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- PDB-3b6s: Crystal Structure of hla-b*2705 Complexed with the Citrullinated ... -

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Basic information

Entry
Database: PDB / ID: 3b6s
TitleCrystal Structure of hla-b*2705 Complexed with the Citrullinated Vasoactive Intestinal Peptide Type 1 Receptor (vipr) Peptide (residues 400-408)
Components
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, B-27 alpha chain
  • VASOACTIVE INTESTINAL POLYPEPTIDE RECEPTOR 1
KeywordsIMMUNE SYSTEM / Immune sistem-complex / MHC (Major Histocompatibility Complex) / HLA-B*2705 / Glycoprotein / Host-virus interaction / Immune response / Membrane / MHC I / Polymorphism / Transmembrane / Ubl conjugation / Disease mutation / Glycation / Immunoglobulin domain / Pyrrolidone carboxylic acid / Secreted
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 Ib / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / detection of bacterium / negative regulation of receptor binding / secretory granule membrane / 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 / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide antigen assembly with MHC class II protein complex / lumenal side of endoplasmic reticulum membrane / 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 / defense response / response to molecule of bacterial origin / MHC class I peptide loading complex / 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 / Modulation by Mtb of host immune system / Glucagon-type ligand receptors / 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 / innate immune response / lysosomal membrane / 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: 1.8 Å
AuthorsBeltrami, A. / Rossmann, M. / Fiorillo, M.T. / Sorrentino, R. / Saenger, W. / Ziegler, A. / Uchanska-Ziegler, A.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Citrullination-dependent Differential Presentation of a Self-peptide by HLA-B27 Subtypes.
Authors: Beltrami, A. / Rossmann, M. / Fiorillo, M.T. / Paladini, F. / Sorrentino, R. / Saenger, W. / Kumar, P. / Ziegler, A. / Uchanska-Ziegler, B.
History
DepositionOct 29, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Aug 30, 2023Group: 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 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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 / 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 30, 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


Theoretical massNumber of molelcules
Total (without water)45,2073
Polymers45,2073
Non-polymers00
Water9,998555
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.661, 82.797, 110.286
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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 / Fragment: EXTRACELLULAR DOMAIN, RESIDUES 25-300
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-B, HLAB / 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 / Fragment: RESIDUES 21-119
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M / Production host: Escherichia coli (E. coli) / References: UniProt: P61769
#3: Protein/peptide VASOACTIVE INTESTINAL POLYPEPTIDE RECEPTOR 1


Mass: 1399.671 Da / Num. of mol.: 1 / Fragment: RESIDUES 400-408 / Mutation: CITRULLINATED IN POSITION 5 / Source method: obtained synthetically / Details: Synthetic / References: UniProt: P32241*PLUS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 555 / 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: 2.56 Å3/Da / Density % sol: 51.92 %
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M Tris HCl, 24% PEG 8000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 281K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.982 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 3, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.982 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 41639 / % possible obs: 95 % / Rmerge(I) obs: 0.093 / Χ2: 1.004 / Net I/σ(I): 13.3
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique allΧ2% possible all
1.8-1.860.48637131.0986.3
1.86-1.940.36438011.03388.2
1.94-2.030.27638861.02389.6
2.03-2.130.20840130.98293.1
2.13-2.270.16741311.0195.4
2.27-2.440.13942811.00697.9
2.44-2.690.11543391.03399.3
2.69-3.080.09443730.97199.8
3.08-3.880.06244621.01499.9
3.88-500.0446400.92699.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3data extraction
ADSCQuantumdata collection
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OGT

1ogt


Resolution: 1.8→41.42 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.928 / SU B: 2.502 / SU ML: 0.08 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.138 / ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.223 2096 5 %RANDOM
Rwork0.184 ---
obs0.186 41581 94.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.459 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.8→41.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3225 0 0 555 3780
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0213327
X-RAY DIFFRACTIONr_angle_refined_deg1.0331.9334527
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6055392
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.68223.022182
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.26215546
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8261535
X-RAY DIFFRACTIONr_chiral_restr0.0730.2458
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022654
X-RAY DIFFRACTIONr_nbd_refined0.1830.21542
X-RAY DIFFRACTIONr_nbtor_refined0.2950.22221
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1330.2556
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1220.239
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1040.243
X-RAY DIFFRACTIONr_mcbond_it0.5491.52023
X-RAY DIFFRACTIONr_mcangle_it0.8823165
X-RAY DIFFRACTIONr_scbond_it1.30531532
X-RAY DIFFRACTIONr_scangle_it2.0824.51362
LS refinement shellResolution: 1.8→1.845 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 138 -
Rwork0.242 2492 -
all-2630 -
obs--82.26 %

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