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- PDB-4aen: HLA-DR1 with covalently linked CLIP106-120 in reversed orientation -

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Basic information

Entry
Database: PDB / ID: 4aen
TitleHLA-DR1 with covalently linked CLIP106-120 in reversed orientation
Components
  • HLA CLASS II HISTOCOMPATIBILITY ANTIGEN GAMMA CHAIN
  • HLA CLASS II HISTOCOMPATIBILITY ANTIGEN, DR ALPHA CHAIN
  • HLA CLASS II HISTOCOMPATIBILITY ANTIGEN, DRB1-1 BETA CHAIN
KeywordsIMMUNE SYSTEM / SELF ANTIGEN / INVARIANT CHAIN / CLIP
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 / regulation of interleukin-4 production / regulation of interleukin-10 production / T cell activation involved in immune response / myeloid dendritic cell antigen processing and presentation / antigen processing and presentation of endogenous peptide antigen via MHC class II / positive regulation of T cell mediated immune response to tumor cell / autolysosome membrane / positive regulation of type 2 immune response / T cell selection / regulation of T-helper cell differentiation / negative thymic T cell selection / positive regulation of prostaglandin biosynthetic process / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / negative regulation of viral entry into host cell / MHC class II receptor activity / MHC class II protein binding / positive regulation of CD4-positive, alpha-beta T cell activation / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / negative regulation of mature B cell apoptotic process / positive regulation of memory T cell differentiation / positive thymic T cell selection / positive regulation of monocyte differentiation / CD4 receptor binding / inflammatory response to antigenic stimulus / positive regulation of kinase activity / positive regulation of chemokine (C-X-C motif) ligand 2 production / positive regulation of neutrophil chemotaxis / vacuole / positive regulation of macrophage cytokine production / prostaglandin biosynthetic process / positive regulation of T cell differentiation / cytokine receptor activity / regulation of macrophage activation / transport vesicle membrane / intermediate filament / polysaccharide binding / T-helper 1 type immune response / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / nitric-oxide synthase binding / cytokine binding / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / response to type II interferon / positive regulation of insulin secretion involved in cellular response to glucose stimulus / antigen processing and presentation / negative regulation of DNA damage response, signal transduction by p53 class mediator / humoral immune response / macrophage differentiation / negative regulation of type II interferon production / chaperone cofactor-dependent protein refolding / Generation of second messenger molecules / immunological synapse / PD-1 signaling / immunoglobulin mediated immune response / epidermis development / T cell receptor binding / detection of bacterium / negative regulation of T cell proliferation / positive regulation of chemokine production / positive regulation of B cell proliferation / protein folding chaperone / negative regulation of inflammatory response to antigenic stimulus / MHC class II antigen presentation / multivesicular body / negative regulation of cell migration / lysosomal lumen / trans-Golgi network membrane / positive regulation of interleukin-8 production / lumenal side of endoplasmic reticulum membrane / Cell surface interactions at the vascular wall / protein tetramerization / intracellular protein transport / clathrin-coated endocytic vesicle membrane / ER to Golgi transport vesicle membrane / structural constituent of cytoskeleton / cognition / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / positive regulation of T cell mediated cytotoxicity / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / endocytic vesicle membrane / positive regulation of interleukin-6 production / positive regulation of peptidyl-tyrosine phosphorylation / Interferon gamma signaling / positive regulation of immune response / positive regulation of fibroblast proliferation / late endosome
Similarity search - Function
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 ...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. / Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / MHC class II, beta chain, N-terminal / Class II histocompatibility antigen, beta domain / Class II histocompatibility antigen, beta domain / MHC class II, alpha chain, N-terminal / Class II histocompatibility antigen, alpha domain / Class II histocompatibility antigen, alpha domain / MHC class II, alpha/beta chain, N-terminal / MHC classes I/II-like antigen recognition protein / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Roll / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
HLA class II histocompatibility antigen, DR alpha chain / HLA class II histocompatibility antigen, DRB1 beta chain / HLA class II histocompatibility antigen, DRB1 beta chain / HLA class II histocompatibility antigen gamma chain
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsSchlundt, A. / Guenther, S. / Sticht, J. / Wieczorek, M. / Roske, Y. / Heinemann, U. / Freund, C.
CitationJournal: J.Mol.Biol. / Year: 2012
Title: Peptide Linkage to the Alpha-Subunit of Mhcii Creates a Stably Inverted Antigen Presentation Complex.
Authors: Schlundt, A. / Gunther, S. / Sticht, J. / Wieczorek, M. / Roske, Y. / Heinemann, U. / Freund, C.
History
DepositionJan 11, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 1, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 10, 2012Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HLA CLASS II HISTOCOMPATIBILITY ANTIGEN, DR ALPHA CHAIN
B: HLA CLASS II HISTOCOMPATIBILITY ANTIGEN, DRB1-1 BETA CHAIN
C: HLA CLASS II HISTOCOMPATIBILITY ANTIGEN GAMMA CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3055
Polymers48,1213
Non-polymers1842
Water4,486249
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7360 Å2
ΔGint-43.9 kcal/mol
Surface area17860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.196, 145.111, 108.777
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222
Components on special symmetry positions
IDModelComponents
11B-2050-

HOH

21C-2002-

HOH

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Components

#1: Protein HLA CLASS II HISTOCOMPATIBILITY ANTIGEN, DR ALPHA CHAIN / MHC CLASS II ANTIGEN DRA


Mass: 23167.883 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR DOMAIN, RESIDUES 26-217
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P01903
#2: Protein HLA CLASS II HISTOCOMPATIBILITY ANTIGEN, DRB1-1 BETA CHAIN / MHC CLASS II ANTIGEN DRB1*1 / DR-1 / DR1


Mass: 23087.791 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR DOMAIN, RESIDUES 30-227
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P04229, UniProt: P01911*PLUS
#3: Protein/peptide HLA CLASS II HISTOCOMPATIBILITY ANTIGEN GAMMA CHAIN / HLA-DR ANTIGENS-ASSOCIATED INVARIANT CHAIN / IA ANTIGEN-ASSOCIATED INVARIANT CHAIN / II / P33 / CD74


Mass: 1865.459 Da / Num. of mol.: 1 / Fragment: RESIDUES 106-120
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P04233
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 249 / Source method: isolated from a natural source / Formula: H2O

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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: 2.75 Å3/Da / Density % sol: 55.3 % / Description: NONE
Crystal growDetails: 2 M (NH4)2SO4, 0.1 M TRIS, PH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 22, 2011 / Details: MIRRORS
RadiationMonochromator: SI-111 CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2.2→34.42 Å / Num. obs: 27008 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 4.5 % / Biso Wilson estimate: 30.6 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 15.8
Reflection shellResolution: 2.2→2.26 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 2.9 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3PDO

3pdo


Resolution: 2.2→34.414 Å / SU ML: 0.56 / σ(F): 1.99 / Phase error: 20.58 / Stereochemistry target values: ML
Details: OWING TO DISORDER FOLLOWING RESIDUES ARE MISSING COMPLETELY A-14-A2, A181-A192, B0-B2, B106-B112, B191-B198, C105. OWING TO DISORDER FOLLOWING RESIDUES COULD ONLY BE MODELED TO THE CBETA- ...Details: OWING TO DISORDER FOLLOWING RESIDUES ARE MISSING COMPLETELY A-14-A2, A181-A192, B0-B2, B106-B112, B191-B198, C105. OWING TO DISORDER FOLLOWING RESIDUES COULD ONLY BE MODELED TO THE CBETA-ATOM A3, B105, B166, C120
RfactorNum. reflection% reflection
Rfree0.2207 1351 5 %
Rwork0.1834 --
obs0.1853 27006 99.93 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 32.502 Å2 / ksol: 0.369 e/Å3
Displacement parametersBiso mean: 25.6 Å2
Baniso -1Baniso -2Baniso -3
1-12.8522 Å20 Å20 Å2
2--5.204 Å20 Å2
3---5.4265 Å2
Refinement stepCycle: LAST / Resolution: 2.2→34.414 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3048 0 12 249 3309
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073143
X-RAY DIFFRACTIONf_angle_d1.0534267
X-RAY DIFFRACTIONf_dihedral_angle_d14.1571147
X-RAY DIFFRACTIONf_chiral_restr0.07461
X-RAY DIFFRACTIONf_plane_restr0.005554
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.27860.29441340.22122549X-RAY DIFFRACTION100
2.2786-2.36980.30481310.2252491X-RAY DIFFRACTION100
2.3698-2.47770.25771350.21712548X-RAY DIFFRACTION100
2.4777-2.60820.24771330.20342537X-RAY DIFFRACTION100
2.6082-2.77160.24281340.19492550X-RAY DIFFRACTION100
2.7716-2.98550.20611340.18822531X-RAY DIFFRACTION100
2.9855-3.28570.23461350.18272581X-RAY DIFFRACTION100
3.2857-3.76070.18951350.1672558X-RAY DIFFRACTION100
3.7607-4.73610.19961370.15162609X-RAY DIFFRACTION100
4.7361-34.41850.20281430.18932701X-RAY DIFFRACTION100

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