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- PDB-8hrh: SN-131/1B2 anti-MUC1 antibody with a glycopeptide -

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Basic information

Entry
Database: PDB / ID: 8hrh
TitleSN-131/1B2 anti-MUC1 antibody with a glycopeptide
Components
  • Heavy chain of SN-131/1B2 antibody Fab
  • Light chain of SN-131/1B2 antibody Fab
KeywordsIMMUNE SYSTEM / antibody
Function / homologyALANINE / ARGININE / ASPARTIC ACID / L-PROLINAMIDE / 1-ACETYL-L-PROLINE / DI(HYDROXYETHYL)ETHER / PROLINE / THREONINE
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.07 Å
AuthorsWakui, H. / Horidome, C. / Yao, M. / Ose, T. / Nishimura, S.-I.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)19H00918 Japan
CitationJournal: Rsc Chem Biol / Year: 2023
Title: Structural and molecular insight into antibody recognition of dynamic neoepitopes in membrane tethered MUC1 of pancreatic cancer cells and secreted exosomes.
Authors: Wakui, H. / Yokoi, Y. / Horidome, C. / Ose, T. / Yao, M. / Tanaka, Y. / Hinou, H. / Nishimura, S.I.
History
DepositionDec 15, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 30, 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: Heavy chain of SN-131/1B2 antibody Fab
B: Light chain of SN-131/1B2 antibody Fab
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,75920
Polymers78,1322
Non-polymers2,62718
Water3,837213
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8630 Å2
ΔGint12 kcal/mol
Surface area18850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.590, 84.590, 271.270
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Space group name HallP652(x,y,z+1/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z+1/2
#9: y,x,-z+2/3
#10: -y,-x,-z+1/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+5/6

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Components

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Antibody , 2 types, 2 molecules AB

#1: Antibody Heavy chain of SN-131/1B2 antibody Fab


Mass: 51471.207 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 Light chain of SN-131/1B2 antibody Fab


Mass: 26661.059 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): Hybridoma / Production host: Mus musculus (house mouse)

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Sugars , 1 types, 1 molecules

#3: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-alpha-D-galactopyranose


Type: oligosaccharide / Mass: 674.604 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DNeup5Aca2-3DGalpb1-3DGalpNAca1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2112h-1a_1-5_2*NCC/3=O][a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O]/1-2-3/a3-b1_b3-c2WURCSPDB2Glycan 1.1.0
[]{[(3+1)][a-D-GalpNAc]{[(3+1)][b-D-Galp]{[(3+2)][a-D-Neup5Ac]{}}}}LINUCSPDB-CARE

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Non-polymers , 11 types, 230 molecules

#4: Chemical ChemComp-N7P / 1-ACETYL-L-PROLINE / N-ACETYLPROLINE


Type: L-peptide linking / Mass: 157.167 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H11NO3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-ASP / ASPARTIC ACID


Type: L-peptide linking / Mass: 133.103 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H7NO4 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-THR / THREONINE


Type: L-peptide linking / Mass: 119.119 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H9NO3 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-ARG / ARGININE


Type: L-peptide linking / Mass: 175.209 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15N4O2 / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-ALA / ALANINE


Type: L-peptide linking / Mass: 89.093 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO2 / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#10: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C4H10O3
#11: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#12: Chemical ChemComp-PRO / PROLINE


Type: L-peptide linking / Mass: 115.130 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO2 / Feature type: SUBJECT OF INVESTIGATION
#13: Chemical ChemComp-LPD / L-PROLINAMIDE


Type: L-peptide linking / Mass: 114.146 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H10N2O
#14: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 213 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 1.79 Å3/Da / Density % sol: 31.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 40% (w/v) PEG300, 5% (w/v) PEG1000, 0.1M Tris

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Mar 7, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.07→49.766 Å / Num. obs: 36078 / % possible obs: 99.9 % / Redundancy: 19.9 % / CC1/2: 0.999 / Rrim(I) all: 0.127 / Net I/σ(I): 16.6
Reflection shellResolution: 2.07→2.2 Å / Redundancy: 20.3 % / Mean I/σ(I) obs: 3.43 / Num. unique obs: 5649 / CC1/2: 0.956 / Rrim(I) all: 0.758 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX1.16-3549refinement
XDSdata scaling
Cootmodel building
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6KX1

6kx1


Resolution: 2.07→49.766 Å / Cross valid method: FREE R-VALUE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2265 1803 5 %Random selection
Rwork0.1923 ---
obs-36063 99.91 %-
Displacement parametersBiso mean: 37.88 Å2
Refinement stepCycle: LAST / Resolution: 2.07→49.766 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3328 0 170 213 3711
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053568
X-RAY DIFFRACTIONf_angle_d0.87924833
X-RAY DIFFRACTIONf_chiral_restr0.0491536
X-RAY DIFFRACTIONf_plane_restr0.0042596
X-RAY DIFFRACTIONf_dihedral_angle_d13.38342088

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