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- PDB-6kx1: Crystal structure of SN-101 mAb in complex with MUC1 glycopeptide -

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Basic information

Entry
Database: PDB / ID: 6kx1
TitleCrystal structure of SN-101 mAb in complex with MUC1 glycopeptide
Components
  • Fab Fragment-SN-101-Heavy chain
  • Fab Fragment-SN-101-Light chain
  • Synthetic MUC1 glycopepide
KeywordsIMMUNE SYSTEM / Antibody / IgG1 / MUC1 / Glycopeptide
Function / homology
Function and homology information


Defective GALNT3 causes HFTC / Defective C1GALT1C1 causes TNPS / Defective GALNT12 causes CRCS1 / Termination of O-glycan biosynthesis / O-linked glycosylation of mucins / negative regulation of cell adhesion mediated by integrin / negative regulation of transcription by competitive promoter binding / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / Dectin-2 family / DNA damage response, signal transduction by p53 class mediator ...Defective GALNT3 causes HFTC / Defective C1GALT1C1 causes TNPS / Defective GALNT12 causes CRCS1 / Termination of O-glycan biosynthesis / O-linked glycosylation of mucins / negative regulation of cell adhesion mediated by integrin / negative regulation of transcription by competitive promoter binding / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / Dectin-2 family / DNA damage response, signal transduction by p53 class mediator / localization / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / transcription coregulator activity / Golgi lumen / p53 binding / Interleukin-4 and Interleukin-13 signaling / vesicle / apical plasma membrane / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular exosome / nucleus / plasma membrane
Similarity search - Function
Domain found in sea urchin sperm protein, enterokinase, agrin / SEA domain superfamily / SEA domain profile. / SEA domain / SEA domain
Similarity search - Domain/homology
2-acetamido-2-deoxy-alpha-D-galactopyranose / Mucin-1
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.773 Å
AuthorsWakui, H. / Tanaka, Y. / Kato, K. / Ose, T. / Matsumoto, I. / Min, Y. / Tachibana, T. / Nishimura, S.-I.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science25220206 Japan
Japan Society for the Promotion of Science19H00918 Japan
CitationJournal: Chem Sci / Year: 2020
Title: A straightforward approach to antibodies recognising cancer specific glycopeptidic neoepitopes
Authors: Wakui, H. / Tanaka, Y. / Ose, T. / Matsumoto, I. / Kato, K. / Min, Y. / Tachibana, T. / Sato, M. / Naruchi, K. / Martin, F.G. / Hinou, H. / Nishimura, S.-I.
History
DepositionSep 9, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 29, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fab Fragment-SN-101-Heavy chain
B: Fab Fragment-SN-101-Light chain
C: Synthetic MUC1 glycopepide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,6564
Polymers53,4353
Non-polymers2211
Water4,270237
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5010 Å2
ΔGint-18 kcal/mol
Surface area18820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)159.920, 39.980, 63.870
Angle α, β, γ (deg.)90.000, 100.560, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Antibody Fab Fragment-SN-101-Heavy chain


Mass: 25541.768 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)
#2: Antibody Fab Fragment-SN-101-Light chain


Mass: 26438.670 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)
#3: Protein/peptide Synthetic MUC1 glycopepide


Mass: 1454.562 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P15941*PLUS
#4: Sugar ChemComp-A2G / 2-acetamido-2-deoxy-alpha-D-galactopyranose / N-acetyl-alpha-D-galactosamine / 2-acetamido-2-deoxy-alpha-D-galactose / 2-acetamido-2-deoxy-D-galactose / 2-acetamido-2-deoxy-galactose / N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE / N-Acetylgalactosamine


Type: D-saccharide, alpha linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGalpNAcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-D-galactopyranosamineCOMMON NAMEGMML 1.0
a-D-GalpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 237 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Sequence detailsACE in chain C is acetylation.

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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: 1.89 Å3/Da / Density % sol: 35.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 300-350 mM NaSCN 20-30% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Mar 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.77→50 Å / Num. obs: 38810 / % possible obs: 99.6 % / Redundancy: 4.98 % / CC1/2: 0.999 / Rrim(I) all: 0.071 / Net I/σ(I): 15.3
Reflection shellResolution: 1.77→1.88 Å / Mean I/σ(I) obs: 1.97 / Num. unique obs: 6165 / CC1/2: 0.723 / Rrim(I) all: 0.926 / % possible all: 98.5

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Processing

Software
NameClassification
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PZ5

1pz5


Resolution: 1.773→39.303 Å / Cross valid method: FREE R-VALUE / σ(F): 1.35
RfactorNum. reflection% reflection
Rfree0.2286 1939 5 %
Rwork0.177 --
obs0.1795 38800 99.6 %
Displacement parametersBiso mean: 31.94 Å2
Refinement stepCycle: LAST / Resolution: 1.773→39.303 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3368 0 14 237 3619
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01023466
X-RAY DIFFRACTIONf_angle_d1.11754721
X-RAY DIFFRACTIONf_chiral_restr0.0621531
X-RAY DIFFRACTIONf_plane_restr0.0074601
X-RAY DIFFRACTIONf_dihedral_angle_d12.45782054

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