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Yorodumi- PDB-5tlj: COMPLEX BETWEEN HUMAN CD27 AND FAB FRAGMENTS OF ANTIBODIES M2177 ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5tlj | |||||||||
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Title | COMPLEX BETWEEN HUMAN CD27 AND FAB FRAGMENTS OF ANTIBODIES M2177 AND M2191 | |||||||||
Components |
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Keywords | IMMUNE SYSTEM | |||||||||
Function / homology | Function and homology information TNFs bind their physiological receptors / negative regulation of T cell apoptotic process / positive regulation of T cell differentiation / positive regulation of B cell differentiation / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / immunoglobulin mediated immune response / extrinsic apoptotic signaling pathway / positive regulation of JNK cascade / positive regulation of non-canonical NF-kappaB signal transduction / transmembrane signaling receptor activity ...TNFs bind their physiological receptors / negative regulation of T cell apoptotic process / positive regulation of T cell differentiation / positive regulation of B cell differentiation / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / immunoglobulin mediated immune response / extrinsic apoptotic signaling pathway / positive regulation of JNK cascade / positive regulation of non-canonical NF-kappaB signal transduction / transmembrane signaling receptor activity / response to ethanol / cell surface receptor signaling pathway / external side of plasma membrane / negative regulation of apoptotic process / extracellular region / plasma membrane Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.5 Å | |||||||||
Authors | Teplyakov, A. / Obmolova, G. / Malia, T. / Gilliland, G.L. | |||||||||
Citation | Journal: Mol. Immunol. / Year: 2017 Title: Epitope-dependent mechanisms of CD27 neutralization revealed by X-ray crystallography. Authors: Obmolova, G. / Teplyakov, A. / Malia, T.J. / Wunderler, N. / Kwok, D. / Barone, L. / Sweet, R. / Ort, T. / Scully, M. / Gilliland, G.L. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5tlj.cif.gz | 348.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5tlj.ent.gz | 279.9 KB | Display | PDB format |
PDBx/mmJSON format | 5tlj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tl/5tlj ftp://data.pdbj.org/pub/pdb/validation_reports/tl/5tlj | HTTPS FTP |
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-Related structure data
Related structure data | 5tlkC 5tl5S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Details | THE DEPOSITORS STATE THAT THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT CONTAINS TWO TERNARY COMPLEXES COMPOSED OF CD27 AND TWO FABS. ONE TERNARY COMPLEX INCLUDES FAB M2177 (CHAINS A AND B), FAB M2191 (CHAINS C AND D), AND CD27 (CHAIN X). THE SECOND TERNARY COMPLEX INCLUDES FAB M2177 (CHAINS E AND F), FAB M2191 (CHAINS G AND H), BUT NO CD27, WHICH IS NOT DEFINED IN THE ELECTRON DENSITY. |
-Components
-Antibody , 4 types, 8 molecules AEBFCGDH
#1: Antibody | Mass: 23712.121 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus, Homo sapiens / Production host: Homo sapiens (human) #2: Antibody | Mass: 24444.291 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus, Homo sapiens / Production host: Homo sapiens (human) #3: Antibody | Mass: 23825.504 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus, Homo sapiens / Production host: Homo sapiens (human) #4: Antibody | Mass: 24371.271 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus, Homo sapiens / Production host: Homo sapiens (human) |
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-Protein / Sugars , 2 types, 2 molecules X
#5: Protein | Mass: 12287.896 Da / Num. of mol.: 1 / Fragment: Extracellular domain residues 21-121 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CD27, TNFRSF7 / Production host: unidentified baculovirus / References: UniProt: P26842 |
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#6: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
-Details
Compound details | THE DEPOSITORS STATE THAT THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT CONTAINS TWO TERNARY COMPLEXES ...THE DEPOSITORS |
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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: 2.29 Å3/Da / Density % sol: 46 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.1 M TRIS PH 8.5, 24% PEG 3350, 0.2 M AMMONIUM CHLORIDE PH range: 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU SATURN 944 / Detector: CCD / Date: Sep 30, 2011 / Details: VARIMAX HF |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 3.5→30 Å / Num. obs: 25023 / % possible obs: 97.8 % / Observed criterion σ(I): -3 / Redundancy: 4.4 % / Biso Wilson estimate: 41.7 Å2 / Rmerge(I) obs: 0.158 / Net I/σ(I): 9.6 |
Reflection shell | Resolution: 3.5→3.6 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.489 / Mean I/σ(I) obs: 2.7 / % possible all: 85.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5TL5 Resolution: 3.5→20 Å / Cor.coef. Fo:Fc: 0.836 / Cor.coef. Fo:Fc free: 0.727 / SU B: 62.932 / SU ML: 0.964 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.973
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 61.4 Å2
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Refinement step | Cycle: LAST / Resolution: 3.5→20 Å
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Refine LS restraints |
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