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- PDB-8g0m: Structure of complex between TV6.6 and CD98hc ECD -

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Basic information

Entry
Database: PDB / ID: 8g0m
TitleStructure of complex between TV6.6 and CD98hc ECD
Components
  • 4F2 cell-surface antigen heavy chain
  • TV 6.6 Fc fragment
KeywordsTRANSPORT PROTEIN / Transport vehicle
Function / homology
Function and homology information


neutral L-amino acid secondary active transmembrane transporter activity / Defective SLC7A7 causes lysinuric protein intolerance (LPI) / methionine transport / tyrosine transport / L-histidine transport / apical pole of neuron / aromatic amino acid transmembrane transporter activity / amino acid transport complex / : / L-leucine import across plasma membrane ...neutral L-amino acid secondary active transmembrane transporter activity / Defective SLC7A7 causes lysinuric protein intolerance (LPI) / methionine transport / tyrosine transport / L-histidine transport / 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 / isoleucine transport / L-alanine import across plasma membrane / phenylalanine transport / valine transport / L-leucine transmembrane transporter activity / calcium:sodium antiporter activity / L-leucine transport / thyroid hormone transport / proline transport / Amino acid transport across the plasma membrane / neutral L-amino acid transmembrane transporter activity / Tryptophan catabolism / exogenous protein binding / anchoring junction / amino acid transport / Basigin interactions / response to exogenous dsRNA / tryptophan transport / basal plasma membrane / calcium ion transport / double-stranded RNA binding / melanosome / virus receptor activity / basolateral plasma membrane / carbohydrate metabolic process / symbiont entry into host cell / cadherin binding / apical plasma membrane / protein heterodimerization activity / lysosomal membrane / synapse / cell surface / protein homodimerization activity / RNA binding / extracellular exosome / nucleoplasm / membrane / plasma membrane
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
Amino acid transporter heavy chain SLC3A2
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsKariolis, M.S. / Lexa, K. / Liau, N.P.D. / Srivastava, D. / Tran, H. / Wells, R.C.
Funding support United States, 1items
OrganizationGrant numberCountry
Other private United States
Citation
Journal: Nat Commun / Year: 2023
Title: CD98hc is a target for brain delivery of biotherapeutics.
Authors: Chew, K.S. / Wells, R.C. / Moshkforoush, A. / Chan, D. / Lechtenberg, K.J. / Tran, H.L. / Chow, J. / Kim, D.J. / Robles-Colmenares, Y. / Srivastava, D.B. / Tong, R.K. / Tong, M. / Xa, K. / ...Authors: Chew, K.S. / Wells, R.C. / Moshkforoush, A. / Chan, D. / Lechtenberg, K.J. / Tran, H.L. / Chow, J. / Kim, D.J. / Robles-Colmenares, Y. / Srivastava, D.B. / Tong, R.K. / Tong, M. / Xa, K. / Yang, A. / Zhou, Y. / Akkapeddi, P. / Annamalai, L. / Bajc, K. / Blanchette, M. / Cherf, G.M. / Earr, T.K. / Gill, A. / Huynh, D. / Joy, D. / Knight, K.N. / Lac, D. / Leung, A.W. / Lexa, K.W. / Liau, N.P.D. / Becerra, I. / Malfavon, M. / McInnes, J. / Nguyen, H.N. / Lozano, E.I. / Pizzo, M.E. / Roche, E. / Sacayon, P. / Calvert, M.E.K. / Daneman, R. / Dennis, M.S. / Duque, J. / Gadkar, K. / Lewcock, J.W. / Mahon, C.S. / Meisner, R. / Solanoy, H. / Thorne, R.G. / Watts, R.J. / Zuchero, Y.J.Y. / Kariolis, M.S.
#1: Journal: Nat Commun / Year: 2023
Title: CD98hc is a target for brain delivery of biotherapeutics.
Authors: Chew, K.S. / Wells, R.C. / Moshkforoush, A. / Chan, D. / Lechtenberg, K.J. / Tran, H.L. / Chow, J. / Kim, D.J. / Robles-Colmenares, Y. / Srivastava, D.B. / Tong, R.K. / Tong, M. / Xa, K. / ...Authors: Chew, K.S. / Wells, R.C. / Moshkforoush, A. / Chan, D. / Lechtenberg, K.J. / Tran, H.L. / Chow, J. / Kim, D.J. / Robles-Colmenares, Y. / Srivastava, D.B. / Tong, R.K. / Tong, M. / Xa, K. / Yang, A. / Zhou, Y. / Akkapeddi, P. / Annamalai, L. / Bajc, K. / Blanchette, M. / Cherf, G.M. / Earr, T.K. / Gill, A. / Huynh, D. / Joy, D. / Knight, K.N. / Lac, D. / Leung, A.W. / Lexa, K.W. / Liau, N.P.D. / Becerra, I. / Malfavon, M. / McInnes, J. / Nguyen, H.N. / Lozano, E.I. / Pizzo, M.E. / Roche, E. / Sacayon, P. / Calvert, M.E.K. / Daneman, R. / Dennis, M.S. / Duque, J. / Gadkar, K. / Lewcock, J.W. / Mahon, C.S. / Meisner, R. / Solanoy, H. / Thorne, R.G. / Watts, R.J. / Zuchero, Y.J.Y. / Kariolis, M.S.
History
DepositionJan 31, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 18, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 4F2 cell-surface antigen heavy chain
B: TV 6.6 Fc fragment
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,6369
Polymers72,7092
Non-polymers1,9277
Water2,828157
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5160 Å2
ΔGint34 kcal/mol
Surface area27710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.152, 167.126, 83.677
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-607-

HOH

21B-707-

HOH

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Components

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Protein / Antibody / Sugars , 3 types, 3 molecules AB

#1: Protein 4F2 cell-surface antigen heavy chain / / CD98 heavy chain / CD98hc / 4F2hc / 4F2 heavy chain antigen / Lymphocyte activation antigen 4F2 ...CD98 heavy chain / CD98hc / 4F2hc / 4F2 heavy chain antigen / Lymphocyte activation antigen 4F2 large subunit / Solute carrier family 3 member 2


Mass: 46951.727 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SLC3A2, MDU1 / Production host: Homo sapiens (human) / References: UniProt: P08195
#2: Antibody TV 6.6 Fc fragment


Mass: 25757.346 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Homo sapiens (human)
#3: Polysaccharide beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose- ...beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1422.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpb1-4DGlcpNAcb1-2DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/5,8,7/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a2112h-1b_1-5][a1221m-1a_1-5]/1-1-2-3-3-1-4-5/a4-b1_a6-h1_b4-c1_c3-d1_c6-e1_e2-f1_f4-g1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{}}}}}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE

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Non-polymers , 3 types, 163 molecules

#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 157 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.29 Å3/Da / Density % sol: 62.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.5
Details: 10% Glycerol, 0.1 M HEPES pH 7.5, 5% PEG 3000, 30% PEG 40

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 1.18071 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Aug 27, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.18071 Å / Relative weight: 1
ReflectionResolution: 2.25→44.681 Å / Num. obs: 45610 / % possible obs: 100 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.054 / Rrim(I) all: 0.058 / Net I/σ(I): 22.1
Reflection shellResolution: 2.25→2.32 Å / Redundancy: 7.2 % / Mean I/σ(I) obs: 2 / Num. unique obs: 4148 / Rrim(I) all: 1.07 / Rsym value: 0.994 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0403refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6IRS

6irs


Resolution: 2.25→44.68 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.938 / SU B: 6.95 / SU ML: 0.165 / Cross valid method: THROUGHOUT / ESU R: 0.224 / ESU R Free: 0.194
Details: HYDROGENS HAVE BEEN ADDED IN THEIR RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.245 2335 5.119 %RANDOM
Rwork0.204 ---
obs-45610 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 63.39 Å2
Baniso -1Baniso -2Baniso -3
1-0.128 Å20 Å20 Å2
2--0.032 Å20 Å2
3----0.161 Å2
Refinement stepCycle: LAST / Resolution: 2.25→44.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4894 0 129 157 5180
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0125146
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164833
X-RAY DIFFRACTIONr_angle_refined_deg1.2191.6536988
X-RAY DIFFRACTIONr_angle_other_deg0.421.57111184
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8515617
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.418525
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.79510844
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0540.2794
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025833
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021147
X-RAY DIFFRACTIONr_nbd_refined0.2140.2906
X-RAY DIFFRACTIONr_nbd_other0.1570.265
X-RAY DIFFRACTIONr_nbtor_refined0.1760.22455
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.2220
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.6756.3492477
X-RAY DIFFRACTIONr_mcbond_other5.6756.3492477
X-RAY DIFFRACTIONr_mcangle_it8.18111.4093091
X-RAY DIFFRACTIONr_mcangle_other8.17911.4093092
X-RAY DIFFRACTIONr_scbond_it5.8016.7732669
X-RAY DIFFRACTIONr_scbond_other5.8016.7732670
X-RAY DIFFRACTIONr_scangle_it8.50812.1993897
X-RAY DIFFRACTIONr_scangle_other8.50712.1993898
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.25→2.31 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.364 162 -
Rwork0.334 3164 -
obs--100 %

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