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- PDB-6xwm: Mechanism of substrate release in neurotransmitter:sodium symport... -

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Basic information

Entry
Database: PDB / ID: 6xwm
TitleMechanism of substrate release in neurotransmitter:sodium symporters: the structure of LeuT in an inward-facing occluded conformation
ComponentsNa(+):neurotransmitter symporter (Snf family)
KeywordsMEMBRANE PROTEIN / Neurotransmitter:sodium symporters (NSS)
Function / homologySodium:neurotransmitter symporter / Sodium:neurotransmitter symporter superfamily / Sodium:neurotransmitter symporter family / Sodium:neurotransmitter symporter family profile. / sodium ion transmembrane transport / membrane / PHENYLALANINE / Na(+):neurotransmitter symporter (Snf family)
Function and homology information
Biological speciesAquifex aeolicus VF5 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsBoesen, T. / Nissen, P. / Gotfryd, K. / Loland, C.J. / Gether, U.
Funding support Denmark, United States, European Union, 9items
OrganizationGrant numberCountry
LundbeckfondenR133-A12689 Denmark
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)P01 DA012408 United States
Lundbeckfonden2009-4585 Denmark
LundbeckfondenDANDRITE-R248-2016-2518 Denmark
The Carlsberg FoundationCF17-0171 Denmark
Danish Council for Independent ResearchSapere Aude 0602-02100B Denmark
Danish Council for Independent ResearchFP1 0602-02100B Denmark
Danish Council for Independent Research4183-00581 Denmark
European Communitys Seventh Framework ProgrammeFP7/2007-2013 HEALTH-F4-2007- 201924European Union
CitationJournal: Nat Commun / Year: 2020
Title: X-ray structure of LeuT in an inward-facing occluded conformation reveals mechanism of substrate release.
Authors: Gotfryd, K. / Boesen, T. / Mortensen, J.S. / Khelashvili, G. / Quick, M. / Terry, D.S. / Missel, J.W. / LeVine, M.V. / Gourdon, P. / Blanchard, S.C. / Javitch, J.A. / Weinstein, H. / Loland, ...Authors: Gotfryd, K. / Boesen, T. / Mortensen, J.S. / Khelashvili, G. / Quick, M. / Terry, D.S. / Missel, J.W. / LeVine, M.V. / Gourdon, P. / Blanchard, S.C. / Javitch, J.A. / Weinstein, H. / Loland, C.J. / Nissen, P. / Gether, U.
History
DepositionJan 24, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 6, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 25, 2020Group: Derived calculations / Structure summary / Category: audit_author / struct_conn
Item: _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id ..._struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Revision 1.2Jan 24, 2024Group: 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

Downloads & links

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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)116,3478
Polymers115,9252
Non-polymers4226
Water39622
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2620 Å2
ΔGint-41 kcal/mol
Surface area37310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.848, 83.985, 86.939
Angle α, β, γ (deg.)65.380, 89.770, 64.560
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 57962.312 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus VF5 (bacteria) / Gene: snf, aq_2077 / Production host: Escherichia coli (E. coli) / References: UniProt: O67854
#2: Chemical ChemComp-PHE / PHENYLALANINE / Phenylalanine


Type: L-peptide linking / Mass: 165.189 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H11NO2 / 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 / Water


Mass: 18.015 Da / Num. of mol.: 22 / 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: 3.93 Å3/Da / Density % sol: 68.73 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: HEPES-NaOH, sodium formate, PEG 3350, glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9999 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 29, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 2.6→46.62 Å / Num. obs: 53681 / % possible obs: 98.8 % / Redundancy: 6.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.034 / Rrim(I) all: 0.087 / Net I/σ(I): 11.1 / Num. measured all: 332230 / Scaling rejects: 230
Reflection shell

Diffraction-ID: 1 / % possible all: 98.2

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs
2.6-2.6861.0672810946510.7220.4651.1661.4
10.72-46.626.40.03448747600.9990.0140.03734.9

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
Aimless0.5.8data scaling
PDB_EXTRACT3.25data extraction
XDSVERSION Oct 15, 2015 BUILT=20151231data reduction
PHENIX1.16_3549phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TT3

3tt3


Resolution: 2.6→45.046 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 25.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.233 2689 5.01 %
Rwork0.2109 50962 -
obs0.212 53651 98.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 171.77 Å2 / Biso mean: 81.2031 Å2 / Biso min: 37.72 Å2
Refinement stepCycle: final / Resolution: 2.6→45.046 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7875 0 28 22 7925
Biso mean--63.9 58.27 -
Num. residues----993
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.6-2.64730.31851490.3139267898
2.6473-2.69820.29441500.2832268298
2.6982-2.75330.30231510.2637259998
2.7533-2.81310.26141550.2396266898
2.8131-2.87860.26891520.2286270398
2.8786-2.95060.24281370.2203263898
2.9506-3.03030.23421240.2241268398
3.0303-3.11950.27071490.227269099
3.1195-3.22010.26951360.2383271399
3.2201-3.33520.24751350.2337266299
3.3352-3.46870.28311380.2334267999
3.4687-3.62650.21781510.2116268399
3.6265-3.81760.24841270.2123269799
3.8176-4.05660.25711290.2203270799
4.0566-4.36960.22051350.2057269799
4.3696-4.80890.20981320.1762271299
4.8089-5.50360.22751350.1957269299
5.5036-6.930.22841510.21782697100
6.93-45.0460.19221530.1882268299
Refinement TLS params.Method: refined / Origin x: 21.5239 Å / Origin y: -4.7879 Å / Origin z: -139.3409 Å
111213212223313233
T0.3868 Å20.0727 Å20.0938 Å2-0.4117 Å2-0.0005 Å2--0.4018 Å2
L1.5355 °20.7536 °20.3936 °2-1.8524 °20.074 °2--0.8328 °2
S0.04 Å °0.1679 Å °-0.2121 Å °-0.0619 Å °0.0515 Å °-0.1419 Å °-0.0907 Å °0.1058 Å °-0.103 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA13 - 510
2X-RAY DIFFRACTION1allA601 - 752
3X-RAY DIFFRACTION1allB13 - 507
4X-RAY DIFFRACTION1allB601 - 752
5X-RAY DIFFRACTION1allS1 - 23

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