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- PDB-3l3d: Crystal structure of HLA-B*4402 in complex with the F3A mutant of... -

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Basic information

Entry
Database: PDB / ID: 3l3d
TitleCrystal structure of HLA-B*4402 in complex with the F3A mutant of a self-peptide derived from DPA*0201
Components
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, B-44 alpha chain
  • peptide from HLA-DPA1 protein
KeywordsIMMUNE SYSTEM / Immunoglobulin domain / Immune response / Major Histocompatibility Complex Class I / MHC-I peptide complex / altered peptide ligand
Function / homology
Function and homology information


antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / 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 ...antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / 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 / 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 / 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 / negative regulation of neuron projection development / protein-folding chaperone binding / ER-Phagosome pathway / protein refolding / early endosome membrane / protein homotetramerization / amyloid fibril formation / adaptive immune response / intracellular iron ion homeostasis / learning or memory / endosome membrane / immune response / endoplasmic reticulum lumen / Amyloid fiber formation / signaling receptor binding / Golgi membrane / 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 II, alpha chain, N-terminal / Class II histocompatibility antigen, alpha domain / Class II histocompatibility antigen, alpha domain / MHC class II, alpha/beta chain, N-terminal / 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 ...MHC class II, alpha chain, N-terminal / Class II histocompatibility antigen, alpha domain / Class II histocompatibility antigen, alpha domain / MHC class II, alpha/beta chain, N-terminal / 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
ACETATE ION / HLA class I histocompatibility antigen, B alpha chain / HLA class I histocompatibility antigen, B alpha chain / Beta-2-microglobulin / HLA class II histocompatibility antigen DP alpha chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsTheodossis, A. / Ely, L.K. / Rossjohn, J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Constraints within major histocompatibility complex class I restricted peptides: presentation and consequences for T-cell recognition
Authors: Theodossis, A. / Guillonneau, C. / Welland, A. / Ely, L.K. / Clements, C.S. / Williamson, N.A. / Webb, A.I. / Wilce, J.A. / Mulder, R.J. / Dunstone, M.A. / Doherty, P.C. / McCluskey, J. / ...Authors: Theodossis, A. / Guillonneau, C. / Welland, A. / Ely, L.K. / Clements, C.S. / Williamson, N.A. / Webb, A.I. / Wilce, J.A. / Mulder, R.J. / Dunstone, M.A. / Doherty, P.C. / McCluskey, J. / Purcell, A.W. / Turner, S.J. / Rossjohn, J.
History
DepositionDec 16, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 26, 2014Group: Database references
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / 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 1.4Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HLA class I histocompatibility antigen, B-44 alpha chain
B: Beta-2-microglobulin
C: peptide from HLA-DPA1 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,8945
Polymers44,7423
Non-polymers1512
Water10,755597
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4220 Å2
ΔGint-16 kcal/mol
Surface area19130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.687, 82.019, 110.440
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein HLA class I histocompatibility antigen, B-44 alpha chain / MHC class I antigen B*44 / Bw-44 / HLA-B*4402


Mass: 31980.258 Da / Num. of mol.: 1 / Fragment: extracellular domains
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: P30481, UniProt: P01889*PLUS
#2: Protein Beta-2-microglobulin / Beta-2-microglobulin form pI 5.3


Mass: 11748.160 Da / Num. of mol.: 1
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

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Protein/peptide , 1 types, 1 molecules C

#3: Protein/peptide peptide from HLA-DPA1 protein / HLA-DPA*0201 peptide


Mass: 1014.069 Da / Num. of mol.: 1 / Mutation: F3A / Source method: obtained synthetically / Details: automated Fmoc-peptide synthesis / References: UniProt: Q95HB9

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Non-polymers , 3 types, 599 molecules

#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 597 / 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: 2.57 Å3/Da / Density % sol: 52.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1M tri-sodium citrate dihydrate, 12-30% PEG 4000, 0.2M ammonium acetate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jan 20, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.8→65.9 Å / Num. all: 43106 / Num. obs: 43106 / % possible obs: 99.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.7 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 7
Reflection shellResolution: 1.8→1.9 Å / Rmerge(I) obs: 0.331 / Mean I/σ(I) obs: 2 / % possible all: 99.1

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Processing

Software
NameVersionClassification
CrystalCleardata collection
AMoREphasing
REFMAC5.5.0088refinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1M6O

1m6o


Resolution: 1.8→40.17 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.932 / SU B: 2.753 / SU ML: 0.085 / Cross valid method: THROUGHOUT / ESU R: 0.131 / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23112 1742 4 %RANDOM
Rwork0.18773 ---
all0.18945 41479 --
obs0.18945 41479 99.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.774 Å2
Baniso -1Baniso -2Baniso -3
1--0.23 Å2-0 Å20 Å2
2---0.72 Å20 Å2
3---0.95 Å2
Refinement stepCycle: LAST / Resolution: 1.8→40.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3156 0 10 597 3763
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0213303
X-RAY DIFFRACTIONr_angle_refined_deg1.3851.944494
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2375395
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.96123.222180
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.80815541
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0981533
X-RAY DIFFRACTIONr_chiral_restr0.1050.2460
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212628
X-RAY DIFFRACTIONr_mcbond_it1.18321955
X-RAY DIFFRACTIONr_mcangle_it2.02433170
X-RAY DIFFRACTIONr_scbond_it2.85241348
X-RAY DIFFRACTIONr_scangle_it4.41261321
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.354 128 -
Rwork0.344 3040 -
obs--99.94 %

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