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- PDB-6c08: Zebrafish SLC38A9 with arginine bound in the cytosol open state -

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Basic information

Entry
Database: PDB / ID: 6c08
TitleZebrafish SLC38A9 with arginine bound in the cytosol open state
Components
  • Sodium-coupled neutral amino acid transporter 9
  • antibody Fab Heavy Chain
  • antibody Fab light chain
KeywordsMEMBRANE PROTEIN / transporter / conformational state / substrate binding / complex
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 / glutamine transport / L-glutamine transmembrane transporter activity / L-amino acid transmembrane transporter activity / L-leucine transmembrane transporter activity / amino acid transmembrane transport / L-leucine transport / amino acid transmembrane transporter activity / arginine binding / 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 / late endosome membrane / lysosome / lysosomal membrane / metal ion binding
Similarity search - Function
Amino acid transporter, transmembrane domain / Transmembrane amino acid transporter protein / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
ARGININE / Sodium-coupled neutral amino acid transporter 9
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.17 Å
AuthorsLei, H.-T. / Gonen, T.
CitationJournal: Nat. Struct. Mol. Biol. / Year: 2018
Title: Crystal structure of arginine-bound lysosomal transporter SLC38A9 in the cytosol-open state.
Authors: Lei, H.T. / Ma, J. / Sanchez Martinez, S. / Gonen, T.
History
DepositionDec 28, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 20, 2018Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: antibody Fab Heavy Chain
B: antibody Fab light chain
C: Sodium-coupled neutral amino acid transporter 9
D: antibody Fab Heavy Chain
E: antibody Fab light chain
F: Sodium-coupled neutral amino acid transporter 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)200,6217
Polymers200,4466
Non-polymers1751
Water0
1
A: antibody Fab Heavy Chain
B: antibody Fab light chain
C: Sodium-coupled neutral amino acid transporter 9


Theoretical massNumber of molelcules
Total (without water)100,2233
Polymers100,2233
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5340 Å2
ΔGint-36 kcal/mol
Surface area36480 Å2
MethodPISA
2
D: antibody Fab Heavy Chain
E: antibody Fab light chain
F: Sodium-coupled neutral amino acid transporter 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,3984
Polymers100,2233
Non-polymers1751
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5260 Å2
ΔGint-36 kcal/mol
Surface area36470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.613, 82.808, 158.922
Angle α, β, γ (deg.)90.000, 100.020, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody antibody Fab Heavy Chain


Mass: 22696.260 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: experimental sequence of heavy chains from antibody fragment is not determined because it is not discussed in the publication.
Source: (natural) Mus musculus (house mouse)
#2: Antibody antibody Fab light chain


Mass: 23410.609 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: Experimental sequence of light chains from antibody fragment is not determined because it is not discussed in the publication.
Source: (natural) Mus musculus (house mouse)
#3: Protein Sodium-coupled neutral amino acid transporter 9 / Solute carrier family 38 member 9


Mass: 54116.090 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: membrane protein / Source: (gene. exp.) Danio rerio (zebrafish) / Gene: slc38a9, zgc:154088 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q08BA4
#4: Chemical ChemComp-ARG / ARGININE / Arginine


Type: L-peptide linking / Mass: 175.209 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15N4O2
Sequence detailsexperimental sequence of antibody fragment is not determined

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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: 4.42 Å3/Da / Density % sol: 72.15 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: PEG400, N-(2-Acetamido)iminodiacetic acid pH 7.2, lithium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 18, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.1→156.5 Å / Num. obs: 63753 / % possible obs: 99.7 % / Redundancy: 8.3 % / Biso Wilson estimate: 114.41 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.118 / Rpim(I) all: 0.044 / Rrim(I) all: 0.127 / Net I/σ(I): 8.3 / Num. measured all: 529570 / Scaling rejects: 391
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
3.1-3.188.51.5413744743910.60.561.6421.198.1
14.21-156.57.40.06453617260.9970.0250.06924.399.1

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
Aimless0.5.32data scaling
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHASERphasing
RefinementResolution: 3.17→156.498 Å / SU ML: 0.51 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 32.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2855 1875 3.14 %
Rwork0.2665 57858 -
obs0.2671 59733 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 202.97 Å2 / Biso mean: 113.9931 Å2 / Biso min: 45.24 Å2
Refinement stepCycle: final / Resolution: 3.17→156.498 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12329 0 12 0 12341
Biso mean--147.08 --
Num. residues----1607
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.17-3.25570.4531440.405344404584100
3.2557-3.35150.3611420.352143804522100
3.3515-3.45970.37811450.304644584603100
3.4597-3.58340.28851420.271944124554100
3.5834-3.72690.32331440.284344394583100
3.7269-3.89650.3161440.265844564600100
3.8965-4.10190.28191430.266444114554100
4.1019-4.3590.26691440.231444414585100
4.359-4.69550.23261440.21544374581100
4.6955-5.16810.25111450.219144714616100
5.1681-5.91590.30371450.243844734618100
5.9159-7.45350.29421450.283844714616100
7.4535-156.6890.27221480.29164569471799

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