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- PDB-6biv: HLA-DRB1 in complex with citrullinated LL37 peptide -

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Basic information

Entry
Database: PDB / ID: 6biv
TitleHLA-DRB1 in complex with citrullinated LL37 peptide
Components
  • HLA class II histocompatibility antigen, DR alpha chain
  • HLA class II histocompatibility antigen, DRB1-4 beta chain
  • LL37_Cit91
KeywordsIMMUNE SYSTEM / HLA / MHC / citrulline / Rheumatoid Arthritis
Function / homology
Function and homology information


cytolysis / 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 / autolysosome membrane / regulation of T-helper cell differentiation / killing by host of symbiont cells / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / MHC class II receptor activity ...cytolysis / 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 / autolysosome membrane / regulation of T-helper cell differentiation / killing by host of symbiont cells / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / MHC class II receptor activity / specific granule / positive regulation of CD4-positive, alpha-beta T cell activation / cellular response to peptidoglycan / neutrophil activation / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / 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 / inflammatory response to antigenic stimulus / CD4 receptor binding / cellular response to interleukin-6 / intermediate filament / Antimicrobial peptides / T-helper 1 type immune response / transport vesicle membrane / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / polysaccharide binding / negative regulation of type II interferon production / humoral immune response / macrophage differentiation / Generation of second messenger molecules / immunological synapse / Co-inhibition by PD-1 / cellular response to interleukin-1 / epidermis development / positive regulation of insulin secretion involved in cellular response to glucose stimulus / detection of bacterium / T cell receptor binding / negative regulation of T cell proliferation / MHC class II antigen presentation / trans-Golgi network membrane / innate immune response in mucosa / cell projection / protein tetramerization / peptide antigen assembly with MHC class II protein complex / lumenal side of endoplasmic reticulum membrane / negative regulation of inflammatory response to antigenic stimulus / lipopolysaccharide binding / 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 T cell mediated cytotoxicity / cognition / specific granule lumen / positive regulation of protein phosphorylation / Interferon gamma signaling / positive regulation of angiogenesis / MHC class II protein complex binding / antimicrobial humoral immune response mediated by antimicrobial peptide / cellular response to tumor necrosis factor / endocytic vesicle membrane / late endosome membrane / antibacterial humoral response / tertiary granule lumen / Downstream TCR signaling / T cell receptor signaling pathway / cellular response to lipopolysaccharide / early endosome membrane / defense response to Gram-negative bacterium / amyloid fibril formation / adaptive immune response / positive regulation of viral entry into host cell / lysosome / positive regulation of ERK1 and ERK2 cascade / positive regulation of canonical NF-kappaB signal transduction / positive regulation of MAPK cascade / defense response to Gram-positive bacterium / defense response to bacterium / immune response / Golgi membrane / innate immune response / lysosomal membrane / external side of plasma membrane / positive regulation of cell population proliferation / Neutrophil degranulation / positive regulation of DNA-templated transcription / cell surface / signal transduction / extracellular space / extracellular exosome / extracellular region / membrane / plasma membrane
Similarity search - Function
Cathelicidin, antimicrobial peptide, C-terminal / LPS binding domain of CAP18 (C terminal) / Cathelicidins signature 1. / Cathelicidin, conserved site / Cathelicidins signature 2. / Cathelicidin-like / Cathelicidin / Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / Cystatin superfamily ...Cathelicidin, antimicrobial peptide, C-terminal / LPS binding domain of CAP18 (C terminal) / Cathelicidins signature 1. / Cathelicidin, conserved site / Cathelicidins signature 2. / Cathelicidin-like / Cathelicidin / Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / Cystatin superfamily / 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, DRB1 beta chain / Cathelicidin antimicrobial peptide
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 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
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id
Revision 2.1Oct 16, 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
B: HLA class II histocompatibility antigen, DR alpha chain
A: HLA class II histocompatibility antigen, DRB1-4 beta chain
C: LL37_Cit91
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,0635
Polymers46,6213
Non-polymers4422
Water1448
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7760 Å2
ΔGint-19 kcal/mol
Surface area17360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.869, 180.303, 73.677
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#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 histocompatibility antigen, DRB1-4 beta chain / MHC class II antigen DRB1*4 / DR4


Mass: 23224.617 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DRB1 / Cell line (production host): HEK293S GnTI- / Production host: Homo sapiens (human) / References: UniProt: P13760, UniProt: P01911*PLUS
#3: Protein/peptide LL37_Cit91


Mass: 1476.564 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P49913*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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 2.38 Å3/Da / Density % sol: 48.36 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.3
Details: 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: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jul 23, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.9→45.08 Å / Num. obs: 10253 / % possible obs: 100 % / Redundancy: 6.9 % / Biso Wilson estimate: 47.37 Å2 / CC1/2: 0.986 / Rmerge(I) obs: 0.06883 / Rpim(I) all: 0.108 / Rrim(I) all: 0.286 / Net I/σ(I): 7.5 / Num. measured all: 70429 / Scaling rejects: 34
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.9-3.0870.445216260.6790.61.616100
8.7-45.086.10.0514340.9970.0220.05699.3

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
Aimless0.2.7data scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MDI

4mdi


Resolution: 2.9→45.076 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.6
RfactorNum. reflection% reflection
Rfree0.2476 494 4.82 %
Rwork0.1972 --
obs0.1997 10241 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 85.91 Å2 / Biso mean: 43.2186 Å2 / Biso min: 21.69 Å2
Refinement stepCycle: final / Resolution: 2.9→45.076 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3040 0 28 8 3076
Biso mean--63.57 31.85 -
Num. residues----380
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043176
X-RAY DIFFRACTIONf_angle_d0.6284331
X-RAY DIFFRACTIONf_chiral_restr0.045478
X-RAY DIFFRACTIONf_plane_restr0.004562
X-RAY DIFFRACTIONf_dihedral_angle_d16.1721861
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.9001-3.19190.30251320.254823812513
3.1919-3.65360.25011030.204524152518
3.6536-4.60240.21711240.17824182542
4.6024-45.08120.25031350.187925332668

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