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- PDB-2qb4: Crystal Structure Analysis of LeuT complexed with L-leucine, sodi... -

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Basic information

Entry
Database: PDB / ID: 2qb4
TitleCrystal Structure Analysis of LeuT complexed with L-leucine, sodium and desipramine
ComponentsTransporter
KeywordsTRANSPORT PROTEIN / membrane protein / neurotransmitter sodium symporter / occluded / secondary amine tricyclic antidepressant / dibenzazepine / Transmembrane / Transport
Function / homologySodium:neurotransmitter symporter / Sodium:neurotransmitter symporter superfamily / Sodium:neurotransmitter symporter family / Sodium:neurotransmitter symporter family profile. / sodium ion transmembrane transport / plasma membrane / Chem-DSM / LEUCINE / Na(+):neurotransmitter symporter (Snf family)
Function and homology information
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.9 Å
AuthorsSingh, S.K. / Yamashita, A. / Gouaux, E.
Citation
Journal: Nature / Year: 2007
Title: Antidepressant binding site in a bacterial homologue of neurotransmitter transporters.
Authors: Singh, S.K. / Yamashita, A. / Gouaux, E.
#1: Journal: Nature / Year: 2005
Title: Crystal structure of a bacterial homologue of Na+/Cl--dependent neurotransmitter transporters
Authors: Yamashita, A. / Singh, S.K. / Kawate, T. / Jin, Y. / Gouaux, E.
History
DepositionJun 15, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.2Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 300BIOMOLECULE: 1 The biological assembly might not be physiologically relevant mainly because of the ...BIOMOLECULE: 1 The biological assembly might not be physiologically relevant mainly because of the results authors obtained in solution. The actual residues in the relevant transmembrane domains (TM9 and TM12) are not conserved in the eukaryotic homologues. Authors are not 100% sure because crosslinking the protein in a lipid bilayer has not been performed.
Remark 600HETEROGEN The authors state that C2 numbering is in crystallographic notation and it is the same as ...HETEROGEN The authors state that C2 numbering is in crystallographic notation and it is the same as C3 numbering in IUPAC. Regarding the bond order difference for the C5-C6 bond, the authors used the topology and parameter files derived from the small molecule crystal structures of clomipramine and imipramine rather than theoretical values.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,24911
Polymers58,0771
Non-polymers2,17210
Water2,540141
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Transporter
hetero molecules

A: Transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,49822
Polymers116,1552
Non-polymers4,34420
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area6910 Å2
ΔGint8 kcal/mol
Surface area40330 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)88.290, 86.770, 81.250
Angle α, β, γ (deg.)90.00, 96.02, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe biological unit is the monomer, which is the asymmetric unit.

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Components

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Protein / Sugars , 2 types, 6 molecules A

#1: Protein Transporter


Mass: 58077.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Strain: VF5 / Gene: snf / Plasmid: pET16b / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3) / References: UniProt: O67854
#2: Sugar
ChemComp-BOG / octyl beta-D-glucopyranoside / Beta-Octylglucoside / octyl beta-D-glucoside / octyl D-glucoside / octyl glucoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 4 types, 146 molecules

#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-LEU / LEUCINE


Type: L-peptide linking / Mass: 131.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO2
#5: Chemical ChemComp-DSM / 3-(10,11-DIHYDRO-5H-DIBENZO[B,F]AZEPIN-5-YL)-N-METHYLPROPAN-1-AMINE / Desipramine;Norpramin


Mass: 266.381 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H22N2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 141 / Source method: isolated from a natural source / Formula: H2O

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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: 2.66 Å3/Da / Density % sol: 53.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 17-22% PEGMME 550, 200 mM NaCl, 100 mM HEPES-NaOH, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 19, 2005 / Details: vertical focusing mirror
RadiationMonochromator: channel-cut Si(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 45802 / % possible obs: 94.7 % / Redundancy: 3.6 % / Biso Wilson estimate: 28.2 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 19.54
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.571 / Mean I/σ(I) obs: 1.49 / Num. unique all: 3607 / % possible all: 74.7

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Processing

Software
NameVersionClassification
CNS1.1refinement
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 2A65

2a65


Resolution: 1.9→27.73 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1897177.69 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: Structure in asymmetric unit starts at R5 because of disorder. Residues E129, T515, and L516 are modeled as alanines because of disorder. Residues N133, A134, V517, P518, and R519 are not ...Details: Structure in asymmetric unit starts at R5 because of disorder. Residues E129, T515, and L516 are modeled as alanines because of disorder. Residues N133, A134, V517, P518, and R519 are not modeled because of disorder. C-terminal residues GTL modeled as GAA because of disorder.
RfactorNum. reflection% reflectionSelection details
Rfree0.217 2265 5 %RANDOM
Rwork0.201 ---
obs0.201 45626 94.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 65.0917 Å2 / ksol: 0.334082 e/Å3
Displacement parametersBiso mean: 41.9 Å2
Baniso -1Baniso -2Baniso -3
1-6.47 Å20 Å2-4.86 Å2
2---1.88 Å20 Å2
3----4.6 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.32 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 1.9→27.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4043 0 151 141 4335
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d19
X-RAY DIFFRACTIONc_improper_angle_d1.05
X-RAY DIFFRACTIONc_mcbond_it1.291.5
X-RAY DIFFRACTIONc_mcangle_it2.042
X-RAY DIFFRACTIONc_scbond_it1.852
X-RAY DIFFRACTIONc_scangle_it2.772.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.306 290 4.5 %
Rwork0.299 6158 -
obs--80.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ion.paramion.top
X-RAY DIFFRACTION3bb
X-RAY DIFFRACTION4desipdesip
X-RAY DIFFRACTION5water_rep.paramwater_rep.top

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