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- PDB-1icf: CRYSTAL STRUCTURE OF MHC CLASS II ASSOCIATED P41 II FRAGMENT IN C... -

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Basic information

Entry
Database: PDB / ID: 1icf
TitleCRYSTAL STRUCTURE OF MHC CLASS II ASSOCIATED P41 II FRAGMENT IN COMPLEX WITH CATHEPSIN L
Components
  • PROTEIN (CATHEPSIN L: HEAVY CHAIN)
  • PROTEIN (CATHEPSIN L: LIGHT CHAIN)
  • PROTEIN (INVARIANT CHAIN)
KeywordsHYDROLASE / 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 / positive regulation of prostaglandin biosynthetic process / T cell selection / elastin catabolic process / positive regulation of type 2 immune response / antigen processing and presentation of peptide antigen / negative thymic T cell selection / host-mediated suppression of symbiont invasion / MHC class II protein binding / RUNX1 regulates transcription of genes involved in differentiation of keratinocytes / negative regulation of mature B cell apoptotic process / endolysosome lumen / positive regulation of kinase activity / positive thymic T cell selection / CD4 receptor binding / positive regulation of monocyte differentiation / vacuole / cellular response to thyroid hormone stimulus / positive regulation of chemokine (C-X-C motif) ligand 2 production / cytokine receptor activity / zymogen activation / Trafficking and processing of endosomal TLR / positive regulation of neutrophil chemotaxis / proteoglycan binding / prostaglandin biosynthetic process / positive regulation of macrophage cytokine production / positive regulation of T cell differentiation / Assembly of collagen fibrils and other multimeric structures / nitric-oxide synthase binding / regulation of macrophage activation / transport vesicle membrane / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / antigen processing and presentation / cytokine binding / cysteine-type endopeptidase activator activity involved in apoptotic process / negative regulation of DNA damage response, signal transduction by p53 class mediator / Collagen degradation / protein autoprocessing / fibronectin binding / immunoglobulin mediated immune response / collagen catabolic process / : / response to type II interferon / serpin family protein binding / positive regulation of chemokine production / receptor-mediated endocytosis of virus by host cell / collagen binding / Attachment and Entry / positive regulation of B cell proliferation / Degradation of the extracellular matrix / MHC class II antigen presentation / endocytic vesicle lumen / protein folding chaperone / multivesicular body / cysteine-type peptidase activity / lysosomal lumen / proteolysis involved in protein catabolic process / negative regulation of cell migration / trans-Golgi network membrane / positive regulation of interleukin-8 production / Cell surface interactions at the vascular wall / Endosomal/Vacuolar pathway / lumenal side of endoplasmic reticulum membrane / intracellular protein transport / positive regulation of apoptotic signaling pathway / clathrin-coated endocytic vesicle membrane / MHC class II protein complex / ER to Golgi transport vesicle membrane / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of interleukin-6 production / positive regulation of fibroblast proliferation / MHC class II protein complex binding / endocytic vesicle membrane / late endosome / amyloid-beta binding / protein-containing complex assembly / collagen-containing extracellular matrix / positive regulation of canonical NF-kappaB signal transduction / histone binding / adaptive immune response / positive regulation of MAPK cascade / positive regulation of ERK1 and ERK2 cascade / Attachment and Entry
Similarity search - Function
Thyroglobulin type-1 / Invariant Chain; Chain I / Cysteine proteinases. Chain C / 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 / Cysteine proteinases. Chain C / 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. / Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Papain-like cysteine endopeptidase / Cysteine peptidase, asparagine active site / Eukaryotic thiol (cysteine) proteases asparagine active site. / Cysteine peptidase, histidine active site / Eukaryotic thiol (cysteine) proteases histidine active site. / : / Peptidase C1A, papain C-terminal / Papain family cysteine protease / Papain family cysteine protease / Cysteine peptidase, cysteine active site / Eukaryotic thiol (cysteine) proteases cysteine active site. / Cysteine proteinases / Cathepsin B; Chain A / Papain-like cysteine peptidase superfamily / Few Secondary Structures / Irregular / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Alpha-Beta Complex / Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
HLA class II histocompatibility antigen gamma chain / Procathepsin L
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsGuncar, G. / Pungercic, G. / Klemencic, I. / Turk, V. / Turk, D.
CitationJournal: 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
DepositionJan 7, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Jan 12, 2000Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Aug 9, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (CATHEPSIN L: HEAVY CHAIN)
B: PROTEIN (CATHEPSIN L: LIGHT CHAIN)
C: PROTEIN (CATHEPSIN L: HEAVY CHAIN)
D: PROTEIN (CATHEPSIN L: LIGHT CHAIN)
I: PROTEIN (INVARIANT CHAIN)
J: PROTEIN (INVARIANT CHAIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,7218
Polymers62,2796
Non-polymers4422
Water12,034668
1
A: PROTEIN (CATHEPSIN L: HEAVY CHAIN)
B: PROTEIN (CATHEPSIN L: LIGHT CHAIN)
I: PROTEIN (INVARIANT CHAIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3614
Polymers31,1403
Non-polymers2211
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6930 Å2
ΔGint-40 kcal/mol
Surface area12970 Å2
MethodPISA, PQS
2
C: PROTEIN (CATHEPSIN L: HEAVY CHAIN)
D: PROTEIN (CATHEPSIN L: LIGHT CHAIN)
J: PROTEIN (INVARIANT CHAIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3614
Polymers31,1403
Non-polymers2211
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6970 Å2
ΔGint-39 kcal/mol
Surface area12850 Å2
MethodPISA, PQS
3
A: PROTEIN (CATHEPSIN L: HEAVY CHAIN)
B: PROTEIN (CATHEPSIN L: LIGHT CHAIN)
I: PROTEIN (INVARIANT CHAIN)
hetero molecules

C: PROTEIN (CATHEPSIN L: HEAVY CHAIN)
D: PROTEIN (CATHEPSIN L: LIGHT CHAIN)
J: PROTEIN (INVARIANT CHAIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,7218
Polymers62,2796
Non-polymers4422
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y+1/2,-z1
Buried area14760 Å2
ΔGint-76 kcal/mol
Surface area24970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.592, 80.594, 64.245
Angle α, β, γ (deg.)90.00, 96.77, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.967984, -0.116869, 0.222146), (-0.108483, -0.992859, -0.049626), (0.226359, 0.023938, -0.97375)
Vector: -27.3, -12.94, 22.04)

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Components

#1: Protein PROTEIN (CATHEPSIN L: HEAVY CHAIN)


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 PROTEIN (CATHEPSIN L: LIGHT CHAIN)


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 PROTEIN (INVARIANT CHAIN) / II FRAGMENT / CD74 FRAGMENT


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 ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 668 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.58 Å3/Da / Density % sol: 52.37 %
Crystal growpH: 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
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
20.2 MNa acetate1reservoir
330 %(v/v)PEG80001reservoir
40.1 MMES1reservoir
520 mMNa acetate1drop
61 mMEDTA1drop

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Data collection

DiffractionMean temperature: 289 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 15, 1997 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 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

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
MAINrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1CJL

1cjl


Resolution: 2→10 Å / Cross valid method: THROUGHOUT / σ(F): 1
RfactorNum. reflection% reflection
Rfree0.213 -8 %
Rwork0.182 --
obs-41514 97 %
Refinement stepCycle: LAST / Resolution: 2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4364 0 28 668 5060
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.011
X-RAY DIFFRACTIONo_bond_d_na
X-RAY DIFFRACTIONo_bond_d_prot
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_d_na
X-RAY DIFFRACTIONo_angle_d_prot
X-RAY DIFFRACTIONo_angle_deg1.38
X-RAY DIFFRACTIONo_angle_deg_na
X-RAY DIFFRACTIONo_angle_deg_prot
X-RAY DIFFRACTIONo_dihedral_angle_d
X-RAY DIFFRACTIONo_dihedral_angle_d_na
X-RAY DIFFRACTIONo_dihedral_angle_d_prot
X-RAY DIFFRACTIONo_improper_angle_d
X-RAY DIFFRACTIONo_improper_angle_d_na
X-RAY DIFFRACTIONo_improper_angle_d_prot
X-RAY DIFFRACTIONo_mcbond_it
X-RAY DIFFRACTIONo_mcangle_it
X-RAY DIFFRACTIONo_scbond_it
X-RAY DIFFRACTIONo_scangle_it
Software
*PLUS
Name: MAIN / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 32.9 Å2

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