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- PDB-6bir: HLA-DRB1 in complex with citrullinated Vimentin peptide -

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Basic information

Entry
Database: PDB / ID: 6bir
TitleHLA-DRB1 in complex with citrullinated Vimentin peptide
Components
  • HLA class II histocompatibility antigen, DR alpha chain
  • MHC class II antigen
  • Vimentin 424Cit419-431
KeywordsIMMUNE SYSTEM / HLA / MHC / citrulline / Rheumatoid Arthritis
Function / homology
Function and homology information


keratin filament binding / lens fiber cell development / regulation of interleukin-4 production / intermediate filament organization / 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 / cellular response to muramyl dipeptide / regulation of T-helper cell differentiation ...keratin filament binding / lens fiber cell development / regulation of interleukin-4 production / intermediate filament organization / 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 / cellular response to muramyl dipeptide / regulation of T-helper cell differentiation / structural constituent of eye lens / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / positive regulation of CD4-positive, alpha-beta T cell activation / astrocyte development / 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 memory T cell differentiation / positive regulation of monocyte differentiation / intermediate filament cytoskeleton / inflammatory response to antigenic stimulus / Striated Muscle Contraction / CD4 receptor binding / intermediate filament / RHOBTB1 GTPase cycle / 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 / cell leading edge / Bergmann glial cell differentiation / negative regulation of type II interferon production / humoral immune response / positive regulation of collagen biosynthetic process / microtubule organizing center / macrophage differentiation / Generation of second messenger molecules / immunological synapse / Co-inhibition by PD-1 / epidermis development / Caspase-mediated cleavage of cytoskeletal proteins / detection of bacterium / positive regulation of insulin secretion involved in cellular response to glucose stimulus / T cell receptor binding / negative regulation of T cell proliferation / phagocytic vesicle / regulation of mRNA stability / MHC class II antigen presentation / trans-Golgi network membrane / lumenal side of endoplasmic reticulum membrane / protein tetramerization / negative regulation of inflammatory response to antigenic stimulus / clathrin-coated endocytic vesicle membrane / ER to Golgi transport vesicle membrane / Late endosomal microautophagy / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / positive regulation of T cell mediated cytotoxicity / structural constituent of cytoskeleton / cellular response to type II interferon / cognition / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / nuclear matrix / positive regulation of immune response / positive regulation of T cell activation / Interferon gamma signaling / Chaperone Mediated Autophagy / neuron projection development / Aggrephagy / endocytic vesicle membrane / peroxisome / MHC class II protein complex binding / Downstream TCR signaling / T cell receptor signaling pathway / late endosome membrane / double-stranded RNA binding / negative regulation of neuron projection development / cellular response to lipopolysaccharide / early endosome membrane / Interleukin-4 and Interleukin-13 signaling / scaffold protein binding / molecular adaptor activity / adaptive immune response / cytoskeleton / lysosome / endosome membrane / immune response / Golgi membrane / protein domain specific binding / axon / external side of plasma membrane / lysosomal membrane / focal adhesion / positive regulation of gene expression / cell surface / signal transduction / extracellular space / extracellular exosome / identical protein binding
Similarity search - Function
Intermediate filament head, DNA-binding domain / : / Intermediate filament head (DNA binding) region / Intermediate filament protein, conserved site / Intermediate filament protein / Intermediate filament (IF) rod domain signature. / Intermediate filament, rod domain / Intermediate filament (IF) rod domain profile. / Intermediate filament protein / Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 ...Intermediate filament head, DNA-binding domain / : / Intermediate filament head (DNA binding) region / Intermediate filament protein, conserved site / Intermediate filament protein / Intermediate filament (IF) rod domain signature. / Intermediate filament, rod domain / Intermediate filament (IF) rod domain profile. / Intermediate filament protein / 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 / Vimentin / MHC class II antigen
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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 2, 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 ...citation / citation_author / entity / 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 / _entity.pdbx_description / _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 / pdbx_validate_main_chain_plane / pdbx_validate_rmsd_angle / 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
A: HLA class II histocompatibility antigen, DR alpha chain
B: MHC class II antigen
C: Vimentin 424Cit419-431
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,0495
Polymers46,6073
Non-polymers4422
Water2,648147
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7980 Å2
ΔGint-17 kcal/mol
Surface area17470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.460, 183.010, 77.080
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 MHC class II antigen


Mass: 23224.621 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DR-beta 1 / Cell line (production host): HEK293S GnTI- / Production host: Homo sapiens (human) / References: UniProt: P79552, UniProt: P01911*PLUS
#3: Protein/peptide Vimentin 424Cit419-431


Mass: 1462.562 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P08670*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.: 147 / 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: 2.69 Å3/Da / Density % sol: 54.2 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Imidazole/MES pH 6.5, 0.01 M ammonium sulfate, 0.01 M di-sodium hydrogen phosphate, 0.01 M sodium nitrate, 12.5% 2-methyl-2,4-pentanediol (MPD), 14% PEG3350, 12.5% PEG1000

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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: Feb 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.3→39.345 Å / Num. obs: 21534 / % possible obs: 99.6 % / Redundancy: 6.8 % / Biso Wilson estimate: 25.61 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.176 / Rpim(I) all: 0.072 / Rrim(I) all: 0.19 / Net I/σ(I): 9.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.3-2.386.30.8261290220410.7920.3450.8982.498
8.91-39.345.70.05724064220.9980.0250.06319.398.5

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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: 2.3→39.344 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.08
RfactorNum. reflection% reflection
Rfree0.2371 1102 5.12 %
Rwork0.1854 --
obs0.1881 21511 99.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 76.28 Å2 / Biso mean: 25.5611 Å2 / Biso min: 9.51 Å2
Refinement stepCycle: final / Resolution: 2.3→39.344 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3046 0 28 147 3221
Biso mean--51.89 27.03 -
Num. residues----376
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073169
X-RAY DIFFRACTIONf_angle_d0.9224313
X-RAY DIFFRACTIONf_chiral_restr0.053471
X-RAY DIFFRACTIONf_plane_restr0.005558
X-RAY DIFFRACTIONf_dihedral_angle_d14.7771859
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3001-2.40480.27151220.2312486260898
2.4048-2.53150.28541330.22312501263499
2.5315-2.69010.28131310.2222532266399
2.6901-2.89770.26631460.207225192665100
2.8977-3.18920.30561580.202925322690100
3.1892-3.65040.22871380.174425552693100
3.6504-4.5980.20551300.147125932723100
4.598-39.34930.17751440.17382691283599

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