+Open data
-Basic information
Entry | Database: PDB / ID: 7uqc | ||||||
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Title | phospho-GlialCAM peptide AA370-389 with Fab MS39p2w174 | ||||||
Components |
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Keywords | IMMUNE SYSTEM / Autoantigen / EBV / Antibody | ||||||
Function / homology | Function and homology information cell cycle / cell-cell junction / protein localization / regulation of cell cycle / cell adhesion / axon / membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å | ||||||
Authors | Lanz, T.V. / Robinson, W.H. / Fernandez, D. | ||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published Title: Evolution of Antibody Reactivity against EBV EBNA1 to Molecular Mimicry with GlialCAM Authors: Lanz, T.V. / Robinson, W.H. / Fernandez, D. #1: Journal: Nature / Year: 2022 Title: Clonally expanded B cells in multiple sclerosis bind EBV EBNA1 and GlialCAM. Authors: Lanz, T.V. / Brewer, R.C. / Ho, P.P. / Moon, J.S. / Jude, K.M. / Fernandez, D. / Fernandes, R.A. / Gomez, A.M. / Nadj, G.S. / Bartley, C.M. / Schubert, R.D. / Hawes, I.A. / Vazquez, S.E. / ...Authors: Lanz, T.V. / Brewer, R.C. / Ho, P.P. / Moon, J.S. / Jude, K.M. / Fernandez, D. / Fernandes, R.A. / Gomez, A.M. / Nadj, G.S. / Bartley, C.M. / Schubert, R.D. / Hawes, I.A. / Vazquez, S.E. / Iyer, M. / Zuchero, J.B. / Teegen, B. / Dunn, J.E. / Lock, C.B. / Kipp, L.B. / Cotham, V.C. / Ueberheide, B.M. / Aftab, B.T. / Anderson, M.S. / DeRisi, J.L. / Wilson, M.R. / Bashford-Rogers, R.J.M. / Platten, M. / Garcia, K.C. / Steinman, L. / Robinson, W.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7uqc.cif.gz | 433.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7uqc.ent.gz | 284.8 KB | Display | PDB format |
PDBx/mmJSON format | 7uqc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7uqc_validation.pdf.gz | 4.5 MB | Display | wwPDB validaton report |
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Full document | 7uqc_full_validation.pdf.gz | 4.5 MB | Display | |
Data in XML | 7uqc_validation.xml.gz | 64.7 KB | Display | |
Data in CIF | 7uqc_validation.cif.gz | 91.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uq/7uqc ftp://data.pdbj.org/pub/pdb/validation_reports/uq/7uqc | HTTPS FTP |
-Related structure data
Related structure data | 7k7rS 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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2 |
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3 |
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4 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein/peptide , 1 types, 2 molecules CF
#3: Protein/peptide | Mass: 2227.210 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HEPACAM / Production host: Homo sapiens (human) / References: UniProt: Q14CZ8 |
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-Antibody , 2 types, 8 molecules AGIDBHJE
#1: Antibody | Mass: 24204.006 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) #2: Antibody | Mass: 23381.055 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) |
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-Non-polymers , 3 types, 331 molecules
#4: Chemical | #5: Chemical | ChemComp-CL / #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.13 Å3/Da / Density % sol: 60.73 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / Details: tbd |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 13, 2022 |
Radiation | Monochromator: Liquid nitrogen-cooled double crystal, non fixed exit slit Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 |
Reflection | Resolution: 2.65→44.11 Å / Num. obs: 69508 / % possible obs: 98.4 % / Redundancy: 3.5 % / Biso Wilson estimate: 44.71 Å2 / CC1/2: 0.977 / CC star: 0.994 / Rmerge(I) obs: 0.1134 / Rpim(I) all: 0.1134 / Rrim(I) all: 0.1603 / Net I/σ(I): 5.42 |
Reflection shell | Resolution: 2.65→2.79 Å / Redundancy: 3.4 % / Rmerge(I) obs: 1.461 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 10053 / CC1/2: 0.347 / Rpim(I) all: 0.94 / % possible all: 97.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7K7R Resolution: 2.65→44.11 Å / SU ML: 0.3527 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.1734 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 49.48 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.65→44.11 Å
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Refine LS restraints |
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LS refinement shell |
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