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- PDB-1iie: HLA-DR ANTIGENS ASSOCIATED INVARIANT CHAIN -

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Basic information

Entry
Database: PDB / ID: 1iie
TitleHLA-DR ANTIGENS ASSOCIATED INVARIANT CHAIN
ComponentsPROTEIN (HLA-DR ANTIGENS ASSOCIATED INVARIANT CHAIN)
KeywordsMAJOR HISTOCOMPATIBILITY COMPLEX / ANTIGEN PROCESSING / OLIGOMERIZATION / CHAPERONIN
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 / T cell selection / negative thymic T cell selection / positive regulation of prostaglandin biosynthetic process / 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 monocyte differentiation / CD4 receptor binding / vacuole / positive regulation of kinase activity / positive regulation of chemokine (C-X-C motif) ligand 2 production / positive regulation of neutrophil chemotaxis / cytokine receptor activity / positive regulation of macrophage cytokine production / prostaglandin biosynthetic process / positive regulation of T cell differentiation / regulation of macrophage activation / transport vesicle membrane / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / cytokine binding / response to type II interferon / nitric-oxide synthase binding / chaperone cofactor-dependent protein refolding / negative regulation of DNA damage response, signal transduction by p53 class mediator / immunoglobulin mediated immune response / antigen processing and presentation / protein folding chaperone / positive regulation of B cell proliferation / positive regulation of chemokine production / MHC class II antigen presentation / multivesicular body / lysosomal lumen / negative regulation of cell migration / trans-Golgi network membrane / positive regulation of interleukin-8 production / lumenal side of endoplasmic reticulum membrane / Cell surface interactions at the vascular wall / 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 / 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 / protein-containing complex assembly / positive regulation of canonical NF-kappaB signal transduction / positive regulation of MAPK cascade / positive regulation of viral entry into host cell / lysosome / positive regulation of ERK1 and ERK2 cascade / protein stabilization / positive regulation of protein phosphorylation / lysosomal membrane / external side of plasma membrane / Golgi membrane / positive regulation of gene expression / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / cell surface / protein-containing complex / extracellular exosome / membrane / identical protein binding / nucleus / plasma membrane / cytoplasm
Similarity search - Function
HLA-dr Antigens Associated Invariant Chain; Chain A / MHC class II-associated invariant chain, trimerisation domain / 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. ...HLA-dr Antigens Associated Invariant Chain; Chain A / MHC class II-associated invariant chain, trimerisation domain / 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. / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
HLA class II histocompatibility antigen gamma chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsJasanoff, A. / Wagner, G. / Wiley, D.C.
Citation
Journal: EMBO J. / Year: 1998
Title: Structure of a trimeric domain of the MHC class II-associated chaperonin and targeting protein Ii.
Authors: Jasanoff, A. / Wagner, G. / Wiley, D.C.
#1: Journal: J.Biomol.NMR / Year: 1998
Title: An Asymmetric Deuterium Labeling Strategy to Identify Interprotomer and Intraprotomer Noes in Oligomeric Proteins
Authors: Jasanoff, A.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1995
Title: Invariant Chain Made in Escherichia coli Has an Exposed N-Terminal Segment that Blocks Antigen Binding to HLA-DR1 and a Trimeric C-Terminal Segment that Binds Empty HLA-DR1
Authors: Park, S.-J. / Sadegh-Nasseri, S. / Wiley, D.C.
History
DepositionFeb 2, 1999Processing site: RCSB
Revision 1.0Feb 16, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 6, 2019Group: Data collection / Derived calculations
Category: pdbx_nmr_spectrometer / pdbx_struct_assembly ...pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Revision 1.4Oct 27, 2021Group: Data collection / Database references
Category: database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.authors / _pdbx_nmr_software.classification / _pdbx_nmr_spectrometer.manufacturer
Revision 1.5Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (HLA-DR ANTIGENS ASSOCIATED INVARIANT CHAIN)
B: PROTEIN (HLA-DR ANTIGENS ASSOCIATED INVARIANT CHAIN)
C: PROTEIN (HLA-DR ANTIGENS ASSOCIATED INVARIANT CHAIN)


Theoretical massNumber of molelcules
Total (without water)26,9533
Polymers26,9533
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area7930 Å2
ΔGint-65 kcal/mol
Surface area13240 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 80LEAST RESTRAINT VIOLATION, GOOD GEOMETRY
RepresentativeModel #14

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Components

#1: Protein PROTEIN (HLA-DR ANTIGENS ASSOCIATED INVARIANT CHAIN) / HLA CLASS II HISTOCOMPATIBILITY ANTIGEN / GAMMA CHAIN


Mass: 8984.300 Da / Num. of mol.: 3
Fragment: ECTOPLASMIC TRIMERIZATION DOMAIN (RESIDUES 118-192)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Description: TRYPSIN-GENERATED FRAGMENT OF RECOMBINANT DOMAIN
Cellular location: TYPE II TRANSMEMBRANE PROTEIN / Gene: CD74 OR DHLAG / Plasmid: PQE9 / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli (E. coli) / Strain (production host): XA90 / Variant (production host): II H94-216 (I94) / References: UniProt: P04233

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121TOCSY
131HSQC
141TRIPLE RESONANCE
NMR detailsText: THE STRUCTURE WAS DETERMINED USING DOUBLE- AND TRIPLE-RESONANCE EXPERIMENTS ON SAMPLES OF II 118-192 LABELED WITH COMBINATIONS OF 2H, 13C, AND 15N

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Sample preparation

Sample conditionspH: 6.7 / Pressure: 1 atm / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX5001
Varian UNITYPLUSVarianUNITYPLUS5002
Varian INOVAVarianINOVA7503

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.1BRUNGERrefinement
X-PLOR3.1BRUNGERstructure calculation
RefinementMethod: simulated annealing / Software ordinal: 1
Details: THE TRIMER STRUCTURE WAS CALCULATED USING A SIMULATED ANNEALING PROTOCOL BASED ON THE DIMER REFINEMENT METHODS OF NILGES, PROTEINS 17 : 297-309 (1993)
NMR ensembleConformer selection criteria: LEAST RESTRAINT VIOLATION, GOOD GEOMETRY
Conformers calculated total number: 80 / Conformers submitted total number: 20

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