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- PDB-7v4w: Crystal structure of Antibody 16A in complex with MUC1 peptide -

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Basic information

Entry
Database: PDB / ID: 7v4w
TitleCrystal structure of Antibody 16A in complex with MUC1 peptide
Components
  • 16A Fab Heavy chain
  • 16A Fab Light chain
  • Mucin-1 subunit alpha
KeywordsIMMUNE SYSTEM / Antibody / anti-MUC1 / Cancer / ANTITUMOR PROTEIN
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 / 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
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsNiu, J. / Xu, L. / Meng, B. / Han, Y.B. / Yang, B.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Site-specific GalNAc modification on a MUC1 neoantigen epitope forms a basis for high-affinity antibody binding
Authors: Han, Y.B. / Xu, L.
History
DepositionAug 15, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 17, 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 30, 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: 16A Fab Light chain
B: 16A Fab Heavy chain
C: Mucin-1 subunit alpha


Theoretical massNumber of molelcules
Total (without water)49,5093
Polymers49,5093
Non-polymers00
Water5,080282
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4630 Å2
ΔGint-37 kcal/mol
Surface area19180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.557, 63.370, 88.681
Angle α, β, γ (deg.)90.000, 97.124, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Antibody 16A Fab Light chain


Mass: 23543.229 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Trichopalpus nigribasis (fry)
#2: Antibody 16A Fab Heavy chain


Mass: 24747.939 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Trichopalpus nigribasis (fry)
#3: Protein/peptide Mucin-1 subunit alpha / MUC1-NT / MUC1-alpha


Mass: 1217.334 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P15941
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 282 / Source method: isolated from a natural source / Formula: H2O
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: 2.23 Å3/Da / Density % sol: 44.79 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / Details: Di-sodium hydrogen phosphate 0.2M, PEG 3350 20%

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 20, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.1→39.25 Å / Num. obs: 23401 / % possible obs: 91.5 % / Redundancy: 1.8 % / Biso Wilson estimate: 29.78 Å2 / CC1/2: 0.964 / Rpim(I) all: 0.068 / Rrim(I) all: 0.129 / Net I/σ(I): 25.3
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 1.3 % / Mean I/σ(I) obs: 3.4 / Num. unique obs: 1379 / CC1/2: 0.544 / Rpim(I) all: 0.241 / Rrim(I) all: 0.39

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YHY

4yhy


Resolution: 2.1→39.25 Å / SU ML: 0.2614 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.9159
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2332 1150 4.91 %
Rwork0.1797 22251 -
obs0.1824 23401 91.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.63 Å2
Refinement stepCycle: LAST / Resolution: 2.1→39.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3292 0 0 282 3574
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00553370
X-RAY DIFFRACTIONf_angle_d0.84074588
X-RAY DIFFRACTIONf_chiral_restr0.0515524
X-RAY DIFFRACTIONf_plane_restr0.0049583
X-RAY DIFFRACTIONf_dihedral_angle_d18.1543457
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.190.2768860.21981690X-RAY DIFFRACTION55.97
2.19-2.310.28651380.22322452X-RAY DIFFRACTION81.68
2.31-2.450.24971470.21012978X-RAY DIFFRACTION97.81
2.45-2.640.281660.21013011X-RAY DIFFRACTION99.06
2.64-2.910.28451380.21073008X-RAY DIFFRACTION99.15
2.91-3.330.24771620.19263025X-RAY DIFFRACTION99.04
3.33-4.190.21621580.1563019X-RAY DIFFRACTION98.73
4.19-39.250.18411550.14983068X-RAY DIFFRACTION98.17

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