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- PDB-7z0q: MHC-II dynamics are maintained in HLA-DR allotypes to ensure cata... -

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Basic information

Entry
Database: PDB / ID: 7z0q
TitleMHC-II dynamics are maintained in HLA-DR allotypes to ensure catalyzed peptide exchange
Components
  • CLIP peptide
  • HLA class II histocompatibility antigen, DR alpha chain
  • HLA-DRB1 protein
KeywordsIMMUNE SYSTEM / HLA-DRB1*0701 / 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 / transport vesicle membrane ...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 / transport vesicle membrane / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / polysaccharide binding / Generation of second messenger molecules / immunological synapse / Co-inhibition by PD-1 / T cell receptor binding / MHC class II antigen presentation / trans-Golgi network membrane / lumenal side of endoplasmic reticulum membrane / peptide antigen assembly with MHC class II protein complex / 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 / positive regulation of T cell mediated cytotoxicity / cognition / Interferon gamma signaling / MHC class II protein complex binding / endocytic vesicle membrane / late endosome membrane / Downstream TCR signaling / 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
HLA-DRB1 protein / HLA class II histocompatibility antigen, DR alpha chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsRoske, Y. / Abualrous, E.T. / Freund, C.
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 23, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 8, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: HLA class II histocompatibility antigen, DR alpha chain
D: HLA-DRB1 protein
G: CLIP peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,58112
Polymers47,0223
Non-polymers5599
Water2,252125
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8500 Å2
ΔGint-19 kcal/mol
Surface area18330 Å2
Unit cell
Length a, b, c (Å)134.094, 134.094, 72.178
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3

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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.: 1
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 HLA-DRB1 protein


Mass: 22967.658 Da / Num. of mol.: 1
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: O19730
#3: Protein/peptide CLIP peptide


Mass: 1847.273 Da / Num. of mol.: 1
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.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / 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: 2.66 Å3/Da / Density % sol: 53.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20% PEG3350, 0.15M Sodiummalonate

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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: Sep 30, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2.1→38.71 Å / Num. obs: 28123 / % possible obs: 98.6 % / Redundancy: 4 % / Biso Wilson estimate: 61.6 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.0763 / Net I/σ(I): 12.06
Reflection shellResolution: 2.1→2.175 Å / Num. unique obs: 2850 / CC1/2: 0.44 / Rrim(I) all: 2.559

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
XSCALEdata scaling
PHASERphasing
BUSTER2.10.3refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4X5X

4x5x


Resolution: 2.1→38.71 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.924 / SU R Cruickshank DPI: 0.205 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.198 / SU Rfree Blow DPI: 0.167 / SU Rfree Cruickshank DPI: 0.172
RfactorNum. reflection% reflectionSelection details
Rfree0.243 1407 5 %RANDOM
Rwork0.215 ---
obs0.216 28123 99.3 %-
Displacement parametersBiso max: 229.64 Å2 / Biso mean: 92.89 Å2 / Biso min: 30 Å2
Baniso -1Baniso -2Baniso -3
1--10.9264 Å20 Å20 Å2
2---10.9264 Å20 Å2
3---21.8528 Å2
Refine analyzeLuzzati coordinate error obs: 0.38 Å
Refinement stepCycle: final / Resolution: 2.1→38.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3014 0 36 125 3175
Biso mean--83.76 75.54 -
Num. residues----368
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1063SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes528HARMONIC5
X-RAY DIFFRACTIONt_it3133HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion383SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3446SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3133HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg4239HARMONIC40.72
X-RAY DIFFRACTIONt_omega_torsion3.63
X-RAY DIFFRACTIONt_other_torsion21.53
LS refinement shellResolution: 2.1→2.18 Å / Rfactor Rfree error: 0 / Total num. of bins used: 14
RfactorNum. reflection% reflection
Rfree0.3573 147 5 %
Rwork0.2714 2791 -
all0.2753 2938 -
obs--98.52 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.77220.7499-0.71472.08961.03869.4482-0.11170.34850.0174-0.38440.61290.0495-1.50191.0182-0.5012-0.1831-0.18870.0274-0.0507-0.1307-0.3265-25.42653.21764.5328
22.3702-0.7452-2.3361.67831.07118.4848-0.17460.1353-0.15840.14910.18-0.05970.99341.3109-0.0054-0.30390.2262-0.0770.0359-0.0693-0.3635-21.629-13.72147.9132
32.75610.0922-3.79820.2668-3.22317.02840.0017-0.38040.03690.44170.14150.2157-0.4840.0574-0.1432-0.09570.1071-0.0296-0.0676-0.0836-0.0161-32.6563-1.513426.9043
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{C|3 - 180}C3 - 180
2X-RAY DIFFRACTION2{D|4 - 191}D4 - 191
3X-RAY DIFFRACTION3{G|6 - 19}G6 - 19

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