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- PDB-1a9b: DECAMER-LIKE CONFORMATION OF A NANO-PEPTIDE BOUND TO HLA-B3501 DU... -

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Basic information

Entry
Database: PDB / ID: 1a9b
TitleDECAMER-LIKE CONFORMATION OF A NANO-PEPTIDE BOUND TO HLA-B3501 DUE TO NONSTANDARD POSITIONING OF THE C-TERMINUS
Components
  • BETA-2-MICROGLOBULINBeta-2 microglobulin
  • HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, B-35 B*3501 (ALPHA CHAIN)
  • PEPTIDE LPPLDITPY
KeywordsCOMPLEX (MHC CLASS I/PEPTIDE) / MHC CLASS I / HISTOCOMPATIBILITY COMPLEX / HLA B3501 / COMPLEX (MHC CLASS I-PEPTIDE) / COMPLEX (MHC CLASS I-PEPTIDE) complex
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 / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / early endosome lumen / positive regulation of receptor binding / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / negative regulation of forebrain neuron differentiation / defense response / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / response to molecule of bacterial origin / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / cellular response to iron ion / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / multicellular organismal-level iron ion homeostasis / positive regulation of T cell mediated cytotoxicity / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / MHC class II protein complex / positive regulation of receptor-mediated endocytosis / cellular response to nicotine / recycling endosome membrane / phagocytic vesicle membrane / specific granule lumen / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / positive regulation of immune response / negative regulation of epithelial cell proliferation / Modulation by Mtb of host immune system / positive regulation of T cell activation / Interferon alpha/beta signaling / sensory perception of smell / negative regulation of neuron projection development / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / late endosome membrane / T cell differentiation in thymus / positive regulation of protein binding / ER-Phagosome pathway / iron ion transport / protein-folding chaperone binding / protein refolding / early endosome membrane / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / adaptive immune response / learning or memory / immune response / Amyloid fiber formation / lysosomal membrane / endoplasmic reticulum lumen / external side of plasma membrane / Golgi membrane / signaling receptor binding / focal adhesion / innate immune response / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / cell surface / endoplasmic reticulum / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / membrane / identical protein binding / 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 classes I/II-like antigen recognition protein ...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 / Immunoglobulins / Immunoglobulin-like fold / 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: 3.2 Å
AuthorsMenssen, R. / Orth, P. / Ziegler, A. / Saenger, W.
CitationJournal: J.Mol.Biol. / Year: 1999
Title: Decamer-like conformation of a nona-peptide bound to HLA-B*3501 due to non-standard positioning of the C terminus.
Authors: Menssen, R. / Orth, P. / Ziegler, A. / Saenger, W.
History
DepositionApr 3, 1998Processing site: BNL
Revision 1.0Oct 21, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2023Group: Data collection / Database references / Refinement description
Category: database_2 / diffrn_source / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site

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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-35 B*3501 (ALPHA CHAIN)
B: BETA-2-MICROGLOBULIN
C: PEPTIDE LPPLDITPY
D: HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, B-35 B*3501 (ALPHA CHAIN)
E: BETA-2-MICROGLOBULIN
F: PEPTIDE LPPLDITPY


Theoretical massNumber of molelcules
Total (without water)89,8706
Polymers89,8706
Non-polymers00
Water0
1
A: HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, B-35 B*3501 (ALPHA CHAIN)
B: BETA-2-MICROGLOBULIN
C: PEPTIDE LPPLDITPY


Theoretical massNumber of molelcules
Total (without water)44,9353
Polymers44,9353
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4460 Å2
ΔGint-22 kcal/mol
Surface area18570 Å2
MethodPISA
2
D: HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, B-35 B*3501 (ALPHA CHAIN)
E: BETA-2-MICROGLOBULIN
F: PEPTIDE LPPLDITPY


Theoretical massNumber of molelcules
Total (without water)44,9353
Polymers44,9353
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4460 Å2
ΔGint-22 kcal/mol
Surface area18570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.740, 116.390, 169.340
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.9944, -0.02705, -0.10219), (0.03046, -0.99903, -0.03191), (-0.10123, -0.03484, 0.99425)
Vector: 51.33088, 70.55732, 3.18913)
DetailsTHERE ARE TWO COMPLEXES PER ASYMMETRIC UNIT, EACH COMPOSED OF THREE POLYPEPTIDE CHAINS. THEY ARE IDENTIFIED AS CHAIN A, B, C FOR ONE COMPLEX AND CHAIN D, E, F FOR THE OTHER COMPLEX. CHAIN A AND D ARE HLA HEAVY CHAIN CHAIN B AND E ARE BETA-2-MICROGLOBULIN CHAIN C AND F ARE PEPTIDE FROM EBNA3C-PROTEIN FROM EBV

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Components

#1: Protein HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, B-35 B*3501 (ALPHA CHAIN)


Mass: 32027.324 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P30685, UniProt: P01889*PLUS
#2: Protein BETA-2-MICROGLOBULIN / Beta-2 microglobulin


Mass: 11879.356 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P61769
#3: Protein/peptide PEPTIDE LPPLDITPY


Mass: 1028.198 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: PEPTIDE FROM EBNA3C-PROTEIN FROM EBV

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

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Sample preparation

CrystalDensity Matthews: 2.51 Å3/Da / Density % sol: 46 %
Crystal growpH: 5.6
Details: 20% MPD, 20% PEG 6000, 1% GLYCEROL, 100 MM SODIUM CITRATE, PH 5.6
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 18 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
17 mg/mlprotein1drop
220 %(v/v)MPD1reservoir
320 %(v/v)PEG60001reservoir
41 %(v/v)glycerol1reservoir
50.1 Msodium citrate1reservoirpH5.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.909
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 1, 1997
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.909 Å / Relative weight: 1
ReflectionResolution: 3.2→28 Å / Num. obs: 13463 / % possible obs: 86.2 % / Observed criterion σ(I): 2 / Redundancy: 7.4 % / Biso Wilson estimate: 29.7 Å2 / Rsym value: 0.097 / Net I/σ(I): 5.4
Reflection shellResolution: 2.31→3.2 Å / Mean I/σ(I) obs: 1.9 / Rsym value: 0.259 / % possible all: 88.6
Reflection
*PLUS
Num. measured all: 99761 / Rmerge(I) obs: 0.097

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HHI

1hhi


Resolution: 3.2→28 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: GROUPED, UNRESTRAINED
RfactorNum. reflection% reflectionSelection details
Rfree0.305 1376 10 %RANDOM
Rwork0.251 ---
obs0.251 13463 86.3 %-
Displacement parametersBiso mean: 21.8 Å2
Refinement stepCycle: LAST / Resolution: 3.2→28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6340 0 0 0 6340
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.2
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.2
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.1
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refine LS restraints NCSNCS model details: NCS RESTRAINTS / Weight Biso : 200000
LS refinement shellResolution: 3.2→3.31 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.377 152 9.6 %
Rwork0.305 1161 -
obs--87.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.HIS
X-RAY DIFFRACTION3TOPH19.SOL
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.2
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.1

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