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- PDB-7yx9: MHC-II dynamics are maintained in HLA-DR allotypes to ensure cata... -

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Basic information

Entry
Database: PDB / ID: 7yx9
TitleMHC-II dynamics are maintained in HLA-DR allotypes to ensure catalyzed peptide exchange
Components
  • CLIP 103-107
  • HLA class II histocompatibility antigen, DR alpha chain
  • MHC class II antigen
KeywordsIMMUNE SYSTEM / HLA-DR / CLIP peptide / MHCII
Function / homology
Function and homology information


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 CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / MHC class II receptor activity / positive regulation of CD4-positive, alpha-beta T cell activation / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / positive regulation of memory T cell differentiation / polysaccharide binding ...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 CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / MHC class II receptor activity / positive regulation of CD4-positive, alpha-beta T cell activation / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / positive regulation of memory T cell differentiation / polysaccharide binding / transport vesicle membrane / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / Generation of second messenger molecules / immunological synapse / PD-1 signaling / T cell receptor binding / MHC class II antigen presentation / trans-Golgi network membrane / lumenal side of endoplasmic reticulum membrane / clathrin-coated endocytic vesicle membrane / ER to Golgi transport vesicle membrane / 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 / positive regulation of immune response / Interferon gamma signaling / endocytic vesicle membrane / positive regulation of T cell activation / Downstream TCR signaling / MHC class II protein complex binding / late endosome membrane / early endosome membrane / adaptive immune response / lysosome / endosome membrane / immune response / Golgi membrane / lysosomal membrane / cell surface / extracellular exosome / plasma membrane
Similarity search - Function
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 ...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 / Immunoglobulin-like fold
Similarity search - Domain/homology
MHC class II antigen / HLA class II histocompatibility antigen, DR alpha chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.76 Å
AuthorsRoske, Y. / Abualrous, E.T.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat.Chem.Biol. / Year: 2023
Title: MHC-II dynamics are maintained in HLA-DR allotypes to ensure catalyzed peptide exchange.
Authors: Abualrous, E.T. / Stolzenberg, S. / Sticht, J. / Wieczorek, M. / Roske, Y. / Gunther, M. / Dahn, S. / Boesen, B.B. / Calvo, M.M. / Biese, C. / Kuppler, F. / Medina-Garcia, A. / Alvaro- ...Authors: Abualrous, E.T. / Stolzenberg, S. / Sticht, J. / Wieczorek, M. / Roske, Y. / Gunther, M. / Dahn, S. / Boesen, B.B. / Calvo, M.M. / Biese, C. / Kuppler, F. / Medina-Garcia, A. / Alvaro-Benito, M. / Hofer, T. / Noe, F. / Freund, C.
History
DepositionFeb 15, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 22, 2023Provider: repository / Type: Initial release
Revision 1.1May 17, 2023Group: Database references / Structure summary / Category: citation / citation_author / struct
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _struct.title
Revision 1.2Oct 11, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Feb 7, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.4Nov 6, 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

Downloads & links

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Assembly

Deposited unit
A: HLA class II histocompatibility antigen, DR alpha chain
B: MHC class II antigen
C: HLA class II histocompatibility antigen, DR alpha chain
D: MHC class II antigen
E: CLIP 103-107
G: CLIP 103-107
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,47417
Polymers96,7916
Non-polymers68311
Water16,340907
1
A: HLA class II histocompatibility antigen, DR alpha chain
B: MHC class II antigen
E: CLIP 103-107
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7689
Polymers48,3953
Non-polymers3726
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8460 Å2
ΔGint-32 kcal/mol
Surface area18530 Å2
MethodPISA
2
C: HLA class II histocompatibility antigen, DR alpha chain
D: MHC class II antigen
G: CLIP 103-107
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7068
Polymers48,3953
Non-polymers3105
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7860 Å2
ΔGint-37 kcal/mol
Surface area18970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.712, 120.803, 68.236
Angle α, β, γ (deg.)90.000, 108.840, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein HLA class II histocompatibility antigen, DR alpha chain / MHC class II antigen DRA


Mass: 22207.057 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DRA, HLA-DRA1 / Plasmid: pFastBacDual-Sf9 / Production host: Baculovirus expression vector pFastBac1-HM / References: UniProt: P01903
#2: Protein MHC class II antigen


Mass: 24512.236 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DRB1 / Plasmid: pFastBacDual-Sf9 / Production host: Baculovirus expression vector pFastBac1-HM / References: UniProt: A0A4E9DJJ3
#3: Protein/peptide CLIP 103-107


Mass: 1676.118 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pFastBacDual-Sf9 / Production host: Baculovirus expression vector pFastBac1-HM
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 907 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.33 Å3/Da / Density % sol: 47.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 25% PEG3350, 0.2M MgCl2, 0.1M Hepes pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 13, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.76→40.51 Å / Num. obs: 328677 / % possible obs: 98.5 % / Redundancy: 3.8 % / Biso Wilson estimate: 26.28 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.099 / Net I/σ(I): 11.39
Reflection shellResolution: 1.76→1.86 Å / Num. unique obs: 22740 / CC1/2: 0.716 / Rrim(I) all: 0.761 / % possible all: 98

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIX1.17_3644refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4X5X

4x5x


Resolution: 1.76→40.51 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 21.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2033 2099 2.43 %
Rwork0.1672 84311 -
obs0.1681 86410 98.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 91.16 Å2 / Biso mean: 22.7616 Å2 / Biso min: 6.9 Å2
Refinement stepCycle: final / Resolution: 1.76→40.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6292 0 44 907 7243
Biso mean--35.43 32.85 -
Num. residues----770
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.76-1.80.31261370.25425517565497
1.8-1.840.27451400.22455622576299
1.84-1.890.27741380.21455553569198
1.89-1.950.29591380.20795543568197
1.95-2.010.25861410.195856525793100
2.01-2.080.22941410.184956725813100
2.08-2.170.23911410.17465651579299
2.17-2.270.22141390.17635576571598
2.27-2.390.22081380.17235554569298
2.39-2.540.23131420.175556955837100
2.54-2.730.22051420.171156935835100
2.73-3.010.21491380.16335550568898
3.01-3.440.16661420.15485676581899
3.44-4.330.15021400.13355650579098
4.34-40.510.15921420.14895707584999

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