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- PDB-5ib1: Crystal structure of HLA-B*27:05 complexed with the self-peptide ... -

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Basic information

Entry
Database: PDB / ID: 5ib1
TitleCrystal structure of HLA-B*27:05 complexed with the self-peptide pVIPR measured at 295 K
Components
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, B-27 alpha chain
  • Vasoactive intestinal polypeptide receptor 1
KeywordsIMMUNE SYSTEM / IMMUNE SYSTEM-COMPLEX / MHC MAJOR HISTOCOMPATIBILITY COMPLEX) / HLA- B*2705
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 / protection from natural killer cell mediated cytotoxicity ...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 / 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 / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / 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 / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / positive regulation of T cell mediated cytotoxicity / multicellular organismal-level iron ion homeostasis / 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 / Glucagon-type ligand receptors / Interferon alpha/beta signaling / 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 / protein-folding chaperone binding / negative regulation of neuron projection development / ER-Phagosome pathway / protein refolding / early endosome membrane / G alpha (s) signalling events / protein homotetramerization / adaptive immune response / amyloid fibril formation / 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 / Golgi membrane / signaling receptor binding / 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 / extracellular space
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
HLA class I histocompatibility antigen, B alpha chain / 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: 1.91 Å
AuthorsJanke, R. / Ballaschk, M. / Schmieder, P. / Uchanska-Ziegler, B. / Ziegler, A. / Loll, B.
CitationJournal: J.Biol.Chem. / Year: 2019
Title: Metal-triggered conformational reorientation of a self-peptide bound to a disease-associated HLA-B*27 subtype.
Authors: Driller, R. / Ballaschk, M. / Schmieder, P. / Uchanska-Ziegler, B. / Ziegler, A. / Loll, B.
History
DepositionFeb 22, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Feb 1, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 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
Revision 1.3Nov 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: HLA class I histocompatibility antigen, B-27 alpha chain
B: Beta-2-microglobulin
C: Vasoactive intestinal polypeptide receptor 1


Theoretical massNumber of molelcules
Total (without water)45,2073
Polymers45,2073
Non-polymers00
Water2,450136
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4860 Å2
ΔGint-17 kcal/mol
Surface area18970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.533, 83.111, 66.543
Angle α, β, γ (deg.)90.00, 109.35, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein HLA class I histocompatibility antigen, B-27 alpha chain / MHC class I antigen B*27


Mass: 31928.160 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-B, HLAB / Plasmid: PHN1 / Production host: Escherichia coli (E. coli) / References: UniProt: P03989, 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 (E. coli) / References: UniProt: P61769
#3: Protein/peptide Vasoactive intestinal polypeptide receptor 1 / VIP-R-1 / Pituitary adenylate cyclase-activating polypeptide type II receptor / PACAP-R2 / VPAC1


Mass: 1399.694 Da / Num. of mol.: 1 / Fragment: UNP residues 400-408 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P32241
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 136 / 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: 2.97 Å3/Da / Density % sol: 58.64 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.1 M Tris HCl, 16% (w/v) PEG 8000

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: May 26, 2011
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.91→30 Å / Num. obs: 40810 / % possible obs: 99.2 % / Redundancy: 3.3 % / Biso Wilson estimate: 32.4 Å2 / CC1/2: 0.998 / Net I/σ(I): 12.92
Reflection shellResolution: 1.91→1.96 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 1.7 / % possible all: 93.4

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: 000)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OF2

1of2


Resolution: 1.91→29.367 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 19.8
RfactorNum. reflection% reflection
Rfree0.1915 2041 5 %
Rwork0.164 --
obs0.1653 40809 99.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.91→29.367 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3189 0 0 136 3325
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073355
X-RAY DIFFRACTIONf_angle_d0.9074571
X-RAY DIFFRACTIONf_dihedral_angle_d14.6872021
X-RAY DIFFRACTIONf_chiral_restr0.056467
X-RAY DIFFRACTIONf_plane_restr0.005602
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.91-1.95450.32911260.26792400X-RAY DIFFRACTION93
1.9545-2.00330.28641360.23722571X-RAY DIFFRACTION99
2.0033-2.05750.24511360.22382592X-RAY DIFFRACTION100
2.0575-2.1180.25851350.2042567X-RAY DIFFRACTION100
2.118-2.18630.22991360.18752580X-RAY DIFFRACTION100
2.1863-2.26450.2111370.18762608X-RAY DIFFRACTION100
2.2645-2.35510.21651370.17222607X-RAY DIFFRACTION100
2.3551-2.46220.22561370.17752600X-RAY DIFFRACTION100
2.4622-2.5920.21771360.18172587X-RAY DIFFRACTION100
2.592-2.75420.23511370.18282586X-RAY DIFFRACTION100
2.7542-2.96670.20061360.17852595X-RAY DIFFRACTION100
2.9667-3.26490.17461370.16752607X-RAY DIFFRACTION100
3.2649-3.73650.14761380.14772610X-RAY DIFFRACTION100
3.7365-4.70450.14991380.12062620X-RAY DIFFRACTION100
4.7045-29.37050.15191390.12722638X-RAY DIFFRACTION99

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