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- PDB-3hcv: Crystal structure of HLA-B*2709 complexed with the double citrull... -

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Basic information

Entry
Database: PDB / ID: 3hcv
TitleCrystal structure of HLA-B*2709 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
  • HLA class I histocompatibility antigen, B-27 alpha chain
KeywordsIMMUNE SYSTEM / IMMUNE SYSTEM-COMPLEX / MHC (MAJOR HISTOCOMPATIBILITY COMPLEX) I / HLA-B*2709 / GLYCOPROTEIN / HOST-VIRUS / IMMUNE RESPONSE / POLYMORPHISM / IMMUNOGLOBULIN DOMAIN / HOST-VIRUS INTERACTION / MEMBRANE / TRANSMEMBRANE / UBL CONJUGATION / DISEASE MUTATION / GLYCATION / PYRROLIDONE CARBOXYLIC ACID / SECRETED / Disulfide bond / MHC I
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: 1.95 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. / Rossmann, M. / Gabdulkhakov, A. / Ziegler, A. / Uchanska-Ziegler, B. / Saenger, W.
History
DepositionMay 6, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 9, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.3Jan 31, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.4Sep 6, 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 / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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 / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_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: DOUBLE CITRULLINATED VASOACTIVE INTESTINAL POLYPEPTIDE RECEPTOR


Theoretical massNumber of molelcules
Total (without water)45,2303
Polymers45,2303
Non-polymers00
Water4,792266
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5430 Å2
ΔGint-5 kcal/mol
Surface area18820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.176, 82.428, 67.017
Angle α, β, γ (deg.)90.000, 110.150, 90.000
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: 31951.219 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, HLAB / Production host: Escherichia coli (E. coli) / References: UniProt: P03989, UniProt: P01889*PLUS
#2: Protein Beta-2-microglobulin / Beta-2-microglobulin form pI 5.3


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 / Source method: obtained synthetically / Details: SYNTHETIC CONSTRUCT / References: UniProt: P32241*PLUS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 266 / 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: 2.93 Å3/Da / Density % sol: 58.08 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1M TRIS HCL,25% PEG 8000, , pH 8.000000, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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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. all: 48072 / Num. obs: 39804 / % possible obs: 82.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 3.75 % / Rmerge(I) obs: 0.06 / Rsym value: 0.06
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 3.76 % / Rmerge(I) obs: 0.432 / Mean I/σ(I) obs: 2.49 / Num. unique all: 2914 / % possible all: 91.9

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ogt

1ogt


Resolution: 1.95→48.04 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.91 / WRfactor Rfree: 0.28 / WRfactor Rwork: 0.227 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.809 / SU B: 8.565 / SU ML: 0.109 / SU Rfree: 0.173 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R Free: 0.173 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.245 1614 5 %RANDOM
Rwork0.199 ---
all0.227 38149 --
obs0.201 32389 84.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 52.24 Å2 / Biso mean: 19.765 Å2 / Biso min: 6.85 Å2
Baniso -1Baniso -2Baniso -3
1--0.96 Å20 Å2-0.43 Å2
2--0 Å20 Å2
3---0.66 Å2
Refinement stepCycle: LAST / Resolution: 1.95→48.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3236 0 0 266 3502
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0213331
X-RAY DIFFRACTIONr_angle_refined_deg1.131.9364525
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6735389
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.31523.027185
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.6315551
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6231535
X-RAY DIFFRACTIONr_chiral_restr0.080.2459
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022636
X-RAY DIFFRACTIONr_nbd_refined0.2060.21483
X-RAY DIFFRACTIONr_nbtor_refined0.2980.22188
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1250.2301
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1440.230
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1530.216
X-RAY DIFFRACTIONr_mcbond_it0.6811.52005
X-RAY DIFFRACTIONr_mcangle_it1.0823138
X-RAY DIFFRACTIONr_scbond_it3.54631554
X-RAY DIFFRACTIONr_scangle_it3.0524.51382
X-RAY DIFFRACTIONr_rigid_bond_restr4.13433559
X-RAY DIFFRACTIONr_sphericity_free3.3893267
X-RAY DIFFRACTIONr_sphericity_bonded2.16933236
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.404 129 -
Rwork0.289 2504 -
all-2633 -
obs--94.31 %

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