.3872-0.0841-0.04590.3907-0.0190.387622.0621-21.929119.4878
80.8404-0.33720.36220.1696-0.30140.8384-0.47510.1107-0.0866-0.26030.45860.0279-0.25520.6334-0.00020.3736-0.12120.02230.5260.00390.617438.941-25.431823.7883
90.43760.31230.2860.35240.10220.2557-0.0333-0.1728-0.1262-0.5026-0.0152-0.3206-0.25820.22-0.00280.592-0.11770.10990.3784-0.00210.507117.4293-22.95999.0827
100.6169-0.4849-0.14510.39710.02670.4625-0.02610.0687-0.04650.0267-0.0048-0.0179-0.272-0.0767-00.44420.1264-0.03760.43370.10020.5321-7.2033-26.0636-21.0364
110.45350.2069-0.14120.3458-0.29160.26040.0408-0.10850.011-0.0790.04540.0053-0.2626-0.021700.50690.1332-0.01040.5354-0.00620.44392.1812-28.3472-11.0224
120.788-0.8335-0.59841.17711.13851.3138-0.12620.1253-0.0102-0.1070.0093-0.2104-0.26730.1558-0.00010.4929-0.04260.0560.49770.03790.423211.2946-29.5694-18.7659
130.5963-0.39480.00510.79640.68720.8857-0.11610.119-0.289-0.2101-0.05520.2134-0.261-0.1433-0.00020.53390.039-0.00640.641-0.0420.5812-5.9511-34.9446-23.5235
140.30.3326-0.01590.63870.61531.5412-0.15480.0163-0.0595-0.04120.0851-0.0433-0.3779-0.105-00.52710.07650.01430.4518-0.01240.4631.6968-23.018-8.7668
150.87010.39860.76280.73660.39660.6764-0.1652-0.00420.0420.4559-0.1055-0.1533-0.3645-0.1579-0.09780.34720.0532-0.00450.4393-0.04920.2829-9.0286-23.9532-2.9415
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 54 )A5 - 54
2X-RAY DIFFRACTION2chain 'A' and (resid 55 through 124 )A55 - 124
3X-RAY DIFFRACTION3chain 'A' and (resid 125 through 152 )A125 - 152
4X-RAY DIFFRACTION4chain 'A' and (resid 153 through 215 )A153 - 215
5X-RAY DIFFRACTION5chain 'A' and (resid 216 through 254 )A216 - 254
6X-RAY DIFFRACTION6chain 'A' and (resid 255 through 369 )A255 - 369
7X-RAY DIFFRACTION7chain 'A' and (resid 370 through 437 )A370 - 437
8X-RAY DIFFRACTION8chain 'A' and (resid 438 through 482 )A438 - 482
9X-RAY DIFFRACTION9chain 'A' and (resid 483 through 601 )A483 - 601
10X-RAY DIFFRACTION10chain 'B' and (resid 5 through 54 )B5 - 54
11X-RAY DIFFRACTION11chain 'B' and (resid 55 through 152 )B55 - 152
12X-RAY DIFFRACTION12chain 'B' and (resid 153 through 214 )B153 - 214
13X-RAY DIFFRACTION13chain 'B' and (resid 215 through 336 )B215 - 336
14X-RAY DIFFRACTION14chain 'B' and (resid 337 through 437 )B337 - 437
15X-RAY DIFFRACTION15chain 'B' and (resid 438 through 601 )B438 - 601

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