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- PDB-3tt3: Crystal Structure of LeuT in the inward-open conformation in comp... -

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Basic information

Entry
Database: PDB / ID: 3tt3
TitleCrystal Structure of LeuT in the inward-open conformation in complex with Fab
Components
  • Leucine transporter LeuT
  • mouse monoclonal 1gG1 Fab fragment, heavy chain
  • mouse monoclonal 1gG1 Fab fragment, kappa light chain
KeywordsTRANSPORT PROTEIN / LeuT fold / transporter / plasma membrane
Function / homology
Function and homology information


sodium ion transmembrane transport / membrane
Similarity search - Function
Sodium:neurotransmitter symporter / Sodium:neurotransmitter symporter superfamily / Sodium:neurotransmitter symporter family / Sodium:neurotransmitter symporter family profile. / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Na(+):neurotransmitter symporter (Snf family)
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.22 Å
AuthorsKrishnamurthy, H. / Gouaux, E.
CitationJournal: Nature / Year: 2012
Title: X-ray structures of LeuT in substrate-free outward-open and apo inward-open states.
Authors: Krishnamurthy, H. / Gouaux, E.
History
DepositionSep 13, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 4, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 18, 2012Group: Database references / Structure summary
Revision 1.2Jan 25, 2012Group: Database references
Revision 1.3Feb 1, 2012Group: Database references
Revision 1.4Jul 29, 2020Group: Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_entity_nonpoly / struct_ref_seq_dif
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Sep 13, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Leucine transporter LeuT
L: mouse monoclonal 1gG1 Fab fragment, heavy chain
H: mouse monoclonal 1gG1 Fab fragment, kappa light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,4124
Polymers106,1043
Non-polymers3081
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)128.838, 169.804, 130.417
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Leucine transporter LeuT


Mass: 57909.273 Da / Num. of mol.: 1 / Mutation: Y268A, K288A, T354V, S355A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Gene: snf, aq_2077 / Plasmid: pET16b / Production host: Escherichia coli (E. coli) / Strain (production host): C41 / References: UniProt: O67854
#2: Antibody mouse monoclonal 1gG1 Fab fragment, heavy chain


Mass: 24208.594 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)
#3: Antibody mouse monoclonal 1gG1 Fab fragment, kappa light chain


Mass: 23985.928 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)
#4: Sugar ChemComp-SOG / octyl 1-thio-beta-D-glucopyranoside / 2-HYDROXYMETHYL-6-OCTYLSULFANYL-TETRAHYDRO-PYRAN-3,4,5-TRIOL / 1-S-OCTYL-BETA-D-THIOGLUCOSIDE / octyl 1-thio-beta-D-glucoside / octyl 1-thio-D-glucoside / octyl 1-thio-glucoside / N-Octyl beta-D-thioglucopyranoside


Type: D-saccharide / Mass: 308.434 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C14H28O5S / Comment: detergent*YM

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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: 3.36 Å3/Da / Density % sol: 63.41 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: 100 mM HEPES, 0.1 M magnesium nitrate, 12-14% PEG1500, 1.5% w/v trimethylamine-N-oxide, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationMonochromator: single crystal Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 3.22→50 Å / Num. all: 23475 / Num. obs: 23381 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 99.7 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 17.78
Reflection shellResolution: 3.22→3.35 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 2 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.7_650)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 2A65, 1Q9Q, 1EJO

2a65

1q9q
PDB Unreleased entry

1ejo


Resolution: 3.22→35.576 Å / SU ML: 0.47 / σ(F): 0 / Phase error: 37.77 / Stereochemistry target values: ML
Details: SIDE CHAIN ATOMS HAVE BEEN MODELED ONLY WHERE ELECTRON DENSITY IS AVAILABLE.
RfactorNum. reflection% reflectionSelection details
Rfree0.3002 1067 5.02 %RANDOM
Rwork0.2572 ---
obs0.2594 21251 90.42 %-
all-0 --
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 55.588 Å2 / ksol: 0.287 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-40.2109 Å2-0 Å20 Å2
2---51.8201 Å20 Å2
3---11.6092 Å2
Refinement stepCycle: LAST / Resolution: 3.22→35.576 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7192 0 8 0 7200
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0117727
X-RAY DIFFRACTIONf_angle_d1.14910105
X-RAY DIFFRACTIONf_dihedral_angle_d11.1012544
X-RAY DIFFRACTIONf_chiral_restr0.0621148
X-RAY DIFFRACTIONf_plane_restr0.0061270
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.22-3.36610.5281900.39082066X-RAY DIFFRACTION75
3.3661-3.54350.38211330.35182307X-RAY DIFFRACTION84
3.5435-3.76520.3751510.29972396X-RAY DIFFRACTION88
3.7652-4.05560.32441560.27472486X-RAY DIFFRACTION91
4.0556-4.4630.27311240.23522631X-RAY DIFFRACTION94
4.463-5.10720.29631170.21322697X-RAY DIFFRACTION96
5.1072-6.42830.33131520.27072743X-RAY DIFFRACTION98
6.4283-35.57860.24031440.23892858X-RAY DIFFRACTION97
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)
12.64870.0437-0.47442.4195-0.90311.8145-0.1446-0.2383-0.07610.2526-0.0431-0.0205-0.06610.2683-0.01080.57170.1133-0.31520.75670.10970.584889.309481.408688.3329
23.63141.6328-1.49972.52350.78124.03040.1363-0.60450.10750.38950.0449-0.53020.08420.42650.07150.40280.1035-0.51460.69050.220.383488.782376.9174100.8388
31.2847-0.32960.05652.8779-0.08022.2388-0.2096-0.1816-0.07020.1450.019-0.498-0.22040.5047-0.00130.50130.1105-0.1820.87320.04180.688995.754285.890387.6641
43.7167-1.5727-1.72222.051.28841.52860.59060.29360.22940.0664-0.1704-1.9570.02050.5766-0.03511.2282-0.4582-0.34041.070.06421.4822104.2287127.052780.4211
52.3583-0.48620.10330.74290.65891.1440.5701-0.0001-0.0307-0.33380.2438-0.1182-0.23220.32210.02641.4189-0.282-0.2510.70490.20561.188487.832141.104274.604
61.83270.80531.47721.04771.00772.28-0.7248-1.04440.05411.10810.8533-0.72720.11920.43650.01741.6783-0.19090.13871.00650.34541.377184.2765152.252570.1014
70.59040.67410.34891.0484-0.39712.3980.00550.31420.48830.4405-0.04410.2297-0.4519-0.5481-0.00021.8051-0.3285-0.00261.12740.21081.353477.219159.692167.125
84.20861.1696-0.75551.9157-0.66774.0037-0.251-0.428-0.10820.87260.29440.1508-0.0434-0.1604-01.26920.048-0.26070.96450.05180.801683.459119.152591.2943
93.1465-1.7111-0.41152.240.15360.2221-0.36280.45790.06870.50620.40110.7096-0.39810.08130.00051.6351-0.2377-0.10611.1494-0.1131.126479.3761132.936380.1822
102.5045-0.1270.68891.0197-0.39560.3195-0.57290.0474-0.077-1.090.54261.1004-1.15680.4145-0.00491.897-0.0473-0.35190.84930.14351.204675.6286140.247770.964
110.8196-0.5157-0.64440.4660.17420.7865-0.1743-0.0266-0.1582-1.59411.01731.2498-0.0415-0.88750.00061.9548-0.3154-0.2041.07750.30341.670470.7686139.417763.8627
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 11:184)
2X-RAY DIFFRACTION2chain 'A' and (resseq 185:254)
3X-RAY DIFFRACTION3chain 'A' and (resseq 255:511)
4X-RAY DIFFRACTION4chain 'L' and (resseq 1:94)
5X-RAY DIFFRACTION5chain 'L' and (resseq 95:131)
6X-RAY DIFFRACTION6chain 'L' and (resseq 132:177)
7X-RAY DIFFRACTION7chain 'L' and (resseq 178:215)
8X-RAY DIFFRACTION8chain 'H' and (resseq 1:83)
9X-RAY DIFFRACTION9chain 'H' and (resseq 84:140)
10X-RAY DIFFRACTION10chain 'H' and (resseq 141:180)
11X-RAY DIFFRACTION11chain 'H' and (resseq 181:219)

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