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

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Basic information

Entry
Database: PDB / ID: 7dii
TitleCrystal structure of LeuT in lipidic cubic phase at pH 7
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 / 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: 2.403 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)115,2608
Polymers114,9052
Non-polymers3546
Water1,63991
1
A: Na(+):neurotransmitter symporter (Snf family)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,6304
Polymers57,4531
Non-polymers1773
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Na(+):neurotransmitter symporter (Snf family)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,6304
Polymers57,4531
Non-polymers1773
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.588, 72.184, 80.806
Angle α, β, γ (deg.)100.890, 97.580, 115.160
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 5 through 58 or resid 60...
21(chain B and (resid 5 through 58 or resid 60...

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
11ARGARGLEULEU(chain A and (resid 5 through 58 or resid 60...AA5 - 585 - 58
12TRPTRPLYSLYS(chain A and (resid 5 through 58 or resid 60...AA60 - 27160 - 271
13ARGARGARGARG(chain A and (resid 5 through 58 or resid 60...AA5 - 5065 - 506
14ARGARGARGARG(chain A and (resid 5 through 58 or resid 60...AA5 - 5065 - 506
15ILEILEVALVAL(chain A and (resid 5 through 58 or resid 60...AA364 - 413364 - 413
16PHEPHEARGARG(chain A and (resid 5 through 58 or resid 60...AA415 - 506415 - 506
17LEULEUHOHHOH(chain A and (resid 5 through 58 or resid 60...AC - I601 - 702
21ARGARGLEULEU(chain B and (resid 5 through 58 or resid 60...BB5 - 585 - 58
22TRPTRPPROPRO(chain B and (resid 5 through 58 or resid 60...BB60 - 13060 - 130
23THRTHRLYSLYS(chain B and (resid 5 through 58 or resid 60...BB135 - 271135 - 271
24GLNGLNPROPRO(chain B and (resid 5 through 58 or resid 60...BB273 - 362273 - 362
25PHEPHEARGARG(chain B and (resid 5 through 58 or resid 60...BB415 - 506415 - 506
26LEULEUHOHHOH(chain B and (resid 5 through 58 or resid 60...BF - J601 - 702

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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-LEU / 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / 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: 2.83 Å3/Da / Density % sol: 56.53 %
Crystal growTemperature: 293.15 K / Method: lipidic cubic phase / pH: 7
Details: 0.1 M NaCl, 0.1 M Na+-HEPES pH 7.0, 32% (v/v) PEG 350 MME 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: BL19U1 / Wavelength: 1.1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 25, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.403→36.06 Å / Num. obs: 47577 / % possible obs: 96.9 % / Redundancy: 3.5 % / Biso Wilson estimate: 41.35 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.044 / Rrim(I) all: 0.083 / Net I/σ(I): 10.6 / Num. measured all: 164247
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.403-2.4442.90.439680623620.8550.310.5412.296.3
6.509-36.063.50.031823323740.9960.0190.03626.897.1

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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

2a65


Resolution: 2.403→32.097 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.99 / Phase error: 23.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2134 2287 4.81 %
Rwork0.192 45229 -
obs0.193 47516 96.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 119.18 Å2 / Biso mean: 50.9853 Å2 / Biso min: 27.01 Å2
Refinement stepCycle: final / Resolution: 2.403→32.097 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7778 0 22 91 7891
Biso mean--40.07 55.17 -
Num. residues----980
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4534X-RAY DIFFRACTION3.619TORSIONAL
12B4534X-RAY DIFFRACTION3.619TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.403-2.45480.26621190.2601282596
2.4548-2.51190.24921530.2408280696
2.5119-2.57470.25451470.2221280896
2.5747-2.64430.24611450.2101278897
2.6443-2.72210.24041380.2033283297
2.7221-2.80990.20391400.1962287297
2.8099-2.91020.23721450.1947279997
2.9102-3.02670.2451440.1924285997
3.0267-3.16430.20411360.1899282197
3.1643-3.3310.19461500.1893284497
3.331-3.53940.22171410.1922284497
3.5394-3.81230.19891370.1901284897
3.8123-4.19520.21161490.198281297
4.1952-4.80050.22381700.187279296
4.8005-6.04150.21771270.1908286597
6.0415-32.0970.16661460.162281497
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)
10.08830.13890.04010.5186-0.31430.3302-0.1328-0.18780.0255-0.1040.0172-0.01-0.0638-0.120500.4066-0.02660.01020.4414-0.05640.4353-11.2241-13.3841-19.9576
20.27120.10090.14870.0906-0.05470.53850.07340.0044-0.0153-0.0659-0.16420.00240.0336-0.0885-00.38670.00290.01860.35260.01480.3285-13.6491-21.2683-29.4357
30.18950.00130.23560.3798-0.23870.33690.22530.2376-0.0193-0.3246-0.17750.09560.2281-0.1076-00.4044-0.03230.01790.37490.02410.3394-16.802-34.628-30.7347
40.02370.0559-0.0910.1336-0.11790.24270.05540.04870.30380.2891-0.19430.06190.0188-0.1218-0.00010.49390.00440.01260.44130.00960.4136-15.7134-24.5319-10.0298
50.33290.21020.3040.5080.32220.5513-0.034-0.1010.0205-0.0075-0.0223-0.10490.0327-0.13-00.3628-0.01790.03970.38980.02060.3459-7.413-20.2247-19.0985
60.49940.00250.68950.27310.3261.06280.0363-0.00760.0348-0.1475-0.0855-0.0941-0.12940.0024-00.3808-0.00850.03830.3267-0.01060.3626-14.2606-9.5276-33.3732
70.13360.0711-0.00660.08120.07820.12960.47110.02060.2347-0.3931-0.4277-0.0332-0.1654-0.1410.00010.46520.0385-0.00140.4294-0.01720.3269-17.3406-19.268-47.5716
81.97862.97151.92069.55895.64183.3563-0.0087-0.1892-0.0695-0.008-0.01340.0474-0.24810.048-0.02580.4663-0.10220.0370.50150.02620.4207-12.4911-18.4186-24.9731
90.30580.4677-0.02960.4905-0.08190.46820.11330.0773-0.0875-0.0137-0.289-0.07430.0294-0.2153-00.3653-0.0142-0.01460.4358-0.01910.3608-1.94454.0470.4506
100.2439-0.0328-0.00590.3530.45351.1390.0462-0.0584-0.05130.0215-0.0882-0.02290.007-0.0389-00.3241-0.014-0.01270.40050.01460.33183.837810.64599.5633
110.50520.1163-0.5660.40490.18410.73560.02550.03320.02990.0195-0.0695-0.0257-0.0171-0.0301-00.35190.0125-0.00370.31540.01920.32898.973918.29192.4775
120.25220.12790.16540.06650.09660.16630.0367-0.18190.09330.11930.0585-0.16080.10780.184200.4276-0.00550.04420.44840.01650.47269.5213-7.5351-2.7493
130.7137-0.0089-0.10660.22750.42411.19750.03950.0089-0.0892-0.0446-0.11160.003-0.0146-0.1239-00.3199-0.0131-0.01250.3442-0.00660.31331.22629.43256.4424
140.2497-0.236-0.35570.42150.49360.5827-0.0573-0.29530.028-0.0318-0.26830.1520.1694-0.0634-00.4551-0.1130.04270.5817-0.0080.5351-10.4072-5.88279.839
150.07570.02220.08680.24820.05140.06830.0391-0.3992-0.3213-0.0171-0.06910.19880.0702-0.23300.3762-0.0401-0.01480.4897-0.00260.3462-0.115312.321228.0747
168.5297-6.13160.33347.47714.73238.06660.0475-0.03110.1075-0.0367-0.0334-0.05620.09410.0424-0.0460.4565-0.05140.05670.51630.00330.43331.6578.12845.411
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 152 )A55 - 152
3X-RAY DIFFRACTION3chain 'A' and (resid 153 through 190 )A153 - 190
4X-RAY DIFFRACTION4chain 'A' and (resid 191 through 215 )A191 - 215
5X-RAY DIFFRACTION5chain 'A' and (resid 216 through 369 )A216 - 369
6X-RAY DIFFRACTION6chain 'A' and (resid 370 through 481 )A370 - 481
7X-RAY DIFFRACTION7chain 'A' and (resid 482 through 506 )A482 - 506
8X-RAY DIFFRACTION8chain 'A' and (resid 601 through 601 )A601
9X-RAY DIFFRACTION9chain 'B' and (resid 5 through 54 )B5 - 54
10X-RAY DIFFRACTION10chain 'B' and (resid 55 through 152 )B55 - 152
11X-RAY DIFFRACTION11chain 'B' and (resid 153 through 215 )B153 - 215
12X-RAY DIFFRACTION12chain 'B' and (resid 216 through 254 )B216 - 254
13X-RAY DIFFRACTION13chain 'B' and (resid 255 through 437 )B255 - 437
14X-RAY DIFFRACTION14chain 'B' and (resid 438 through 481 )B438 - 481
15X-RAY DIFFRACTION15chain 'B' and (resid 482 through 506 )B482 - 506
16X-RAY DIFFRACTION16chain 'B' and (resid 601 through 601 )B601

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