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- PDB-4ah2: HLA-DR1 with covalently linked CLIP106-120 in canonical orientation -

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Basic information

Entry
Database: PDB / ID: 4ah2
TitleHLA-DR1 with covalently linked CLIP106-120 in canonical orientation
Components
  • HLA CLASS II HISTOCOMPATIBILITY ANTIGEN GAMMA CHAIN, HLA CLASS II HISTOCOMPATIBILITY ANTIGEN\,DRB1-1 BETA CHAIN
  • HLA CLASS II HISTOCOMPATIBILITY ANTIGEN, DR ALPHA CHAIN
KeywordsIMMUNE SYSTEM / MHC II / 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 / macrophage migration inhibitory factor binding / negative regulation of T cell differentiation / 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 / macrophage migration inhibitory factor binding / negative regulation of T cell differentiation / positive regulation of macrophage migration inhibitory factor signaling pathway / protein trimerization / macrophage migration inhibitory factor receptor complex / regulation of interleukin-4 production / positive regulation of cytokine-mediated signaling pathway / regulation of interleukin-10 production / myeloid dendritic cell antigen processing and presentation / antigen processing and presentation of endogenous peptide antigen via MHC class II / autolysosome membrane / regulation of T-helper cell differentiation / positive regulation of prostaglandin biosynthetic process / T cell activation involved in immune response / T cell selection / positive regulation of type 2 immune response / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / MHC class II receptor activity / host-mediated suppression of symbiont invasion / positive regulation of CD4-positive, alpha-beta T cell activation / negative thymic T cell selection / MHC class II protein binding / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / negative regulation of mature B cell apoptotic process / positive regulation of T cell mediated immune response to tumor cell / positive regulation of kinase activity / positive regulation of memory T cell differentiation / positive regulation of monocyte differentiation / positive thymic T cell selection / inflammatory response to antigenic stimulus / vacuole / CD4 receptor binding / cytokine receptor activity / positive regulation of neutrophil chemotaxis / positive regulation of chemokine (C-X-C motif) ligand 2 production / intermediate filament / prostaglandin biosynthetic process / positive regulation of macrophage cytokine production / T-helper 1 type immune response / positive regulation of T cell differentiation / transport vesicle membrane / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / regulation of macrophage activation / antigen processing and presentation / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / cytokine binding / nitric-oxide synthase binding / negative regulation of DNA damage response, signal transduction by p53 class mediator / polysaccharide binding / negative regulation of type II interferon production / : / immunoglobulin mediated immune response / humoral immune response / macrophage differentiation / Generation of second messenger molecules / immunological synapse / Co-inhibition by PD-1 / epidermis development / response to type II interferon / positive regulation of insulin secretion involved in cellular response to glucose stimulus / detection of bacterium / T cell receptor binding / positive regulation of chemokine production / negative regulation of T cell proliferation / positive regulation of B cell proliferation / multivesicular body / protein folding chaperone / MHC class II antigen presentation / lysosomal lumen / negative regulation of cell migration / trans-Golgi network membrane / Cell surface interactions at the vascular wall / positive regulation of interleukin-8 production / lumenal side of endoplasmic reticulum membrane / protein tetramerization / peptide antigen assembly with MHC class II protein complex / intracellular protein transport / negative regulation of inflammatory response to antigenic stimulus / MHC class II protein complex / clathrin-coated endocytic vesicle membrane / ER to Golgi transport vesicle membrane / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / positive regulation of T cell activation / peptide antigen binding / structural constituent of cytoskeleton / positive regulation of interleukin-6 production / positive regulation of T cell mediated cytotoxicity / cognition / positive regulation of protein phosphorylation / positive regulation of fibroblast proliferation / Interferon gamma signaling / MHC class II protein complex binding
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 ...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 / Roll / Immunoglobulin-like fold / Immunoglobulins / 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 gamma chain
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.36 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
DepositionFeb 3, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 1, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 10, 2012Group: Database references
Revision 1.2Mar 15, 2017Group: Source and taxonomy
Revision 1.3Dec 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
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)48,4726
Polymers48,1032
Non-polymers3684
Water3,963220
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6890 Å2
ΔGint-33 kcal/mol
Surface area17630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.644, 65.616, 131.331
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 22353.223 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 GAMMA CHAIN, HLA CLASS II HISTOCOMPATIBILITY ANTIGEN\,DRB1-1 BETA CHAIN / HLA-DR ANTIGENS-ASSOCIATED INVARIANT CHAIN / IA ANTIGEN-ASSOCIATED INVARIANT CHAIN\ / II / P33 / ...HLA-DR ANTIGENS-ASSOCIATED INVARIANT CHAIN / IA ANTIGEN-ASSOCIATED INVARIANT CHAIN\ / II / P33 / CD74 / MHC CLASS II ANTIGEN DRB1*1 / DR-1 / DR


Mass: 25749.902 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR DOMAIN, RESIDUES 106-120,30-227
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: P04233, UniProt: P04229
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 220 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsCLIP WAS ATTACHED TO THE N-TERMINUS OF MHC BETA-CHAIN DURING EXPRESSION VIA A (GGGGS)3 LINKER.

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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: 2.7 Å3/Da / Density % sol: 54.44 % / Description: NONE
Crystal growpH: 7 / Details: 0.2 M LICL, 20% (W/V) PEG6000, 0.1 M HEPES, PH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841
DetectorType: MARRESEARCH MX-225 / Detector: CCD / Date: Jan 13, 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: 2.36→32.84 Å / Num. obs: 21133 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 4.8 % / Biso Wilson estimate: 27.9 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 10.7
Reflection shellResolution: 2.36→2.42 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 2.4 / % possible all: 99.9

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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: 2.36→32.833 Å / SU ML: 0.76 / σ(F): 1.99 / Phase error: 22.41 / Stereochemistry target values: ML
Details: RESIDUES A0 TO A3, A181 TO A192, B-16 TO B-1, B105 TO B110, B190 TO B198 ARE MISSING COMPLETELY DUE TO DISORDER, RESIDUES B111, B112, B166 COULD ONLY BE MODELED TO THE CBETA-ATOM DUE TO DISORDER
RfactorNum. reflection% reflection
Rfree0.2402 1057 5 %
Rwork0.1914 --
obs0.1939 21132 99.9 %
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 27.165 Å2 / ksol: 0.343 e/Å3
Displacement parametersBiso mean: 29.8 Å2
Baniso -1Baniso -2Baniso -3
1--6.9457 Å20 Å20 Å2
2---4.6013 Å20 Å2
3---11.547 Å2
Refinement stepCycle: LAST / Resolution: 2.36→32.833 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3057 0 24 220 3301
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083161
X-RAY DIFFRACTIONf_angle_d1.0194285
X-RAY DIFFRACTIONf_dihedral_angle_d15.9991155
X-RAY DIFFRACTIONf_chiral_restr0.071461
X-RAY DIFFRACTIONf_plane_restr0.005555
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.36-2.46740.26211300.2322464X-RAY DIFFRACTION100
2.4674-2.59750.30431290.23842449X-RAY DIFFRACTION100
2.5975-2.76010.29851310.22792492X-RAY DIFFRACTION100
2.7601-2.97310.26271300.21522474X-RAY DIFFRACTION100
2.9731-3.2720.25931310.19732487X-RAY DIFFRACTION100
3.272-3.74490.23341320.18522513X-RAY DIFFRACTION100
3.7449-4.7160.20751340.15152540X-RAY DIFFRACTION100
4.716-32.83590.2081400.18152656X-RAY DIFFRACTION100

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