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- PDB-5deg: Crystal structure of B*27:06 bound to the pVIPR peptide -

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Basic information

Entry
Database: PDB / ID: 5deg
TitleCrystal structure of B*27:06 bound to the pVIPR peptide
Components
  • Beta-2-microglobulin
  • MHC class I antigen
  • Peptide derived of VASOACTIVE INTESTINAL POLYPEPTIDE RECEPTOR 1 (pVIPR)
KeywordsIMMUNE SYSTEM / IMMUNE SYSTEM-COMPLEX / MHC MAJOR HISTOCOMPATIBILITY COMPLEX) / HLA- B*2706
Function / homology
Function and homology information


vasoactive intestinal polypeptide receptor activity / G protein-coupled peptide receptor activity / regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / regulation of interleukin-6 production / antigen processing and presentation / peptide hormone binding / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / TAP binding ...vasoactive intestinal polypeptide receptor activity / G protein-coupled peptide receptor activity / regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / regulation of interleukin-6 production / antigen processing and presentation / peptide hormone binding / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / TAP binding / protection from natural killer cell mediated cytotoxicity / detection of bacterium / secretory granule membrane / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / 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 / lumenal side of endoplasmic reticulum membrane / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / regulation of erythrocyte differentiation / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / defense response / multicellular organismal-level iron ion homeostasis / Glucagon-type ligand receptors / negative regulation of neurogenesis / peptide antigen assembly with MHC class II protein complex / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of cellular senescence / peptide antigen binding / negative regulation of epithelial cell proliferation / antigen processing and presentation of exogenous peptide antigen via MHC class II / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / positive regulation of immune response / Modulation by Mtb of host immune system / Interferon alpha/beta signaling / sensory perception of smell / positive regulation of T cell activation / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / iron ion transport / ER-Phagosome pathway / early endosome membrane / protein-folding chaperone binding / T cell differentiation in thymus / protein refolding / G alpha (s) signalling events / protein homotetramerization / intracellular iron ion homeostasis / adaptive immune response / amyloid fibril formation / membrane => GO:0016020 / learning or memory / cell surface receptor signaling pathway / receptor complex / immune response / G protein-coupled receptor signaling pathway / Amyloid fiber formation / endoplasmic reticulum lumen / lysosomal membrane / external side of plasma membrane / Golgi membrane / innate immune response / focal adhesion / signaling receptor binding / positive regulation of cell population proliferation / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus
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. / Hormone receptor domain / GPCR, family 2, extracellular hormone receptor domain / G-protein coupled receptors family 2 profile 1. / Domain present in hormone receptors / 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, vasoactive intestinal peptide receptor 1 / GPCR, family 2, vasoactive intestinal peptide receptor / G-protein coupled receptors family 2 signature 1. / Hormone receptor domain / GPCR, family 2, extracellular hormone receptor domain / G-protein coupled receptors family 2 profile 1. / Domain present in hormone receptors / 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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
HLA class I histocompatibility antigen, B alpha chain / Vasoactive intestinal polypeptide receptor 1 / Beta-2-microglobulin / HLA-B alpha chain (B*2706)
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å
AuthorsLoll, B. / Fabian, H. / Hee, C.S. / Huser, H. / Uchanska-Ziegler, B. / Ziegler, A.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research FoundationSFB 449 Germany
German Research FoundationUC 8/1-3 Germany
CitationJournal: Arthritis Rheumatol / Year: 2016
Title: Increased Conformational Flexibility of HLA-B*27 Subtypes Associated With Ankylosing Spondylitis.
Authors: Loll, B. / Fabian, H. / Huser, H. / Hee, C.S. / Ziegler, A. / Uchanska-Ziegler, B. / Ziegler, A.
History
DepositionAug 25, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Nov 18, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 20, 2016Group: Database references
Revision 1.2Jan 27, 2016Group: Database references
Revision 1.3Dec 18, 2019Group: Author supporting evidence / Database references
Category: citation / pdbx_audit_support / pdbx_related_exp_data_set
Item: _citation.country / _pdbx_audit_support.funding_organization
Revision 1.4Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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: MHC class I antigen
B: Beta-2-microglobulin
C: Peptide derived of VASOACTIVE INTESTINAL POLYPEPTIDE RECEPTOR 1 (pVIPR)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4045
Polymers45,2203
Non-polymers1842
Water7,062392
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5300 Å2
ΔGint-16 kcal/mol
Surface area19140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.768, 81.684, 64.433
Angle α, β, γ (deg.)90.00, 107.53, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein MHC class I antigen


Mass: 31941.133 Da / Num. of mol.: 1 / Fragment: residues 25-300
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-B / Plasmid: PHN1 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q7YQB0, UniProt: P01889*PLUS
#2: Protein Beta-2-microglobulin


Mass: 11879.356 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Plasmid: PHN1 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P61769
#3: Protein/peptide Peptide derived of VASOACTIVE INTESTINAL POLYPEPTIDE RECEPTOR 1 (pVIPR)


Mass: 1399.694 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P32241*PLUS
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 392 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.9 Å3/Da / Density % sol: 57.5 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 20%(w/v) PEG 8000, 100 mM Tris-HCl pH 7.0 / Temp details: 291

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.005 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: May 10, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.005 Å / Relative weight: 1
ReflectionResolution: 1.83→30 Å / Num. obs: 43847 / % possible obs: 99.1 % / Redundancy: 3.6 % / Biso Wilson estimate: 20.4 Å2 / Rsym value: 0.036 / Net I/σ(I): 34.7
Reflection shellResolution: 1.83→1.9 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 6 / % possible all: 92.2

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2a83

2a83


Resolution: 1.83→20 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.945 / SU B: 4.015 / SU ML: 0.066 / Cross valid method: THROUGHOUT / ESU R: 0.123 / ESU R Free: 0.11 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19308 2205 5 %RANDOM
Rwork0.17097 ---
obs0.17214 41622 99.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.591 Å2
Baniso -1Baniso -2Baniso -3
1-0.29 Å20 Å20.48 Å2
2---0.77 Å20 Å2
3---0.76 Å2
Refinement stepCycle: 1 / Resolution: 1.83→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3190 0 12 392 3594
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0213588
X-RAY DIFFRACTIONr_bond_other_d0.0010.022569
X-RAY DIFFRACTIONr_angle_refined_deg1.2671.9324897
X-RAY DIFFRACTIONr_angle_other_deg0.79836189
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9855423
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.37222.938211
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.99215628
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9491543
X-RAY DIFFRACTIONr_chiral_restr0.0820.2498
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214014
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02802
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6081.52034
X-RAY DIFFRACTIONr_mcbond_other0.161.5800
X-RAY DIFFRACTIONr_mcangle_it1.10523338
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.65931554
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.7274.51543
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.833→1.88 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 143 -
Rwork0.271 2989 -
obs--96.46 %
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)
12.2713-0.1148-0.34660.78940.03050.55250.0282-0.1637-0.00950.1071-0.00840.01570.0039-0.023-0.01980.0243-0.00620.00320.01690.00220.001510.39017.806233.7922
21.10010.29420.28023.36343.50548.3457-0.00310.3224-0.0551-0.5877-0.06310.0838-0.1689-0.11430.06620.15980.0103-0.00620.1256-0.01160.0537-9.8373.58274.8955
34.0162-1.13261.19752.9952-1.12762.10270.01210.31340.3556-0.1783-0.03470.1102-0.0368-0.05280.02260.0693-0.0061-0.00560.06050.0440.05520.618621.918313.5989
428.0544-0.9311-8.75070.03350.28892.7305-0.2131-2.6162-0.31680.01510.0935-0.00460.06780.81920.11960.0948-0.0008-0.00610.27920.04610.109215.32337.175341.2273
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 185
2X-RAY DIFFRACTION2A186 - 276
3X-RAY DIFFRACTION3B0 - 99
4X-RAY DIFFRACTION4C1 - 9

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