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- PDB-3dtx: Crystal structure of HLA-B*2705 complexed with the double citrull... -

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Entry
Database: PDB / ID: 3dtx
TitleCrystal structure of HLA-B*2705 complexed with the double citrullinated vasoactive intestinal peptide type 1 receptor (VIPR) peptide (residues 400-408)
Components
  • Beta-2-microglobulin
  • Double citrullinated vasoactive intestinal polypeptide receptor
  • MHC class I antigen (Fragment)
KeywordsIMMUNE SYSTEM / IMMUNE SYSTEM-COMPLEX / MHC (MAJOR HISTOCOMPATIBILITY COMPLEX) I / HLA-B*2705 / GLYCOPROTEIN / HOST-VIRUS / IMMUNE RESPONSE / IMMUNOGLOBULIN DOMAIN / HOST-VIRUS INTERACTION / MEMBRANE / TRANSMEMBRANE / DISEASE MUTATION / GLYCATION / SECRETED / MHC I / Pyrrolidone carboxylic acid
Function / homology
Function and homology information


pituitary adenylate cyclase-activating polypeptide receptor activity / vasoactive intestinal polypeptide receptor activity / regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / G protein-coupled peptide receptor activity / regulation of interleukin-6 production / peptide hormone binding / TAP binding / antigen processing and presentation of peptide antigen via MHC class I ...pituitary adenylate cyclase-activating polypeptide receptor activity / vasoactive intestinal polypeptide receptor activity / regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / G protein-coupled peptide receptor activity / regulation of interleukin-6 production / peptide hormone binding / TAP binding / antigen processing and presentation of peptide antigen via MHC class I / protection from natural killer cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / detection of bacterium / secretory granule membrane / negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / transferrin transport / cellular response to iron ion / Endosomal/Vacuolar pathway / lumenal side of endoplasmic reticulum membrane / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide antigen assembly with MHC class II protein complex / cellular response to iron(III) ion / MHC class II protein complex / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / regulation of erythrocyte differentiation / HFE-transferrin receptor complex / response to molecule of bacterial origin / MHC class I peptide loading complex / defense response / T cell mediated cytotoxicity / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / MHC class I protein complex / positive regulation of T cell activation / peptide antigen binding / positive regulation of receptor-mediated endocytosis / negative regulation of neurogenesis / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / multicellular organismal-level iron ion homeostasis / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / specific granule lumen / phagocytic vesicle membrane / adenylate cyclase-activating G protein-coupled receptor signaling pathway / recycling endosome membrane / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / MHC class II protein complex binding / Interferon alpha/beta signaling / Glucagon-type ligand receptors / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / positive regulation of cellular senescence / tertiary granule lumen / DAP12 signaling / T cell differentiation in thymus / negative regulation of neuron projection development / protein-folding chaperone binding / ER-Phagosome pathway / protein refolding / early endosome membrane / protein homotetramerization / G alpha (s) signalling events / amyloid fibril formation / adaptive immune response / intracellular iron ion homeostasis / learning or memory / cell surface receptor signaling pathway / receptor complex / immune response / G protein-coupled receptor signaling pathway / endoplasmic reticulum lumen / Amyloid fiber formation / signaling receptor binding / Golgi membrane / lysosomal membrane / innate immune response / external side of plasma membrane / focal adhesion / positive regulation of cell population proliferation / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / cell surface / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity
Similarity search - Function
GPCR, family 2, vasoactive intestinal peptide receptor 1 / GPCR, family 2, vasoactive intestinal peptide receptor / G-protein coupled receptors family 2 signature 1. / : / GPCR, family 2, extracellular hormone receptor domain / G-protein coupled receptors family 2 profile 1. / Domain present in hormone receptors / Hormone receptor domain / GPCR family 2, extracellular hormone receptor domain superfamily / G-protein coupled receptors family 2 signature 2. ...GPCR, family 2, vasoactive intestinal peptide receptor 1 / GPCR, family 2, vasoactive intestinal peptide receptor / G-protein coupled receptors family 2 signature 1. / : / GPCR, family 2, extracellular hormone receptor domain / G-protein coupled receptors family 2 profile 1. / Domain present in hormone receptors / Hormone receptor domain / GPCR family 2, extracellular hormone receptor domain superfamily / G-protein coupled receptors family 2 signature 2. / GPCR, family 2, secretin-like, conserved site / GPCR, family 2, secretin-like / 7 transmembrane receptor (Secretin family) / GPCR, family 2-like / G-protein coupled receptors family 2 profile 2. / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
MHC class I antigen / HLA class I histocompatibility antigen, B alpha chain / Vasoactive intestinal polypeptide receptor 1 / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsBeltrami, A. / Gabdulkhakov, A. / Rossmann, M. / Ziegler, A. / Uchanska-Ziegler, B. / Saenger, W.
CitationJournal: To be Published
Title: Citrullination-and mhc polymorphism-dependent conformational changes of a self peptide
Authors: Beltrami, A. / Gabdulkhakov, A. / Rossmann, M. / Ziegler, A. / Uchanska-Ziegler, B. / Saenger, W.
History
DepositionJul 16, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 5, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 12, 2011Group: Derived calculations
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity / entity_name_com / entity_src_gen / pdbx_entity_src_syn / pdbx_initial_refinement_model / struct_conn / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_seq_type / _pdbx_entity_src_syn.pdbx_beg_seq_num / _pdbx_entity_src_syn.pdbx_end_seq_num / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
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_peptide_omega / 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 2.1Dec 27, 2023Group: Derived calculations / Category: struct_conn
Revision 2.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MHC class I antigen (Fragment)
B: Beta-2-microglobulin
C: Double citrullinated vasoactive intestinal polypeptide receptor


Theoretical massNumber of molelcules
Total (without water)45,2073
Polymers45,2073
Non-polymers00
Water3,891216
1
A: MHC class I antigen (Fragment)
B: Beta-2-microglobulin
C: Double citrullinated vasoactive intestinal polypeptide receptor

A: MHC class I antigen (Fragment)
B: Beta-2-microglobulin
C: Double citrullinated vasoactive intestinal polypeptide receptor


Theoretical massNumber of molelcules
Total (without water)90,4146
Polymers90,4146
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y+1/2,-z1
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5790 Å2
ΔGint-5 kcal/mol
Surface area19100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.842, 81.931, 65.771
Angle α, β, γ (deg.)90.00, 108.88, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein MHC class I antigen (Fragment)


Mass: 31928.160 Da / Num. of mol.: 1 / Fragment: EXTRACELLUAR DOMAIN, RESIDUES 25-300
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-B / Production host: Escherichia coli (E. coli) / References: UniProt: A3F718, UniProt: P01889*PLUS
#2: Protein Beta-2-microglobulin


Mass: 11879.356 Da / Num. of mol.: 1 / Fragment: RESIDUES 21-119
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Production host: Escherichia coli (E. coli) / References: UniProt: P61769
#3: Protein/peptide Double citrullinated vasoactive intestinal polypeptide receptor


Mass: 1399.648 Da / Num. of mol.: 1 / Fragment: RESIDUES 400-408 / Source method: obtained synthetically / Details: THIS SEQUENCE OCCURS NATURALLY IN HUMANS.
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 216 / 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: 2.87 Å3/Da / Density % sol: 57.1 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M TRIS HCL, 25% PEG 8000,, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.905 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Mar 9, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.905 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 29222 / Num. obs: 28855 / % possible obs: 96.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Rsym value: 0.13 / Net I/σ(I): 8.56
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 1.955 / Rsym value: 0.456 / % possible all: 85.14

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OGT

1ogt


Resolution: 2.1→50 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.901 / SU B: 5.279 / SU ML: 0.142 / Cross valid method: THROUGHOUT / ESU R: 0.229 / ESU R Free: 0.201 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26183 1452 5 %RANDOM
Rwork0.20901 ---
obs0.21164 28855 96.64 %-
all-29222 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.05 Å2
Baniso -1Baniso -2Baniso -3
1--1.91 Å20 Å2-0.23 Å2
2---0.77 Å20 Å2
3---2.53 Å2
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3189 0 0 216 3405
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0213356
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2871.9324560
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.5955390
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.46523.027185
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.1815564
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3471538
X-RAY DIFFRACTIONr_chiral_restr0.1030.2463
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022657
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1880.21419
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2970.22187
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.2287
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1790.232
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1490.214
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.881.52015
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.05623159
X-RAY DIFFRACTIONr_scbond_it1.46931569
X-RAY DIFFRACTIONr_scangle_it2.2364.51396
X-RAY DIFFRACTIONr_rigid_bond_restr1.00433541
X-RAY DIFFRACTIONr_sphericity_free3.8313418
X-RAY DIFFRACTIONr_sphericity_bonded1.45833225
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 89 -
Rwork0.234 1760 -
obs--85.09 %

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