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- PDB-6i9q: Structure of the mouse CD98 heavy chain ectodomain -

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Basic information

Entry
Database: PDB / ID: 6i9q
TitleStructure of the mouse CD98 heavy chain ectodomain
Components4F2 cell-surface antigen heavy chain
KeywordsMEMBRANE PROTEIN / CD98hc / 4F2hc / amino acid transport / CD98 light chain / LAT-1 / LAT-2 / integrin beta subunit binding / single-pass type II membrane protein
Function / homology
Function and homology information


Amino acid transport across the plasma membrane / Tryptophan catabolism / apical pole of neuron / aromatic amino acid transmembrane transporter activity / amino acid transport complex / : / L-leucine import across plasma membrane / L-alanine transmembrane transporter activity / L-alanine import across plasma membrane / phenylalanine transport ...Amino acid transport across the plasma membrane / Tryptophan catabolism / apical pole of neuron / aromatic amino acid transmembrane transporter activity / amino acid transport complex / : / L-leucine import across plasma membrane / L-alanine transmembrane transporter activity / L-alanine import across plasma membrane / phenylalanine transport / L-leucine transmembrane transporter activity / neutral amino acid transport / L-leucine transport / neutral L-amino acid transmembrane transporter activity / anchoring junction / response to exogenous dsRNA / tryptophan transport / basal plasma membrane / melanosome / double-stranded RNA binding / basolateral plasma membrane / carbohydrate metabolic process / symbiont entry into host cell / apical plasma membrane / lysosomal membrane / neuronal cell body / synapse / cell surface / nucleoplasm / plasma membrane / cytoplasm
Similarity search - Function
Solute carrier family 3 member 2, N-terminal domain / 4F2 cell-surface antigen heavy chain / Solute carrier family 3 member 2 N-terminus / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Glycosyl hydrolase, all-beta / Glycoside hydrolase superfamily
Similarity search - Domain/homology
4F2 cell-surface antigen heavy chain
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsSchiefner, A. / Deuschle, F.-C. / Skerra, A.
CitationJournal: Proteins / Year: 2019
Title: Structural differences between the ectodomains of murine and human CD98hc.
Authors: Deuschle, F.C. / Schiefner, A. / Skerra, A.
History
DepositionNov 24, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 17, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 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

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Assembly

Deposited unit
A: 4F2 cell-surface antigen heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5264
Polymers48,3671
Non-polymers1603
Water3,585199
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area620 Å2
ΔGint-5 kcal/mol
Surface area18300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.384, 97.384, 218.980
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-850-

HOH

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Components

#1: Protein 4F2 cell-surface antigen heavy chain / / 4F2hc / Solute carrier family 3 member 2


Mass: 48366.570 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Slc3a2, Mdu1 / Plasmid: pASK-IBA5+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P10852
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 199 / 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: 2.68 Å3/Da / Density % sol: 54.17 % / Description: thin plates
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 24 % (w/v) PEG 3350, 0.1 M Bis-tris propane/HCl, 0.2 M sodium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 22, 2018
RadiationMonochromator: KMC-2 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.1→34.45 Å / Num. obs: 31196 / % possible obs: 99.9 % / Redundancy: 26.556 % / Biso Wilson estimate: 42.827 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.13 / Rrim(I) all: 0.133 / Χ2: 1.008 / Net I/σ(I): 21.43
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.1-2.228.0811.4532.8239840.8111.4899.9
2.2-2.327.88814.1233440.8991.018100
2.3-2.527.4390.6386.4951710.9620.65100
2.5-325.3570.28513.3177330.9930.29100
3-3.527.7330.11730.7539690.9990.119100
3.5-426.3920.07346.83223910.075100
4-623.7030.05555.8327110.05699.9
6-827.5510.04762.5483610.048100
8-1025.7120.03870.7630610.039100
10-34.4522.5480.03669.0434310.03796.1

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Processing

Software
NameVersionClassification
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2DH2

2dh2


Resolution: 2.1→34.45 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.947 / SU B: 4.404 / SU ML: 0.115 / SU R Cruickshank DPI: 0.1786 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.179 / ESU R Free: 0.161
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2184 1505 4.8 %RANDOM
Rwork0.1749 ---
obs0.1771 29690 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 145.23 Å2 / Biso mean: 39.43 Å2 / Biso min: 19.44 Å2
Baniso -1Baniso -2Baniso -3
1--0.13 Å20 Å2-0 Å2
2---0.13 Å20 Å2
3---0.26 Å2
Refinement stepCycle: final / Resolution: 2.1→34.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3321 0 9 199 3529
Biso mean--42.39 44.39 -
Num. residues----422
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0143419
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173084
X-RAY DIFFRACTIONr_angle_refined_deg1.5831.6444639
X-RAY DIFFRACTIONr_angle_other_deg0.9511.6357241
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1775425
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.38522.898176
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.60615586
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9721520
X-RAY DIFFRACTIONr_chiral_restr0.0790.2432
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023839
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02621
LS refinement shellResolution: 2.1→2.154 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.372 111 -
Rwork0.269 2159 -
all-2270 -
obs--100 %

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