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- PDB-7df1: Crystal structure of human CD98 heavy chain extracellular domain ... -

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Basic information

Entry
Database: PDB / ID: 7df1
TitleCrystal structure of human CD98 heavy chain extracellular domain in complex with S1-F4 scFv
Components
  • 4F2 cell-surface antigen heavy chain
  • IGL c2062_light_IGKV4-1_IGKJ5
  • S1-F4 VH
KeywordsANTITUMOR PROTEIN / Complex / tumor growth / antibody
Function / homology
Function and homology information


apical pole of neuron / tyrosine transport / L-histidine transport / amino acid transport complex / L-leucine import across plasma membrane / L-alanine transmembrane transporter activity / L-alanine import across plasma membrane / Defective SLC7A7 causes lysinuric protein intolerance (LPI) / aromatic amino acid transmembrane transporter activity / phenylalanine transport ...apical pole of neuron / tyrosine transport / L-histidine transport / amino acid transport complex / L-leucine import across plasma membrane / L-alanine transmembrane transporter activity / L-alanine import across plasma membrane / Defective SLC7A7 causes lysinuric protein intolerance (LPI) / aromatic amino acid transmembrane transporter activity / phenylalanine transport / methionine transport / L-leucine transmembrane transporter activity / isoleucine transport / valine transport / proline transport / L-leucine transport / thyroid hormone transport / neutral L-amino acid transmembrane transporter activity / Tryptophan catabolism / Amino acid transport across the plasma membrane / exogenous protein binding / anchoring junction / Basigin interactions / response to exogenous dsRNA / amino acid transport / tryptophan transport / basal plasma membrane / calcium ion transport / melanosome / double-stranded RNA binding / virus receptor activity / basolateral plasma membrane / carbohydrate metabolic process / immune response / apical plasma membrane / cadherin binding / protein heterodimerization activity / lysosomal membrane / synapse / symbiont entry into host cell / cell surface / protein homodimerization activity / extracellular space / 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 / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Immunoglobulin V-Type ...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 / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Glycosidases / Immunoglobulin subtype / Immunoglobulin / Glycoside hydrolase superfamily / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
IGL c2062_light_IGKV4-1_IGKJ5 / Amino acid transporter heavy chain SLC3A2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.806 Å
AuthorsLiu, X. / Ding, J. / Sui, J. / Tian, X.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China) China
CitationJournal: Nat Biomed Eng / Year: 2022
Title: An anti-CD98 antibody displaying pH-dependent Fc-mediated tumour-specific activity against multiple cancers in CD98-humanized mice.
Authors: Tian, X. / Liu, X. / Ding, J. / Wang, F. / Wang, K. / Liu, J. / Wei, Z. / Hao, X. / Li, Y. / Wei, X. / Zhang, H. / Sui, J.
History
DepositionNov 6, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 7, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 4F2 cell-surface antigen heavy chain
B: 4F2 cell-surface antigen heavy chain
C: 4F2 cell-surface antigen heavy chain
D: 4F2 cell-surface antigen heavy chain
H: S1-F4 VH
L: IGL c2062_light_IGKV4-1_IGKJ5
E: S1-F4 VH
I: IGL c2062_light_IGKV4-1_IGKJ5
F: S1-F4 VH
J: IGL c2062_light_IGKV4-1_IGKJ5
G: S1-F4 VH
K: IGL c2062_light_IGKV4-1_IGKJ5


Theoretical massNumber of molelcules
Total (without water)298,26512
Polymers298,26512
Non-polymers00
Water00
1
H: S1-F4 VH
L: IGL c2062_light_IGKV4-1_IGKJ5

A: 4F2 cell-surface antigen heavy chain


Theoretical massNumber of molelcules
Total (without water)74,5663
Polymers74,5663
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_454-x-1/2,-y,z-1/21
2
E: S1-F4 VH
I: IGL c2062_light_IGKV4-1_IGKJ5

B: 4F2 cell-surface antigen heavy chain


Theoretical massNumber of molelcules
Total (without water)74,5663
Polymers74,5663
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_454-x-1/2,-y,z-1/21
3
C: 4F2 cell-surface antigen heavy chain
F: S1-F4 VH
J: IGL c2062_light_IGKV4-1_IGKJ5


Theoretical massNumber of molelcules
Total (without water)74,5663
Polymers74,5663
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: 4F2 cell-surface antigen heavy chain
G: S1-F4 VH
K: IGL c2062_light_IGKV4-1_IGKJ5


Theoretical massNumber of molelcules
Total (without water)74,5663
Polymers74,5663
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)125.802, 165.212, 176.191
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 46243.961 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SLC3A2, MDU1 / Production host: Escherichia coli (E. coli) / References: UniProt: P08195
#2: Antibody
S1-F4 VH


Mass: 14741.354 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK 293-F / Production host: Homo sapiens (human)
#3: Antibody
IGL c2062_light_IGKV4-1_IGKJ5 / IGL c2147_light_IGKV4-1_IGKJ5


Mass: 13581.007 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK 293-F / Production host: Homo sapiens (human) / References: UniProt: A0A5C2G3X0
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: 3.27 Å3/Da / Density % sol: 62.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M sodium citrate tribasic dihydrate pH 5.0, 9% PEG20000, 5% PEG400, 9% glycerol

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 16, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.806→50.05 Å / Num. obs: 90217 / % possible obs: 99.8 % / Redundancy: 6.97 % / CC1/2: 0.998 / Rmerge(I) obs: 0.118 / Net I/σ(I): 12.69
Reflection shellResolution: 2.81→2.88 Å / Num. unique obs: 6299 / CC1/2: 0.896

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2DH2

2dh2


Resolution: 2.806→50.044 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 32.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2486 2009 2.23 %
Rwork0.217 --
obs0.2177 89964 99.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.806→50.044 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19740 0 0 0 19740
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00220192
X-RAY DIFFRACTIONf_angle_d0.55427388
X-RAY DIFFRACTIONf_dihedral_angle_d14.31411980
X-RAY DIFFRACTIONf_chiral_restr0.0413014
X-RAY DIFFRACTIONf_plane_restr0.0033518
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.806-2.87580.38741380.33216057X-RAY DIFFRACTION98
2.8758-2.95360.32391480.28696226X-RAY DIFFRACTION100
2.9536-3.04050.31261370.27786223X-RAY DIFFRACTION100
3.0405-3.13860.30621440.28176248X-RAY DIFFRACTION100
3.1386-3.25080.33511460.28316222X-RAY DIFFRACTION100
3.2508-3.38090.28311420.25566252X-RAY DIFFRACTION100
3.3809-3.53470.28321380.23876258X-RAY DIFFRACTION100
3.5347-3.7210.24591390.2236266X-RAY DIFFRACTION100
3.721-3.95410.24421460.21736277X-RAY DIFFRACTION100
3.9541-4.25920.24451440.19736308X-RAY DIFFRACTION100
4.2592-4.68750.21931470.17196294X-RAY DIFFRACTION100
4.6875-5.36520.18311450.17396360X-RAY DIFFRACTION100
5.3652-6.75690.21751400.19616410X-RAY DIFFRACTION100
6.7569-50.0440.20821550.18566554X-RAY DIFFRACTION99

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