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- PDB-1adq: CRYSTAL STRUCTURE OF A HUMAN IGM RHEUMATOID FACTOR FAB IN COMPLEX... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1adq | ||||||
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Title | CRYSTAL STRUCTURE OF A HUMAN IGM RHEUMATOID FACTOR FAB IN COMPLEX WITH ITS AUTOANTIGEN IGG FC | ||||||
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![]() | COMPLEX (IMMUNOGLOBULIN/AUTOANTIGEN) / COMPLEX (IMMUNOGLOBULIN-AUTOANTIGEN) / RHEUMATOID FACTOR AUTO-ANTIBODY COMPLEX / COMPLEX (IMMUNOGLOBULIN-AUTOANTIGEN) complex | ||||||
Function / homology | ![]() IgG immunoglobulin complex / Classical antibody-mediated complement activation / Initial triggering of complement / FCGR activation / Role of phospholipids in phagocytosis / immunoglobulin complex, circulating / immunoglobulin receptor binding / FCGR3A-mediated IL10 synthesis / complement activation, classical pathway / Regulation of Complement cascade ...IgG immunoglobulin complex / Classical antibody-mediated complement activation / Initial triggering of complement / FCGR activation / Role of phospholipids in phagocytosis / immunoglobulin complex, circulating / immunoglobulin receptor binding / FCGR3A-mediated IL10 synthesis / complement activation, classical pathway / Regulation of Complement cascade / FCGR3A-mediated phagocytosis / antigen binding / B cell receptor signaling pathway / Regulation of actin dynamics for phagocytic cup formation / antibacterial humoral response / Interleukin-4 and Interleukin-13 signaling / adaptive immune response / blood microparticle / extracellular space / extracellular exosome / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Corper, A.L. / Taussig, M.J. / Sutton, B.J. | ||||||
![]() | ![]() Title: Structure of human IgM rheumatoid factor Fab bound to its autoantigen IgG Fc reveals a novel topology of antibody-antigen interaction. Authors: Corper, A.L. / Sohi, M.K. / Bonagura, V.R. / Steinitz, M. / Jefferis, R. / Feinstein, A. / Beale, D. / Taussig, M.J. / Sutton, B.J. #1: ![]() Title: Crystallization of a Complex between the Fab Fragment of a Human Immunoglobulin M (Igm) Rheumatoid Factor (Rf-an) and the Fc Fragment of Human Igg4 Authors: Sohi, M.K. / Corper, A.L. / Wan, T. / Steinitz, M. / Jefferis, R. / Beale, D. / He, M. / Feinstein, A. / Sutton, B.J. / Taussig, M.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 121.8 KB | Display | ![]() |
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PDB format | ![]() | 94.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 439.7 KB | Display | ![]() |
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Full document | ![]() | 449.2 KB | Display | |
Data in XML | ![]() | 22.7 KB | Display | |
Data in CIF | ![]() | 31.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 23484.457 Da / Num. of mol.: 1 / Fragment: FC / Source method: isolated from a natural source Details: ISOLATED FROM THE SERA OF PATIENTS WITH MULTIPLE MYELOMA Source: (natural) ![]() |
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#2: Antibody | Mass: 22567.885 Da / Num. of mol.: 1 / Fragment: FAB / Source method: isolated from a natural source Details: RF-AN CELL LINE WAS PREPARED FROM PERIPHERAL BLOOD LYMPHOCYTES OF AN RA PATIENT BY TRANSFORMATION WITH EPSTEIN-BARR VIRUS Source: (natural) ![]() |
#3: Antibody | Mass: 24665.742 Da / Num. of mol.: 1 / Fragment: FAB / Source method: isolated from a natural source Details: RF-AN CELL LINE WAS PREPARED FROM PERIPHERAL BLOOD LYMPHOCYTES OF AN RA PATIENT BY TRANSFORMATION WITH EPSTEIN-BARR VIRUS Source: (natural) ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.9 Å3/Da / Density % sol: 58 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 7 Details: CRYSTALS WERE GROWN BY HANGING DROP VAPOR DIFFUSION. THE HANGING DROPS CONSISTED OF 2UL OF PROTEIN SOLUTION CONTAINING EACH PROTEIN AT 1MG/ML IN 0.1 % SODIUM AZIDE, 20MM TRIS-HCL AT PH 7.0, ...Details: CRYSTALS WERE GROWN BY HANGING DROP VAPOR DIFFUSION. THE HANGING DROPS CONSISTED OF 2UL OF PROTEIN SOLUTION CONTAINING EACH PROTEIN AT 1MG/ML IN 0.1 % SODIUM AZIDE, 20MM TRIS-HCL AT PH 7.0, MIXED WITH AN EQUAL VOLUME OF THE RESERVOIR SOLUTION TO BE SCREENED. CRYSTALS WERE OBTAINED WITH RESERVOIR SOLUTIONS CONTAINING 17.5 - 22.5 % (W/V) POLYETHYLENE GLYCOL (MEAN MW 8000) IN 0.1 % SODIUM AZIDE, 100MM TRIS-HCL, PH 7.0, AT TEMPERATURES BETWEEN 17.5 AND 21.5 (CELSIUS)., vapor diffusion - hanging drop PH range: APPROX. / Temp details: 290.5 - 294.5 | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 17.5-21.5 ℃ / Method: vapor diffusion, hanging dropDetails: drop consists of equal volume of protein and reservoir solutions | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 278 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Jun 1, 1994 / Details: COLLIMATOR |
Radiation | Monochromator: GRAPHITE / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 3.15→15 Å / Num. obs: 14109 / % possible obs: 98.3 % / Observed criterion σ(I): 3 / Redundancy: 3.1 % / Biso Wilson estimate: 25.4 Å2 / Rmerge(I) obs: 0.113 / Net I/σ(I): 5.3 |
Reflection shell | Resolution: 3.15→3.31 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.265 / Mean I/σ(I) obs: 2.8 / % possible all: 98.8 |
Reflection shell | *PLUS % possible obs: 98.8 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1FC1, 2IG2 Resolution: 3.15→8 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 100000 / Data cutoff low absF: 80 / Isotropic thermal model: GROUPED B-FACTOR REFINEMENT / Cross valid method: THROUGHOUT / σ(F): 0 Details: DISORDERED REGION A263-A300 WAS MODELED STEREOCHEMICALLY. FAB IN COMPLEX WITH ITS AUTOANTIGEN IGG FC. CONSTANT DOMAINS OF RF-AN SHOWED SIGNIFICANT DISORDER AND WERE PARTLY MODELED ...Details: DISORDERED REGION A263-A300 WAS MODELED STEREOCHEMICALLY. FAB IN COMPLEX WITH ITS AUTOANTIGEN IGG FC. CONSTANT DOMAINS OF RF-AN SHOWED SIGNIFICANT DISORDER AND WERE PARTLY MODELED STEREOCHEMICALLY. RESIDUES L51 AND L171 OCCUR IN WELL DEFINED REGIONS OF THE STRUCTURE (OCCUPANCY = 1). BOTH OCCUR IN LOOP REGIONS AND CONTINUE TO HAVE DISALLOWED PHI/PSI VALUES EVEN AFTER REBUILDING.
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Displacement parameters | Biso mean: 33.1 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.15→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.15→3.26 Å / Rfactor Rfree error: 0.05 / Total num. of bins used: 10
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Xplor file |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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