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- PDB-1h3t: Crystal structure of the human igg1 fc-fragment,glycoform (mn2f)2 -
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Open data
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Basic information
Entry | Database: PDB / ID: 1h3t | |||||||||
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Title | Crystal structure of the human igg1 fc-fragment,glycoform (mn2f)2 | |||||||||
![]() | IG GAMMA-1 CHAIN C REGION | |||||||||
![]() | IMMUNE SYSTEM / IMMUNOGLOBULIN / GLYCOSYLATION / FCGR / ANTIBODY / EFFECTOR FUNCTIONS | |||||||||
Function / homology | ![]() Fc-gamma receptor I complex binding / complement-dependent cytotoxicity / IgG immunoglobulin complex / antibody-dependent cellular cytotoxicity / Classical antibody-mediated complement activation / Initial triggering of complement / FCGR activation / Role of phospholipids in phagocytosis / immunoglobulin complex, circulating / immunoglobulin receptor binding ...Fc-gamma receptor I complex binding / complement-dependent cytotoxicity / IgG immunoglobulin complex / antibody-dependent cellular cytotoxicity / 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 | ![]() ![]() | |||||||||
![]() | Krapp, S. / Mimura, Y. / Jefferis, R. / Huber, R. / Sondermann, P. | |||||||||
![]() | ![]() Title: Structural Analysis of Human Igg-Fc Glycoforms Reveals a Correlation between Glycosylation and Structural Integrity Authors: Krapp, S. / Mimura, Y. / Jefferis, R. / Huber, R. / Sondermann, P. | |||||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 97.9 KB | Display | ![]() |
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PDB format | ![]() | 72.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 805 KB | Display | ![]() |
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Full document | ![]() | 820.2 KB | Display | |
Data in XML | ![]() | 19.4 KB | Display | |
Data in CIF | ![]() | 26.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1h3uC ![]() 1h3vC ![]() 1h3wC ![]() 1h3xC ![]() 1h3yC ![]() 1fc1S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: Protein | Mass: 25126.541 Da / Num. of mol.: 2 / Fragment: CH2, CH3, RESIDUES 225-447 / Source method: isolated from a natural source / Source: (natural) ![]() #2: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6) ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #3: Sugar | ChemComp-BMA / | #4: Water | ChemComp-HOH / | Sequence details | THE PRIMARY SEQUENCE FOR THIS ENTRY IS VERY SIMILAR TO SWISSPROT ENTRY P01857 (GC1_HUMAN) WITH 96% ...THE PRIMARY SEQUENCE FOR THIS ENTRY IS VERY SIMILAR TO SWISSPROT ENTRY P01857 (GC1_HUMAN) WITH 96% SEQUENCE IDENTITY. | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.78 Å3/Da / Density % sol: 55 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.5 / Details: DIALYSIS AGAINST WATER, pH 6.50 | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 6 / Method: vapor diffusion, sitting drop | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 15, 2001 / Details: MIRRORS |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. obs: 21295 / % possible obs: 98.1 % / Observed criterion σ(I): 2 / Redundancy: 4 % / Rmerge(I) obs: 0.06 |
Reflection shell | Rmerge(I) obs: 0.2 / % possible all: 93.4 |
Reflection | *PLUS Lowest resolution: 50 Å |
Reflection shell | *PLUS % possible obs: 93.4 % / Rmerge(I) obs: 0.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1FC1 Resolution: 2.4→50 Å / Cross valid method: THROUGHOUT / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 2.4→50 Å
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Refine LS restraints |
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Refinement | *PLUS Lowest resolution: 50 Å / Rfactor Rwork: 0.28 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |