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- PDB-1jgd: HLA-B*2709 bound to deca-peptide s10R -

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Basic information

Entry
Database: PDB / ID: 1jgd
TitleHLA-B*2709 bound to deca-peptide s10R
Components
  • BETA-2-MICROGLOBULIN
  • HUMAN LYMPHOCYTE ANTIGEN HLA-B27
  • peptide s10R
KeywordsIMMUNE SYSTEM / MHC (Major Histocompatibility Complex) / HLA (Human Leukocyte Antigen)
Function / homology
Function and homology information


regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / regulation of interleukin-6 production / 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 / detection of bacterium / secretory granule membrane ...regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / regulation of interleukin-6 production / 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 / 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 / positive regulation of T cell mediated cytotoxicity / multicellular organismal-level iron ion homeostasis / specific granule lumen / phagocytic vesicle membrane / 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 / 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 / protein homotetramerization / adaptive immune response / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / immune response / endoplasmic reticulum lumen / Amyloid fiber formation / Golgi membrane / signaling receptor binding / lysosomal membrane / innate immune response / external side of plasma membrane / focal adhesion / 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 / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane / cytosol
Similarity search - Function
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 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 / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsHillig, R.C. / Huelsmeyer, M. / Saenger, W. / Volz, A. / Uchanska-Ziegler, B. / Ziegler, A.
Citation
Journal: J.Biol.Chem. / Year: 2004
Title: Thermodynamic and structural analysis of peptide- and allele-dependent properties of two HLA-B27 subtypes exhibiting differential disease association
Authors: Hillig, R.C. / Huelsmeyer, M. / Saenger, W. / Welfle, K. / Misselwitz, R. / Welfle, H. / Kozerski, C. / Volz, A. / Uchanska-Ziegler, B. / Ziegler, A.
#1: Journal: J.Biol.Chem. / Year: 2002
Title: HLA-B27 subtypes differentially associated with disease exhibit subtle structural alterations
Authors: Hulsmeyer, M. / Hillig, R.C. / Volz, A. / Ruhl, M. / Schroder, W. / Saenger, W. / Ziegler, A. / Uchanska-Ziegler, B.
#2: Journal: J.IMMUNOL. / Year: 1994
Title: Identification of a Novel HLA-B27 Subtype by Restriction Analysis of a Cytotoxic gamma delta T Cell Clone
Authors: Del Porto, P. / D'Amato, M. / Fiorillo, M.T. / Tuosto, L. / Piccolella, E. / Sorrention, R.
#3: Journal: Nature / Year: 1991
Title: The Structure of HLA-B27 Reveals Nonamer Self-peptides Bound in an Extended Conformation
Authors: Madden, D.R. / Gorga, J.C. / Strominger, J.L. / Wiley, D.C.
#4: Journal: Cell(Cambridge,Mass.) / Year: 1992
Title: The Three-dimensional Structure of HLA-B27 at 2.1 A Resolution Suggests a General Mechanism for Tight Peptide Binding to MHC
Authors: Madden, D.R. / Gorga, J.C. / Strominger, J.L. / Wiley, D.C.
History
DepositionJun 25, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.4Aug 16, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 9, 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: HUMAN LYMPHOCYTE ANTIGEN HLA-B27
B: BETA-2-MICROGLOBULIN
C: peptide s10R
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2394
Polymers45,1473
Non-polymers921
Water8,143452
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4930 Å2
ΔGint-15 kcal/mol
Surface area18600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.844, 48.438, 88.532
Angle α, β, γ (deg.)90.00, 121.291, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe biological assembly is a heterotrimeric complex consisting of one HLA-B*2709 (heavy) chain, one beta-2-microglobulin (light) chain and one decameric model peptide s10R.

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Components

#1: Protein HUMAN LYMPHOCYTE ANTIGEN HLA-B27


Mass: 31951.219 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-B or 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
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 peptide s10R


Mass: 1316.516 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This peptide was chemically synthesized.
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 452 / 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: 2.7 Å3/Da / Density % sol: 54 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG 8000, Tris-HCl, NaCl; glycerol as cryo protectant, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.05 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 21, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.05 Å / Relative weight: 1
ReflectionResolution: 1.9→14 Å / Num. all: 37162 / Num. obs: 37162 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6 % / Biso Wilson estimate: 26.3 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 28.8
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.386 / Mean I/σ(I) obs: 4.6 / % possible all: 98.6
Reflection
*PLUS
% possible obs: 99.6 %
Reflection shell
*PLUS
Highest resolution: 1.9 Å / % possible obs: 98.6 % / Num. unique obs: 1849

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1JGE

1jge


Resolution: 1.9→20 Å / Isotropic thermal model: TLS / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.194 1905 5.1 %RANDOM
Rwork0.169 ---
obs0.17 37162 99.5 %-
all-37162 --
Displacement parametersBiso mean: 23.21 Å2
Baniso -1Baniso -2Baniso -3
1-0.44 Å20 Å21.45 Å2
2--0.82 Å20 Å2
3---0.26 Å2
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3184 0 6 452 3642
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0170.021
X-RAY DIFFRACTIONp_angle_d1.872
X-RAY DIFFRACTIONp_mcbond_it0.9841.5
X-RAY DIFFRACTIONp_mcangle_it1.6292
X-RAY DIFFRACTIONp_scbond_it2.8623
X-RAY DIFFRACTIONp_scangle_it4.6184.5
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-IDNum. reflection obs% reflection obs (%)
1.92-1.980.261410.19X-RAY DIFFRACTION255498.54
1.98-2.030.221310.18X-RAY DIFFRACTION249799.7
2.03-2.090.21170.17X-RAY DIFFRACTION244099.19
2.09-2.160.21340.17X-RAY DIFFRACTION236099.17
2.16-2.220.21300.16X-RAY DIFFRACTION230399.84
2.22-2.310.191230.16X-RAY DIFFRACTION224099.49
2.31-2.40.231170.17X-RAY DIFFRACTION210999.55
2.4-2.50.221010.16X-RAY DIFFRACTION210399.68
2.5-2.610.221270.17X-RAY DIFFRACTION199499.76
2.61-2.740.231030.17X-RAY DIFFRACTION1903100
2.74-2.90.191020.17X-RAY DIFFRACTION180299.9
2.9-3.090.18870.17X-RAY DIFFRACTION174299.95
3.09-3.270.19910.17X-RAY DIFFRACTION162799.94
3.27-3.580.21990.17X-RAY DIFFRACTION151599.88
3.58-3.950.18680.16X-RAY DIFFRACTION141299.93
3.95-4.430.14710.16X-RAY DIFFRACTION1269100
4.43-5.20.16640.15X-RAY DIFFRACTION1151100
5.2-6.60.17410.18X-RAY DIFFRACTION995100
6.6-10.50.26390.2X-RAY DIFFRACTION786100
10.5-140.18190.19X-RAY DIFFRACTION45587.62
Refinement
*PLUS
Lowest resolution: 14 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.9
LS refinement shell
*PLUS
Highest resolution: 1.9 Å

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