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- PDB-7kgv: Crystal structure of sodium-coupled neutral amino acid transporte... -

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Basic information

Entry
Database: PDB / ID: 7kgv
TitleCrystal structure of sodium-coupled neutral amino acid transporter SLC38A9 in the N-terminal plugged form
Components
  • Monoclonal antibody Fab heavy chain
  • Monoclonal antibody Fab light chain
  • Sodium-coupled neutral amino acid transporter 9
KeywordsTRANSPORT PROTEIN / SLC38A9 / MEMBRANE PROTEIN
Function / homology
Function and homology information


Macroautophagy / MTOR signalling / Energy dependent regulation of mTOR by LKB1-AMPK / TP53 Regulates Metabolic Genes / Regulation of PTEN gene transcription / Amino acids regulate mTORC1 / mTORC1-mediated signalling / asparagine transport / L-asparagine transmembrane transporter activity / sterol sensor activity ...Macroautophagy / MTOR signalling / Energy dependent regulation of mTOR by LKB1-AMPK / TP53 Regulates Metabolic Genes / Regulation of PTEN gene transcription / Amino acids regulate mTORC1 / mTORC1-mediated signalling / asparagine transport / L-asparagine transmembrane transporter activity / sterol sensor activity / amino acid sensor activity / L-arginine transmembrane transport / L-arginine transmembrane transporter activity / L-glutamine transmembrane transporter activity / glutamine transport / L-leucine transmembrane transporter activity / amino acid transmembrane transport / L-amino acid transmembrane transporter activity / L-leucine transport / regulation of cellular response to hypoxia / amino acid transmembrane transporter activity / amino acid metabolic process / arginine binding / regulation of glycolytic process / regulation of gluconeogenesis / cholesterol binding / positive regulation of TOR signaling / positive regulation of TORC1 signaling / guanyl-nucleotide exchange factor activity / cellular response to amino acid stimulus / late endosome membrane / late endosome / lysosome / lysosomal membrane / metal ion binding / membrane
Similarity search - Function
Amino acid transporter, transmembrane domain / Transmembrane amino acid transporter protein / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Neutral amino acid transporter 9
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsLei, H. / Mu, X. / Hattne, J. / Gonen, T.
CitationJournal: Structure / Year: 2021
Title: A conformational change in the N terminus of SLC38A9 signals mTORC1 activation.
Authors: Lei, H.T. / Mu, X. / Hattne, J. / Gonen, T.
History
DepositionOct 19, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2020Provider: repository / Type: Initial release
Revision 1.1May 19, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.title / _citation.year
Revision 1.2Oct 18, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sodium-coupled neutral amino acid transporter 9
B: Sodium-coupled neutral amino acid transporter 9
C: Monoclonal antibody Fab heavy chain
D: Monoclonal antibody Fab heavy chain
E: Monoclonal antibody Fab light chain
F: Monoclonal antibody Fab light chain


Theoretical massNumber of molelcules
Total (without water)215,9536
Polymers215,9536
Non-polymers00
Water00
1
A: Sodium-coupled neutral amino acid transporter 9
D: Monoclonal antibody Fab heavy chain
F: Monoclonal antibody Fab light chain


Theoretical massNumber of molelcules
Total (without water)107,9773
Polymers107,9773
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Sodium-coupled neutral amino acid transporter 9
C: Monoclonal antibody Fab heavy chain
E: Monoclonal antibody Fab light chain


Theoretical massNumber of molelcules
Total (without water)107,9773
Polymers107,9773
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)157.798, 82.514, 158.590
Angle α, β, γ (deg.)90.000, 106.024, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "A"
d_2ens_1(chain "B" and (resid 80 through 83 or resid 104...
d_1ens_2(chain "C" and (resid 1 through 134 or resid 138 through 219))
d_2ens_2chain "D"
d_1ens_3chain "E"
d_2ens_3chain "F"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1SERMETA1 - 361
d_21ens_1SERASPB6 - 9
d_22ens_1LYSSERB17 - 72
d_23ens_1VALASPB77 - 132
d_24ens_1GLULEUB134 - 153
d_25ens_1SERASNB155 - 228
d_26ens_1VALGLNB236 - 311
d_27ens_1HISLYSB325 - 376
d_28ens_1THRMETB382 - 404
d_11ens_2GLNALAC1 - 134
d_12ens_2THRALAC136 - 217
d_21ens_2GLNALAD1 - 216
d_11ens_3ASPASNE1 - 215
d_21ens_3ASPASNF1 - 215

NCS ensembles :
ID
ens_1
ens_2
ens_3

NCS oper:
IDCodeMatrixVector
1given(0.988280802555, -0.0249784754422, 0.150589279386), (-0.0233785563474, -0.999649957517, -0.0123856989866), (0.150845942619, 0.0087199885812, -0.988518822984)0.48026842964, -11.4368391464, -0.730945729456
2given(0.991035505095, -0.00536025992416, 0.133491180437), (-0.00539761712282, -0.999985429393, -8.20399539E-5), (0.133489675145, -0.000639229774053, -0.991049997737)0.00216103519476, -11.5117698044, -0.140828438746
3given(0.992533842003, -0.00279940959102, 0.121937425692), (-0.00321181248721, -0.999989767851, 0.00318566378183), (0.121927260033, -0.00355351925921, -0.992532677428)0.112840973691, -11.6414877549, 0.126983571979

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Components

#1: Protein Sodium-coupled neutral amino acid transporter 9 / Solute carrier family 38 member 9


Mass: 62003.750 Da / Num. of mol.: 2 / Mutation: N227Q, N235Q, N252Q, N263Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: slc38a9, zgc:154088 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q08BA4
#2: Antibody Monoclonal antibody Fab heavy chain


Mass: 22575.121 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#3: Antibody Monoclonal antibody Fab light chain


Mass: 23397.824 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
Has protein modificationY

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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: 4.6 Å3/Da / Density % sol: 77.69 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 26-30% (w/v) PEG400, 100 mM ADA pH 6.0, 350 mM Li2SO4.

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 6, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.4→49.37 Å / Num. obs: 54452 / % possible obs: 99.9 % / Redundancy: 11.8 % / Biso Wilson estimate: 97.19 Å2 / CC1/2: 0.989 / Rpim(I) all: 0.084 / Net I/σ(I): 6.5
Reflection shellResolution: 3.4→3.52 Å / Redundancy: 6.1 % / Mean I/σ(I) obs: 1 / Num. unique obs: 5375 / CC1/2: 0.35 / Rpim(I) all: 1.071 / % possible all: 99.8

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Processing

Software
NameVersionClassification
XDS20170601data reduction
Aimless0.5.23data scaling
PHASERphasing
PHENIX1.18.2_3874+SVNrefinement
Coot0.8.9.2model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1f8t

1f8t


Resolution: 3.4→49.37 Å / SU ML: 0.5098 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.9836
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2843 1697 3.12 %
Rwork0.2509 52699 -
obs0.2519 54396 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 110.31 Å2
Refinement stepCycle: LAST / Resolution: 3.4→49.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12613 0 0 0 12613
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.010512941
X-RAY DIFFRACTIONf_angle_d1.324917615
X-RAY DIFFRACTIONf_chiral_restr0.06562041
X-RAY DIFFRACTIONf_plane_restr0.00882174
X-RAY DIFFRACTIONf_dihedral_angle_d16.16114461
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS1.12736715902
ens_2d_2CX-RAY DIFFRACTIONTorsion NCS0.73849691611
ens_3d_2EX-RAY DIFFRACTIONTorsion NCS0.596082660469
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4-3.50.35651430.35154320X-RAY DIFFRACTION99.38
3.5-3.610.34811420.31524318X-RAY DIFFRACTION99.78
3.61-3.740.3181410.28684391X-RAY DIFFRACTION99.93
3.74-3.890.30391230.274368X-RAY DIFFRACTION99.91
3.89-4.070.27921430.25294384X-RAY DIFFRACTION99.96
4.07-4.280.28431400.22544358X-RAY DIFFRACTION99.93
4.28-4.550.26941390.20014372X-RAY DIFFRACTION99.91
4.55-4.90.24251410.19124377X-RAY DIFFRACTION99.91
4.9-5.40.22461580.19864384X-RAY DIFFRACTION99.98
5.4-6.180.27441280.22994441X-RAY DIFFRACTION100
6.18-7.770.29941450.27754428X-RAY DIFFRACTION100
7.78-49.370.29551540.27524558X-RAY DIFFRACTION99.85
Refinement TLS params.Method: refined / Origin x: 32.0197503688 Å / Origin y: -5.71553027097 Å / Origin z: 4.06604648172 Å
111213212223313233
T0.699264423387 Å2-0.0178134724581 Å2-0.0408754602327 Å2-0.682782209705 Å20.119187500227 Å2--0.915709007665 Å2
L0.383685155612 °2-0.0545885189746 °2-0.0537866780419 °2-0.308330074334 °20.322302696804 °2--0.723249793012 °2
S0.0253542304421 Å °0.0141470317427 Å °0.0312653119199 Å °-0.0594531582476 Å °-0.0689032525969 Å °-0.0839302887018 Å °-0.0645719718572 Å °0.12318838394 Å °0.0424004915426 Å °
Refinement TLS groupSelection details: all

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