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Yorodumi- PDB-1icf: CRYSTAL STRUCTURE OF MHC CLASS II ASSOCIATED P41 II FRAGMENT IN C... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1icf | ||||||
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Title | CRYSTAL STRUCTURE OF MHC CLASS II ASSOCIATED P41 II FRAGMENT IN COMPLEX WITH CATHEPSIN L | ||||||
Components |
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Keywords | HYDROLASE / CYSTEINE PROTEINASE / CATHEPSIN / MHC CLASS II / INVARIANT CHAIN / THYROGLOBULIN TYPE-1 DOMAIN | ||||||
Function / homology | Function and homology information negative regulation of peptide secretion / macrophage migration inhibitory factor signaling pathway / NOS2-CD74 complex / MHC class II protein binding, via antigen binding groove / antigen processing and presentation of endogenous antigen / positive regulation of dendritic cell antigen processing and presentation / negative regulation of T cell differentiation / macrophage migration inhibitory factor binding / positive regulation of macrophage migration inhibitory factor signaling pathway / enkephalin processing ...negative regulation of peptide secretion / macrophage migration inhibitory factor signaling pathway / NOS2-CD74 complex / MHC class II protein binding, via antigen binding groove / antigen processing and presentation of endogenous antigen / positive regulation of dendritic cell antigen processing and presentation / negative regulation of T cell differentiation / macrophage migration inhibitory factor binding / positive regulation of macrophage migration inhibitory factor signaling pathway / enkephalin processing / cathepsin L / CD4-positive, alpha-beta T cell lineage commitment / protein trimerization / macrophage migration inhibitory factor receptor complex / macrophage apoptotic process / positive regulation of cytokine-mediated signaling pathway / chromaffin granule / T cell activation involved in immune response / negative thymic T cell selection / positive regulation of type 2 immune response / T cell selection / positive regulation of prostaglandin biosynthetic process / elastin catabolic process / negative regulation of viral entry into host cell / antigen processing and presentation of peptide antigen / MHC class II protein binding / RUNX1 regulates transcription of genes involved in differentiation of keratinocytes / negative regulation of mature B cell apoptotic process / positive thymic T cell selection / endolysosome lumen / positive regulation of monocyte differentiation / CD4 receptor binding / vacuole / positive regulation of chemokine (C-X-C motif) ligand 2 production / positive regulation of kinase activity / positive regulation of neutrophil chemotaxis / cellular response to thyroid hormone stimulus / cytokine receptor activity / zymogen activation / Trafficking and processing of endosomal TLR / positive regulation of macrophage cytokine production / prostaglandin biosynthetic process / positive regulation of T cell differentiation / regulation of macrophage activation / proteoglycan binding / transport vesicle membrane / Assembly of collagen fibrils and other multimeric structures / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / cytokine binding / nitric-oxide synthase binding / response to type II interferon / negative regulation of DNA damage response, signal transduction by p53 class mediator / chaperone cofactor-dependent protein refolding / cysteine-type endopeptidase activator activity involved in apoptotic process / protein autoprocessing / Collagen degradation / immunoglobulin mediated immune response / fibronectin binding / antigen processing and presentation / collagen catabolic process / serpin family protein binding / cysteine-type peptidase activity / Attachment and Entry / positive regulation of B cell proliferation / protein folding chaperone / positive regulation of apoptotic signaling pathway / positive regulation of chemokine production / endocytic vesicle lumen / collagen binding / MHC class II antigen presentation / Degradation of the extracellular matrix / multivesicular body / proteolysis involved in protein catabolic process / lysosomal lumen / negative regulation of cell migration / trans-Golgi network membrane / positive regulation of interleukin-8 production / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / Cell surface interactions at the vascular wall / clathrin-coated endocytic vesicle membrane / intracellular protein transport / ER to Golgi transport vesicle membrane / positive regulation of interleukin-6 production / MHC class II protein complex / endocytic vesicle membrane / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of fibroblast proliferation / positive regulation of peptidyl-tyrosine phosphorylation / late endosome / MHC class II protein complex binding / amyloid-beta binding / histone binding / protein-containing complex assembly / collagen-containing extracellular matrix / positive regulation of canonical NF-kappaB signal transduction / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / positive regulation of MAPK cascade / adaptive immune response Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Guncar, G. / Pungercic, G. / Klemencic, I. / Turk, V. / Turk, D. | ||||||
Citation | Journal: EMBO J. / Year: 1999 Title: Crystal structure of MHC class II-associated p41 Ii fragment bound to cathepsin L reveals the structural basis for differentiation between cathepsins L and S. Authors: Guncar, G. / Pungercic, G. / Klemencic, I. / Turk, V. / Turk, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1icf.cif.gz | 137.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1icf.ent.gz | 106.2 KB | Display | PDB format |
PDBx/mmJSON format | 1icf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ic/1icf ftp://data.pdbj.org/pub/pdb/validation_reports/ic/1icf | HTTPS FTP |
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-Related structure data
Related structure data | 1cjlS 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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3 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.967984, -0.116869, 0.222146), Vector: |
-Components
#1: Protein | Mass: 19095.020 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Organ: KIDNEY / References: UniProt: P07711, cathepsin L #2: Protein/peptide | Mass: 4783.409 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Organ: KIDNEY / References: UniProt: P07711, cathepsin L #3: Protein | Mass: 7261.075 Da / Num. of mol.: 2 / Fragment: THYROGLOBULIN TYPE-1 DOMAIN / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Organ: KIDNEY / References: UniProt: P04233 #4: Sugar | #5: Water | ChemComp-HOH / | |
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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: 2.58 Å3/Da / Density % sol: 52.37 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.1 Details: SITTING DROP VAPOR DIFFUSION METHOD RESERVOIR CONTAINED 1ML OF 0.2 M NA- ACETATE TRIHYDRATE, 30% W/V PEG 8K AND 0.1M MES, PH 6.1. DROP WAS COMPOSED OF 2 MICRO L OF RESERVOIR SOLUTION AND 2 ...Details: SITTING DROP VAPOR DIFFUSION METHOD RESERVOIR CONTAINED 1ML OF 0.2 M NA- ACETATE TRIHYDRATE, 30% W/V PEG 8K AND 0.1M MES, PH 6.1. DROP WAS COMPOSED OF 2 MICRO L OF RESERVOIR SOLUTION AND 2 MICRO L OF THE COMPLEX (10 MG/ML) IN 20MM NA-ACETATE AND 1MM EDTA, PH 5.0. | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 5 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 289 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 15, 1997 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→99 Å / Num. obs: 42072 / % possible obs: 97 % / Observed criterion σ(I): 1 / Redundancy: 3.16 % / Rsym value: 0.11 |
Reflection | *PLUS Num. measured all: 132945 / Rmerge(I) obs: 0.11 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1CJL Resolution: 2→10 Å / Cross valid method: THROUGHOUT / σ(F): 1
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Refinement step | Cycle: LAST / Resolution: 2→10 Å
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Refine LS restraints |
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Software | *PLUS Name: MAIN / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 32.9 Å2 |