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Yorodumi- PDB-7v7k: Crystal structure of Antibody 16A in complex with MUC1 Glycopepti... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7v7k | ||||||
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Title | Crystal structure of Antibody 16A in complex with MUC1 Glycopeptide(GlycoST) | ||||||
Components |
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Keywords | IMMUNE SYSTEM / Antibody / anti-MUC1 / Cancer / Glycopeptide / PEPTIDE BINDING 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 / 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 | ||||||
Biological species | Mus musculus (house mouse) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Niu, J. / Xu, L. / Meng, B. / Han, Y.B. / Yang, B. | ||||||
Funding support | China, 1items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7v7k.cif.gz | 174.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7v7k.ent.gz | 138.3 KB | Display | PDB format |
PDBx/mmJSON format | 7v7k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v7/7v7k ftp://data.pdbj.org/pub/pdb/validation_reports/v7/7v7k | HTTPS FTP |
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-Related structure data
Related structure data | 7v3qC 7v4wC 7v64C 7v8qC 7vacC 7vazC 4yhyS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Antibody | 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) | ||||
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#2: Antibody | 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 | Mass: 1217.334 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P15941 | ||||
#4: Sugar | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.81 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 1.0 M Lithium chloride, 0.1 M Tris pH 8.5, 20%(w/v) PEG 6000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 20, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→39.7 Å / Num. obs: 21331 / % possible obs: 93.4 % / Redundancy: 1.6 % / CC1/2: 0.994 / Rpim(I) all: 0.072 / Rrim(I) all: 0.129 / Net I/σ(I): 10.5 |
Reflection shell | Resolution: 2.2→2.28 Å / Num. unique obs: 1731 / CC1/2: 0.58 / Rpim(I) all: 0.49 / Rrim(I) all: 0.73 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4YHY Resolution: 2.2→39.7 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 25.79 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 102.45 Å2 / Biso mean: 32.4499 Å2 / Biso min: 15.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.2→39.7 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7
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