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- PDB-1l3h: NMR structure of P41icf, a potent inhibitor of human cathepsin L -

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Basic information

Entry
Database: PDB / ID: 1l3h
TitleNMR structure of P41icf, a potent inhibitor of human cathepsin L
ComponentsMHC CLASS II-ASSOCIATED P41 INVARIANT CHAIN FRAGMENT (P41icf)
KeywordsIMMUNE SYSTEM / ALPHA HELIX / BETA SHEET / DISULFIDE BONDS
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 / protein trimerization ...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 / protein trimerization / macrophage migration inhibitory factor receptor complex / positive regulation of cytokine-mediated signaling pathway / T cell activation involved in immune response / positive regulation of type 2 immune response / positive regulation of prostaglandin biosynthetic process / T cell selection / negative thymic T cell selection / negative regulation of viral entry into host cell / MHC class II protein binding / negative regulation of mature B cell apoptotic process / positive thymic T cell selection / positive regulation of kinase activity / CD4 receptor binding / positive regulation of monocyte differentiation / vacuole / positive regulation of chemokine (C-X-C motif) ligand 2 production / positive regulation of neutrophil chemotaxis / cytokine receptor activity / prostaglandin biosynthetic process / positive regulation of macrophage cytokine production / positive regulation of T cell differentiation / regulation of macrophage activation / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / transport vesicle membrane / nitric-oxide synthase binding / response to type II interferon / antigen processing and presentation / cytokine binding / negative regulation of DNA damage response, signal transduction by p53 class mediator / chaperone cofactor-dependent protein refolding / immunoglobulin mediated immune response / positive regulation of chemokine production / positive regulation of B cell proliferation / protein folding chaperone / MHC class II antigen presentation / multivesicular body / lysosomal lumen / trans-Golgi network membrane / negative regulation of cell migration / positive regulation of interleukin-8 production / Cell surface interactions at the vascular wall / lumenal side of endoplasmic reticulum membrane / intracellular protein transport / clathrin-coated endocytic vesicle membrane / ER to Golgi transport vesicle membrane / MHC class II protein complex / positive regulation of interleukin-6 production / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of peptidyl-tyrosine phosphorylation / positive regulation of fibroblast proliferation / endocytic vesicle membrane / late endosome / MHC class II protein complex binding / amyloid-beta binding / protein-containing complex assembly / positive regulation of canonical NF-kappaB signal transduction / positive regulation of MAPK cascade / positive regulation of ERK1 and ERK2 cascade / positive regulation of viral entry into host cell / lysosome / protein stabilization / positive regulation of protein phosphorylation / Golgi membrane / external side of plasma membrane / lysosomal membrane / positive regulation of gene expression / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / cell surface / protein-containing complex / extracellular exosome / identical protein binding / membrane / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Thyroglobulin type-1 / Invariant Chain; Chain I / MHC class II-associated invariant chain, trimerisation / MHC class II-associated invariant chain/CLIP, MHC II-interacting / MHC class II-associated invariant chain / MHC class II-associated invariant chain, trimerisation domain superfamily / HLA class II histocompatibility antigen, gamma subunit / Class II MHC-associated invariant chain trimerisation domain / CLIP, MHC2 interacting / : ...Thyroglobulin type-1 / Invariant Chain; Chain I / MHC class II-associated invariant chain, trimerisation / MHC class II-associated invariant chain/CLIP, MHC II-interacting / MHC class II-associated invariant chain / MHC class II-associated invariant chain, trimerisation domain superfamily / HLA class II histocompatibility antigen, gamma subunit / Class II MHC-associated invariant chain trimerisation domain / CLIP, MHC2 interacting / : / Thyroglobulin type-1 repeat signature. / Thyroglobulin type-1 / Thyroglobulin type-1 superfamily / Thyroglobulin type-1 repeat / Thyroglobulin type-1 domain profile. / Thyroglobulin type I repeats. / Few Secondary Structures / Irregular
Similarity search - Domain/homology
HLA class II histocompatibility antigen gamma chain
Similarity search - Component
MethodSOLUTION NMR / torsion angle dynamics, simulated annealing with restrained molecular dynamics
AuthorsChiva, C. / Barthe, P. / Codina, A. / Giralt, E.
CitationJournal: J.Am.Chem.Soc. / Year: 2003
Title: Synthesis and NMR structure of P41ICF, a potent inhibitor of human cathepsin L
Authors: Chiva, C. / Barthe, P. / Codina, A. / Gairi, M. / Molina, F. / Granier, C. / Pugniere, M. / Inui, T. / Nishio, H. / Nishiuchi, Y. / Kimura, T. / Sakakibara, S. / Albericio, F. / Giralt, E.
History
DepositionFeb 27, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.4Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MHC CLASS II-ASSOCIATED P41 INVARIANT CHAIN FRAGMENT (P41icf)


Theoretical massNumber of molelcules
Total (without water)7,2611
Polymers7,2611
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)30 / 600structures with the lowest energy,target function
RepresentativeModel #1fewest violations

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Components

#1: Protein MHC CLASS II-ASSOCIATED P41 INVARIANT CHAIN FRAGMENT (P41icf) / HLA class II histocompatibility antigen / gamma chain


Mass: 7261.075 Da / Num. of mol.: 1 / Fragment: THYROGLOBULIN-LIKE DOMAIN / Source method: obtained synthetically / Details: This sequence occurs naturally in humans. / References: UniProt: P04233
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111DQF-COSY
1212D TOCSY
1312D NOESY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques.

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Sample preparation

DetailsContents: 1mM P41icf; 20mM phosphate buffer, 0.01mM NaN3 / Solvent system: 85% H20, 15% D2O
Sample conditionspH: 5.7 / Pressure: ambient / Temperature: 288 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX8001
Bruker DRXBrukerDRX6002

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipeDelaglioprocessing
NMRViewJohnsondata analysis
DYANA1.5Guntertstructure solution
Amber5Caserefinement
RefinementMethod: torsion angle dynamics, simulated annealing with restrained molecular dynamics
Software ordinal: 1
Details: the structures are based on a total of 981 restraints, 925 are NOE-derived distance constraints, 56 dihedral angle restraints
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the lowest energy,target function
Conformers calculated total number: 600 / Conformers submitted total number: 30

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