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- PDB-5ib4: Crystal structure of HLA-B*27:05 complexed with the self-peptide ... -

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Basic information

Entry
Database: PDB / ID: 5ib4
TitleCrystal structure of HLA-B*27:05 complexed with the self-peptide pVIPR and Nickel
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 / 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 / recycling endosome membrane / adenylate cyclase-activating G protein-coupled receptor signaling pathway / 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 / negative regulation of neuron projection development / protein-folding chaperone binding / ER-Phagosome pathway / protein refolding / early endosome membrane / G alpha (s) signalling events / protein homotetramerization / 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 / 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
NICKEL (II) ION / 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: 1.95 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _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.ptnr1_symmetry / _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_symmetry
Revision 1.3Nov 13, 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 I histocompatibility antigen, B-27 alpha chain
B: Beta-2-microglobulin
C: Vasoactive intestinal polypeptide receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5097
Polymers45,2073
Non-polymers3024
Water3,513195
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5380 Å2
ΔGint-35 kcal/mol
Surface area19180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.130, 81.740, 65.120
Angle α, β, γ (deg.)90.00, 107.83, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 2 molecules AB

#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

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Protein/peptide , 1 types, 1 molecules C

#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

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Non-polymers , 3 types, 199 molecules

#4: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 195 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 57.08 %
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: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 1.127 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Mar 10, 2012
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.127 Å / Relative weight: 1
ReflectionResolution: 1.95→35 Å / Num. obs: 69349 / % possible obs: 94.6 % / Redundancy: 3.6 % / Biso Wilson estimate: 31.1 Å2 / CC1/2: 0.995 / Net I/σ(I): 14.76
Reflection shellResolution: 1.95→2 Å / Redundancy: 1.4 % / Mean I/σ(I) obs: 6.43 / % possible all: 65.6

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: 000)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OF2

1of2


Resolution: 1.95→34.122 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 0.45 / Phase error: 19.83
RfactorNum. reflection% reflection
Rfree0.2022 3451 4.98 %
Rwork0.1641 --
obs0.166 69336 94.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.95→34.122 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3189 0 14 195 3398
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0163476
X-RAY DIFFRACTIONf_angle_d1.2984728
X-RAY DIFFRACTIONf_dihedral_angle_d15.8662104
X-RAY DIFFRACTIONf_chiral_restr0.078475
X-RAY DIFFRACTIONf_plane_restr0.009625
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-1.97670.2226940.16371761X-RAY DIFFRACTION62
1.9767-2.00490.2048960.16261893X-RAY DIFFRACTION70
2.0049-2.03490.2317930.17112154X-RAY DIFFRACTION75
2.0349-2.06670.2361290.16222215X-RAY DIFFRACTION82
2.0667-2.10050.18751290.15812506X-RAY DIFFRACTION87
2.1005-2.13680.19711180.15852639X-RAY DIFFRACTION95
2.1368-2.17560.18841600.15772689X-RAY DIFFRACTION99
2.1756-2.21740.20361660.15752785X-RAY DIFFRACTION100
2.2174-2.26270.17771140.16432766X-RAY DIFFRACTION100
2.2627-2.31190.21981580.16142815X-RAY DIFFRACTION100
2.3119-2.36570.24351510.17282721X-RAY DIFFRACTION100
2.3657-2.42480.2121370.17162833X-RAY DIFFRACTION100
2.4248-2.49030.19641760.16142753X-RAY DIFFRACTION100
2.4903-2.56360.20011310.16192791X-RAY DIFFRACTION100
2.5636-2.64630.20591590.16962730X-RAY DIFFRACTION100
2.6463-2.74090.22281410.16952824X-RAY DIFFRACTION100
2.7409-2.85050.2511070.17362837X-RAY DIFFRACTION100
2.8505-2.98020.2121540.16942761X-RAY DIFFRACTION100
2.9802-3.13720.18481690.16232747X-RAY DIFFRACTION100
3.1372-3.33360.20041370.16042770X-RAY DIFFRACTION100
3.3336-3.59080.18311430.14862791X-RAY DIFFRACTION100
3.5908-3.95160.17481540.14572764X-RAY DIFFRACTION100
3.9516-4.52230.14811470.14412774X-RAY DIFFRACTION100
4.5223-5.69340.19091400.15762807X-RAY DIFFRACTION100
5.6934-34.12680.28281480.2252759X-RAY DIFFRACTION100
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)
12.9791-0.4245-0.69411.5610.07791.1170.01910.24980.0356-0.13540.00430.05470.0193-0.0375-0.01670.15090.0059-0.01840.1160.00730.11253.827-2.7721-3.3861
21.84720.1180.56222.86610.56371.989-0.1373-0.55820.47180.30590.0373-0.1591-0.24370.11620.04690.25830.0105-0.04310.2654-0.09720.237214.430611.470716.8658
36.13471.3743-2.17340.3076-0.52722.36850.01381.10850.1811-0.15590.04580.18490.0735-0.3759-0.07660.178-0.0078-0.01870.22780.0070.1606-0.0191-3.8439-10.5517
41.21180.36361.14721.1741-0.14251.8523-0.1319-0.7485-0.15680.75640.3027-0.11030.59120.4989-0.05030.58490.2313-0.02880.61140.02530.244526.1828-6.193724.1969
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and ((resseq 1:176))
2X-RAY DIFFRACTION2chain 'B'
3X-RAY DIFFRACTION3chain 'C'
4X-RAY DIFFRACTION4chain 'A' and ((resseq 177:276))

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