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- PDB-7vac: Crystal structure of antibody 14A in complex with MUC1 glycopepti... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7vac | ||||||
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Title | Crystal structure of antibody 14A in complex with MUC1 glycopeptide(GlycoST) | ||||||
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![]() | IMMUNE SYSTEM / Antibody / anti-MUC1 / Glycopeptide / PEPTIDE BINDING PROTEIN | ||||||
Function / homology | ![]() 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 | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Niu, J. / Xu, L. / Meng, B. / Han, Y.B. / Yang, B. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 506.1 KB | Display | ![]() |
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PDB format | ![]() | 420.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.9 MB | Display | ![]() |
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Full document | ![]() | 1.9 MB | Display | |
Data in XML | ![]() | 47.9 KB | Display | |
Data in CIF | ![]() | 65.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7v3qC ![]() 7v4wC ![]() 7v64C ![]() 7v7kC ![]() 7v8qC ![]() 7vazC ![]() 4yhyS C: citing same article ( S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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3 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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Components
#1: Antibody | Mass: 23512.129 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Antibody | Mass: 24568.670 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Protein/peptide | Mass: 1217.334 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) ![]() #4: Sugar | ChemComp-NGA / Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.38 Å3/Da / Density % sol: 63.64 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 0.1 M Sodium citrate pH 5.5, Isopropanol 10%, PEG 4000 20% |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 19, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 3.5→40.69 Å / Num. obs: 26442 / % possible obs: 99.7 % / Redundancy: 6.2 % / CC1/2: 0.998 / Rpim(I) all: 0.048 / Rrim(I) all: 0.164 / Net I/σ(I): 11.7 |
Reflection shell | Resolution: 3.5→3.63 Å / Mean I/σ(I) obs: 2 / Num. unique obs: 2588 / CC1/2: 0.816 / Rpim(I) all: 0.253 / Rrim(I) all: 0.841 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4YHY Resolution: 3.5→40.69 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 20.5 / 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: 159.7 Å2 / Biso mean: 55.4481 Å2 / Biso min: 20 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.5→40.69 Å
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Refine LS restraints NCS |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9
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Refinement TLS params. | Method: refined / Origin x: 27.5567 Å / Origin y: -46.789 Å / Origin z: -32.9233 Å
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Refinement TLS group | Selection details: all |