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- PDB-6biy: HLA-DRB1 in complex with Histone 2B peptide -

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Basic information

Entry
Database: PDB / ID: 6biy
TitleHLA-DRB1 in complex with Histone 2B peptide
Components
  • (HLA class II ...) x 2
  • Histone2B_69-81
KeywordsIMMUNE SYSTEM / HLA / MHC / citrulline / Rheumatoid Arthritis
Function / homology
Function and homology information


sperm DNA condensation / regulation of interleukin-4 production / regulation of interleukin-10 production / 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 / regulation of T-helper cell differentiation / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / MHC class II receptor activity ...sperm DNA condensation / regulation of interleukin-4 production / regulation of interleukin-10 production / 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 / regulation of T-helper cell differentiation / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / MHC class II receptor activity / mononuclear cell migration / positive regulation of CD4-positive, alpha-beta T cell activation / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / nucleosome disassembly / positive regulation of memory T cell differentiation / positive regulation of monocyte differentiation / CD4 receptor binding / female germ cell nucleus / inflammatory response to antigenic stimulus / positive regulation of kinase activity / transport vesicle membrane / intermediate filament / polysaccharide binding / T-helper 1 type immune response / plasminogen activation / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / positive regulation of insulin secretion involved in cellular response to glucose stimulus / humoral immune response / macrophage differentiation / negative regulation of type II interferon production / Generation of second messenger molecules / immunological synapse / PD-1 signaling / chromosome organization / epidermis development / Replacement of protamines by nucleosomes in the male pronucleus / T cell receptor binding / Packaging Of Telomere Ends / detection of bacterium / negative regulation of T cell proliferation / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Deposition of new CENPA-containing nucleosomes at the centromere / negative regulation of inflammatory response to antigenic stimulus / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Inhibition of DNA recombination at telomere / Meiotic synapsis / MHC class II antigen presentation / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / DNA methylation / Condensation of Prophase Chromosomes / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / trans-Golgi network membrane / PRC2 methylates histones and DNA / Defective pyroptosis / HDACs deacetylate histones / lumenal side of endoplasmic reticulum membrane / RNA Polymerase I Promoter Escape / Nonhomologous End-Joining (NHEJ) / protein tetramerization / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / clathrin-coated endocytic vesicle membrane / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / ER to Golgi transport vesicle membrane / B-WICH complex positively regulates rRNA expression / G2/M DNA damage checkpoint / DNA Damage/Telomere Stress Induced Senescence / structural constituent of cytoskeleton / Meiotic recombination / cognition / Pre-NOTCH Transcription and Translation / peptide antigen assembly with MHC class II protein complex / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / MHC class II protein complex / Transcriptional regulation of granulopoiesis / positive regulation of T cell mediated cytotoxicity / structural constituent of chromatin / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / endocytic vesicle membrane / Interferon gamma signaling / positive regulation of immune response / nucleosome / nucleosome assembly / Downstream TCR signaling / positive regulation of T cell activation / E3 ubiquitin ligases ubiquitinate target proteins / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / MHC class II protein complex binding / late endosome membrane
Similarity search - Function
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 / Histone H2B signature. ...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 / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / MHC classes I/II-like antigen recognition protein / Histone-fold / 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 DR-beta (HLA-DR B) / Histone H2B type 1-A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05004900063 Å
AuthorsTing, Y.T. / Scally, S.W. / Rossjohn, J.
CitationJournal: J. Biol. Chem. / Year: 2018
Title: The interplay between citrullination and HLA-DRB1 polymorphism in shaping peptide binding hierarchies in rheumatoid arthritis.
Authors: Ting, Y.T. / Petersen, J. / Ramarathinam, S.H. / Scally, S.W. / Loh, K.L. / Thomas, R. / Suri, A. / Baker, D.G. / Purcell, A.W. / Reid, H.H. / Rossjohn, J.
History
DepositionNov 3, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 17, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Database references / Structure summary / Category: citation / citation_author / struct
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _struct.title
Revision 1.2Mar 14, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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 DR-beta (HLA-DR B)
C: Histone2B_69-81
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,4486
Polymers46,7233
Non-polymers7253
Water4,720262
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7780 Å2
ΔGint-24 kcal/mol
Surface area18240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.826, 182.478, 76.807
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

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HLA class II ... , 2 types, 2 molecules AB

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


Mass: 21919.594 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DRA, HLA-DRA1 / Cell line (production host): HEK293S GnTI- / Production host: Homo sapiens (human) / References: UniProt: P01903
#2: Protein HLA class II DR-beta (HLA-DR B)


Mass: 23294.709 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293S GnTI- / Production host: Homo sapiens (human) / References: UniProt: Q29890, UniProt: P01911*PLUS

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Protein/peptide / Sugars , 2 types, 3 molecules C

#3: Protein/peptide Histone2B_69-81


Mass: 1508.677 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q96A08*PLUS
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 2 types, 263 molecules

#5: Chemical ChemComp-B3P / 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL


Mass: 282.334 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H26N2O6 / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 262 / 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: 2.67 Å3/Da / Density % sol: 53.93 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.3
Details: 20-28% PEG 3350, 0.2M Potassium Nitrate, 0.1M Bis-Tris-Propane pH 7.3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 23, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.05→39.22 Å / Num. obs: 30243 / % possible obs: 99.6 % / Redundancy: 4.4 % / Biso Wilson estimate: 24.9180573111 Å2 / CC1/2: 0.989 / Rmerge(I) obs: 0.05276 / Net I/σ(I): 9.9
Reflection shellResolution: 2.05→2.12 Å / CC1/2: 0.739

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MDI

4mdi


Resolution: 2.05004900063→39.2227033472 Å / SU ML: 0.247940179927 / Cross valid method: FREE R-VALUE / σ(F): 1.33351604688 / Phase error: 23.5089546655
RfactorNum. reflection% reflection
Rfree0.231849295707 1536 5.08440913605 %
Rwork0.182544376258 --
obs0.185114762639 30210 99.528876882 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 28.6355946896 Å2
Refinement stepCycle: LAST / Resolution: 2.05004900063→39.2227033472 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3116 0 46 262 3424
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007040038194333265
X-RAY DIFFRACTIONf_angle_d0.8655697152414451
X-RAY DIFFRACTIONf_chiral_restr0.0551829240824479
X-RAY DIFFRACTIONf_plane_restr0.0052578809876578
X-RAY DIFFRACTIONf_dihedral_angle_d6.227649582482277
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.11620.2689995260221190.2413311552352598X-RAY DIFFRACTION99.9264435454
2.1162-2.19180.2668671041621340.2178752188192566X-RAY DIFFRACTION99.8890122087
2.1918-2.27960.2976035037941510.2113111917532567X-RAY DIFFRACTION99.8897464168
2.2796-2.38330.2917810163351430.2050188885852595X-RAY DIFFRACTION99.7813411079
2.3833-2.5090.2674024769581260.201797823342591X-RAY DIFFRACTION99.9632082414
2.509-2.66610.2760030258371400.2009200126832597X-RAY DIFFRACTION99.9269806499
2.6661-2.87190.2875002575321410.2006334122972607X-RAY DIFFRACTION99.7459165154
2.8719-3.16080.2738373753581350.1942469129712614X-RAY DIFFRACTION99.7098295248
3.1608-3.61790.1892561598111390.1735847496082609X-RAY DIFFRACTION99.3133357427
3.6179-4.55710.1936684549711720.1400295311312606X-RAY DIFFRACTION98.9668685429
4.5571-39.22990.1865317165421360.1682158240512724X-RAY DIFFRACTION97.8446801232

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