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- PDB-7v64: Crystal structure of Antibody 16A in complex with MUC1 Glycopepti... -

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Basic information

Entry
Database: PDB / ID: 7v64
TitleCrystal structure of Antibody 16A in complex with MUC1 Glycopeptide(GlycoT)
Components
  • 16A fab Heavy chain
  • 16A fab Light chain
  • Mucin-1 subunit alpha
KeywordsIMMUNE SYSTEM / Antibody / anti-MUC1 / Cancer / Glycopeptide / 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 / : / 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
2-acetamido-2-deoxy-beta-D-galactopyranose / Mucin-1
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.56 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 19, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 24, 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 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 16A fab Light chain
B: 16A fab Heavy chain
C: Mucin-1 subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,7304
Polymers49,5093
Non-polymers2211
Water9,422523
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4930 Å2
ΔGint-27 kcal/mol
Surface area18830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.534, 81.225, 137.331
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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: Sugar ChemComp-NGA / 2-acetamido-2-deoxy-beta-D-galactopyranose / N-acetyl-beta-D-galactosamine / 2-acetamido-2-deoxy-beta-D-galactose / 2-acetamido-2-deoxy-D-galactose / 2-acetamido-2-deoxy-galactose / N-ACETYL-D-GALACTOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGalpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-galactopyranosamineCOMMON NAMEGMML 1.0
b-D-GalpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 523 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 44.76 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 1.0 M Lithium chloride, 0.1 M Tris pH 8.5, 20% PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 19, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.56→40.61 Å / Num. obs: 62756 / % possible obs: 98.1 % / Redundancy: 6.4 % / CC1/2: 0.999 / Net I/σ(I): 23.7
Reflection shellResolution: 1.56→1.62 Å / Mean I/σ(I) obs: 2.2 / Num. unique obs: 5598 / CC1/2: 0.849 / Rpim(I) all: 0.258 / Rrim(I) all: 0.855

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Processing

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

4yhy


Resolution: 1.56→40.61 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 19.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2028 3205 5.11 %
Rwork0.1791 59551 -
obs0.1803 62756 97.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 74.76 Å2 / Biso mean: 20.2127 Å2 / Biso min: 6.41 Å2
Refinement stepCycle: final / Resolution: 1.56→40.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3294 0 28 523 3845
Biso mean--23.46 33.22 -
Num. residues----434
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 23

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.56-1.580.29881170.25332004212176
1.58-1.610.27961310.23532462259396
1.61-1.630.27521420.22292526266897
1.63-1.660.25541410.2192542268397
1.66-1.690.27541410.21122521266297
1.69-1.720.27881340.20772561269598
1.72-1.760.27571360.1992544268098
1.76-1.80.2761330.19452611274498
1.8-1.840.2351210.19052549267098
1.84-1.890.22391430.18742624276799
1.89-1.940.19241350.18242583271899
1.94-1.990.21661570.178126022759100
1.99-2.060.2061620.16725842746100
2.06-2.130.16931450.169225992744100
2.13-2.220.17141370.16862644278199
2.22-2.320.18661240.172626872811100
2.32-2.440.19611510.179626072758100
2.44-2.590.2291280.178526652793100
2.59-2.790.19161420.180526682810100
2.79-3.070.22311350.178426792814100
3.07-3.520.19631590.161726762835100
3.52-4.430.1671490.158427432892100
4.43-40.610.16961420.185128703012100

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