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- PDB-6s4m: Crystal structure of the human organic anion transporter MFSD10 (... -

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Basic information

Entry
Database: PDB / ID: 6s4m
TitleCrystal structure of the human organic anion transporter MFSD10 (TETRAN)
ComponentsMajor facilitator superfamily domain-containing protein 10
KeywordsTRANSPORT PROTEIN / MEMBRANE TRANSPORTER / MFSD10 / TETRAN / SLC22A32 / AMTF1 / STRUCTURAL GENOMICS CONSORTIUM / SGC
Function / homology
Function and homology information


tetracycline transmembrane transporter activity / sodium-independent organic anion transport / organic anion transmembrane transporter activity / nuclear inner membrane / brush border membrane / cytoplasmic vesicle membrane / membrane => GO:0016020 / apoptotic process
Similarity search - Function
Major facilitator superfamily / Major Facilitator Superfamily / Major facilitator superfamily domain / Major facilitator superfamily (MFS) profile. / MFS transporter superfamily
Similarity search - Domain/homology
CITRIC ACID / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / Major facilitator superfamily domain-containing protein 10
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsPascoa, T.C. / Pike, A.C.W. / Bushell, S.R. / Quigley, A. / Chu, A. / Mukhopadhyay, S.M.M. / Shrestha, L. / Venkaya, S. / Chalk, R. / Burgess-Brown, N.A. ...Pascoa, T.C. / Pike, A.C.W. / Bushell, S.R. / Quigley, A. / Chu, A. / Mukhopadhyay, S.M.M. / Shrestha, L. / Venkaya, S. / Chalk, R. / Burgess-Brown, N.A. / Edwards, A.M. / Arrowsmith, C.H. / Bountra, C. / Carpenter, E.P. / Structural Genomics Consortium (SGC)
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust United Kingdom
CitationJournal: To be published
Title: Crystal structure of the human organic anion transporter TETRAN (MFSD10)
Authors: Pascoa, T.C. / Pike, A.C.W. / Bushell, S.R. / Quigley, A. / Chu, A. / Mukhopadhyay, S.M.M. / Shrestha, L. / Venkaya, S. / Chalk, R. / Burgess-Brown, N.A. / Edwards, A.M. / Arrowsmith, C.H. / ...Authors: Pascoa, T.C. / Pike, A.C.W. / Bushell, S.R. / Quigley, A. / Chu, A. / Mukhopadhyay, S.M.M. / Shrestha, L. / Venkaya, S. / Chalk, R. / Burgess-Brown, N.A. / Edwards, A.M. / Arrowsmith, C.H. / Bountra, C. / Carpenter, E.P. / Structural Genomics Consortium (SGC)
History
DepositionJun 28, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 13, 2020Provider: repository / Type: Initial release
Revision 2.0Jul 14, 2021Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Refinement description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_refine_tls / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / reflns_shell / software / struct_asym / struct_conf / struct_site / struct_site_gen
Item: _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] ..._atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _pdbx_refine_tls.L[1][1] / _pdbx_refine_tls.L[1][2] / _pdbx_refine_tls.L[1][3] / _pdbx_refine_tls.L[2][2] / _pdbx_refine_tls.L[2][3] / _pdbx_refine_tls.L[3][3] / _pdbx_refine_tls.S[1][1] / _pdbx_refine_tls.S[1][2] / _pdbx_refine_tls.S[1][3] / _pdbx_refine_tls.S[2][1] / _pdbx_refine_tls.S[2][2] / _pdbx_refine_tls.S[2][3] / _pdbx_refine_tls.S[3][1] / _pdbx_refine_tls.S[3][2] / _pdbx_refine_tls.S[3][3] / _pdbx_refine_tls.T[1][1] / _pdbx_refine_tls.T[1][2] / _pdbx_refine_tls.T[1][3] / _pdbx_refine_tls.T[2][2] / _pdbx_refine_tls.T[2][3] / _pdbx_refine_tls.T[3][3] / _pdbx_refine_tls.origin_x / _pdbx_refine_tls.origin_y / _pdbx_refine_tls.origin_z / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.value / _refine.B_iso_max / _refine.B_iso_mean / _refine.B_iso_min / _refine.aniso_B[1][1] / _refine.aniso_B[1][2] / _refine.aniso_B[1][3] / _refine.aniso_B[2][2] / _refine.aniso_B[3][3] / _refine.correlation_coeff_Fo_to_Fc / _refine.correlation_coeff_Fo_to_Fc_free / _refine.details / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.overall_SU_B / _refine.overall_SU_ML / _refine.pdbx_ls_sigma_F / _refine.pdbx_overall_ESU_R / _refine.pdbx_overall_ESU_R_Free / _refine.pdbx_stereochemistry_target_values / _refine.solvent_model_details / _refine_hist.cycle_id / _refine_hist.number_atoms_total / _refine_hist.pdbx_B_iso_mean_ligand / _refine_hist.pdbx_B_iso_mean_solvent / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_residues_total / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_free_error / _refine_ls_shell.R_factor_R_work / _refine_ls_shell.number_reflns_all / _reflns_shell.d_res_high / _reflns_shell.d_res_low / _software.version / _struct_conf.end_auth_comp_id / _struct_conf.end_auth_seq_id / _struct_conf.end_label_comp_id / _struct_conf.end_label_seq_id / _struct_conf.pdbx_PDB_helix_length
Description: Ligand identity
Details: Protein was crystallised in the presence of 0.2M lithium citrate. No citrate was modelled originally, but there is clear density for citrate in the substrate-binding site. This is now ...Details: Protein was crystallised in the presence of 0.2M lithium citrate. No citrate was modelled originally, but there is clear density for citrate in the substrate-binding site. This is now corrected in this coordinate replacement.
Provider: author / Type: Coordinate replacement
Revision 2.1Jan 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: Major facilitator superfamily domain-containing protein 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,9444
Polymers48,0381
Non-polymers9053
Water1,08160
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area440 Å2
ΔGint1 kcal/mol
Surface area17460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.994, 70.375, 63.440
Angle α, β, γ (deg.)90.000, 115.450, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Major facilitator superfamily domain-containing protein 10 / Tetracycline transporter-like protein


Mass: 48038.430 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MFSD10, TETRAN / Plasmid: pFB-CT10HF-LIC / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q14728
#2: Chemical ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H40O4
#3: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C6H8O7
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 60 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.35 Å3/Da / Density % sol: 47.79 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 6.5
Details: 0.1M ADA pH6.5 -- 0.2M lithium citrate -- 30% PEG400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9687 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 6, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9687 Å / Relative weight: 1
ReflectionResolution: 2.4→31.74 Å / Num. obs: 17297 / % possible obs: 98.7 % / Redundancy: 4.9 % / Biso Wilson estimate: 36.8 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.208 / Rpim(I) all: 0.104 / Rrim(I) all: 0.234 / Χ2: 1 / Net I/σ(I): 5.7
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 5 % / Rmerge(I) obs: 1.657 / Mean I/σ(I) obs: 1 / Num. unique obs: 1822 / CC1/2: 0.399 / Rpim(I) all: 0.822 / Rrim(I) all: 1.853 / Χ2: 1 / % possible all: 98.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDS20190315data reduction
Aimless0.7.4data scaling
PHASER2.8.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3wdo

3wdo


Resolution: 2.4→30 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.904 / SU B: 25.357 / SU ML: 0.262 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.512 / ESU R Free: 0.283 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2583 831 4.8 %RANDOM
Rwork0.2087 ---
obs0.2112 16449 98.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 89.31 Å2 / Biso mean: 36.098 Å2 / Biso min: 22.85 Å2
Baniso -1Baniso -2Baniso -3
1--0.88 Å2-0 Å2-1.11 Å2
2--0.72 Å20 Å2
3---0.84 Å2
Refinement stepCycle: final / Resolution: 2.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3169 0 60 60 3289
Biso mean--66.88 37.56 -
Num. residues----426
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0133309
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173265
X-RAY DIFFRACTIONr_angle_refined_deg1.4581.6224498
X-RAY DIFFRACTIONr_angle_other_deg1.2521.5557477
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0115425
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.2119.12125
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.63115482
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7891520
X-RAY DIFFRACTIONr_chiral_restr0.070.2413
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023673
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02775
LS refinement shellResolution: 2.4→2.462 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 70 -
Rwork0.333 1183 -
all-1253 -
obs--97.59 %
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)
12.17691.41571.68911.59391.62123.21560.003-0.1522-0.04890.0601-0.0664-0.17790.00060.01350.06350.0320.00360.04490.02070.0240.238917.15373.1678-15.2311
20.84820.0404-0.05670.9241-0.41381.15120.00230.0027-0.02910.0146-0.0574-0.0476-0.00880.01330.05510.0113-0.00480.03970.0051-0.01210.1542.985-2.0378-17.1367
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A18 - 88
2X-RAY DIFFRACTION2A89 - 443

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