+Open data
-Basic information
Entry | Database: PDB / ID: 1ucb | ||||||
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Title | STRUCTURE OF UNCOMPLEXED FAB COMPARED TO COMPLEX (1CLY, 1CLZ) | ||||||
Components | (CHIMERIC HUMAN/MOUSE IGG FAB FRAGMENT BR96) x 2 | ||||||
Keywords | IMMUNOGLOBULIN / FAB / ANTIBODY / ANTI-TUMOR / CHIMERA | ||||||
Function / homology | Function and homology information IgD immunoglobulin complex / IgM immunoglobulin complex / IgA immunoglobulin complex / IgE immunoglobulin complex / CD22 mediated BCR regulation / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / Initial triggering of complement / IgG immunoglobulin complex / immunoglobulin mediated immune response ...IgD immunoglobulin complex / IgM immunoglobulin complex / IgA immunoglobulin complex / IgE immunoglobulin complex / CD22 mediated BCR regulation / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / Initial triggering of complement / IgG immunoglobulin complex / immunoglobulin mediated immune response / FCGR activation / Role of phospholipids in phagocytosis / Role of LAT2/NTAL/LAB on calcium mobilization / Scavenging of heme from plasma / antigen binding / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / Regulation of Complement cascade / Cell surface interactions at the vascular wall / FCGR3A-mediated phagocytosis / FCERI mediated MAPK activation / B cell receptor signaling pathway / Regulation of actin dynamics for phagocytic cup formation / FCERI mediated NF-kB activation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / blood microparticle / Potential therapeutics for SARS / adaptive immune response / immune response / extracellular space / extracellular exosome / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Sheriff, S. / Bajorath, J. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1996 Title: X-ray structure of the uncomplexed anti-tumor antibody BR96 and comparison with its antigen-bound form. Authors: Sheriff, S. / Chang, C.Y. / Jeffrey, P.D. / Bajorath, J. #1: Journal: J.Mol.Biol. / Year: 1994 Title: Crystallization and Preliminary X-Ray Analysis of the Monoclonal Anti-Tumor Antibody Br96 and its Complex with the Lewis Y Determinant Authors: Chang, C.Y. / Jeffrey, P.D. / Bajorath, J. / Hellstrom, I. / Hellstrom, K.E. / Sheriff, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ucb.cif.gz | 92 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ucb.ent.gz | 73.3 KB | Display | PDB format |
PDBx/mmJSON format | 1ucb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uc/1ucb ftp://data.pdbj.org/pub/pdb/validation_reports/uc/1ucb | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Antibody | Mass: 24077.883 Da / Num. of mol.: 1 Fragment: MOUSE VH AND VL DOMAINS, HUMAN CL KAPPA AND CH1 IGG1 DOMAINS Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) Description: MOUSE/HUMAN CHIMERA. MOUSE HYBRIDOMA PRODUCED BY FUSIONING BALB/C SPLEEN CELLS WITH 2X63-AG 8.653 MOUSE MYELOMA CELLS. HUMAN CONSTANT REGIONS INTRODUCED BY HOMOLOGOUS RECOMBINATION. CL ...Description: MOUSE/HUMAN CHIMERA. MOUSE HYBRIDOMA PRODUCED BY FUSIONING BALB/C SPLEEN CELLS WITH 2X63-AG 8.653 MOUSE MYELOMA CELLS. HUMAN CONSTANT REGIONS INTRODUCED BY HOMOLOGOUS RECOMBINATION. CL IS HUMAN KAPPA, CH1 IS HUMAN IGG1 DOMAIN. Fragment: CL AND CH1 / Organ: SPLEEN / Cell (production host): SPLEEN, MYELOMA / Production host: Mus musculus (house mouse) / Strain (production host): BALB/C, 2X63-AG 8.653 / References: UniProt: P01834 |
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#2: Antibody | Mass: 23609.449 Da / Num. of mol.: 1 Fragment: MOUSE VH AND VL DOMAINS, HUMAN CL KAPPA AND CH1 IGG1 DOMAINS Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) Description: MOUSE/HUMAN CHIMERA. MOUSE HYBRIDOMA PRODUCED BY FUSIONING BALB/C SPLEEN CELLS WITH 2X63-AG 8.653 MOUSE MYELOMA CELLS. HUMAN CONSTANT REGIONS INTRODUCED BY HOMOLOGOUS RECOMBINATION. CL ...Description: MOUSE/HUMAN CHIMERA. MOUSE HYBRIDOMA PRODUCED BY FUSIONING BALB/C SPLEEN CELLS WITH 2X63-AG 8.653 MOUSE MYELOMA CELLS. HUMAN CONSTANT REGIONS INTRODUCED BY HOMOLOGOUS RECOMBINATION. CL IS HUMAN KAPPA, CH1 IS HUMAN IGG1 DOMAIN. Fragment: CL AND CH1 / Organ: SPLEEN / Cell (production host): SPLEEN, MYELOMA / Production host: Mus musculus (house mouse) / Strain (production host): BALB/C, 2X63-AG 8.653 |
#3: Chemical | ChemComp-SO4 / |
#4: Water | ChemComp-HOH / |
Sequence details | THE FAB LIGHT CHAIN (RESIDUES 1 - 214) HAS BEEN ASSIGNED CHAIN INDICATOR L. THE FAB HEAVY CHAIN ...THE FAB LIGHT CHAIN (RESIDUES 1 - 214) HAS BEEN ASSIGNED CHAIN INDICATOR L. THE FAB HEAVY CHAIN (RESIDUES 1 - 227) HAS BEEN ASSIGNED CHAIN INDICATOR H. THE FAB FRAGMENT IS NUMBERED BY THE CONVENTION |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 49 % | |||||||||||||||
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Crystal grow | pH: 4.6 Details: 0.1 M SODIUM ACETATE (PH 4.6), 0.1 M AMMONIUM SULFATE, 15 % PEG 8000. | |||||||||||||||
Crystal grow | *PLUS pH: 7 / Method: unknown | |||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 295 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: SIEMENS-NICOLET X100 / Detector: AREA DETECTOR / Date: Mar 1, 1993 / Details: MIRROR |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→36 Å / Num. obs: 14826 / % possible obs: 87 % / Observed criterion σ(I): 0 / Redundancy: 2 % / Rmerge(I) obs: 0.045 / Net I/σ(I): 16.1 |
Reflection shell | Resolution: 2.5→2.8 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.107 / Mean I/σ(I) obs: 4 / % possible all: 65 |
Reflection | *PLUS Num. measured all: 29571 |
Reflection shell | *PLUS Highest resolution: 2.53 Å / Lowest resolution: 2.8 Å / % possible obs: 65 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: FV OF 1CLZ WITH CDRS REMOVED 1CLY (HUMAN IGG1, HUMAN KAPPA) AND OF 1CLZ (MOUSE IGG3, MOUSE KAPPA) Resolution: 2.5→8 Å / Cross valid method: EX POST FACTO / σ(F): 1
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Displacement parameters | Biso mean: 29 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.28 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→8 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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