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- PDB-3ln4: Crystal structure of HLA-B*4103 in complex with a 16mer self-pept... -

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Basic information

Entry
Database: PDB / ID: 3ln4
TitleCrystal structure of HLA-B*4103 in complex with a 16mer self-peptide derived from heterogeneous nuclear ribonucleoproteins C1/C2
Components
  • 16-mer peptide from Heterogeneous nuclear ribonucleoproteins C1/C2
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, B-41 alpha chain
KeywordsIMMUNE SYSTEM / Immunoglobulin domain / Immune response / Major Histocompatibility Complex Class I / MHC-I peptide complex / peptide-binding motifs / Disulfide bond
Function / homology
Function and homology information


N6-methyladenosine-containing RNA reader activity / regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / SUMOylation of RNA binding proteins / telomerase holoenzyme complex / telomerase RNA binding / regulation of interleukin-6 production / RHOBTB1 GTPase cycle / 3'-UTR-mediated mRNA stabilization ...N6-methyladenosine-containing RNA reader activity / regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / SUMOylation of RNA binding proteins / telomerase holoenzyme complex / telomerase RNA binding / regulation of interleukin-6 production / RHOBTB1 GTPase cycle / 3'-UTR-mediated mRNA stabilization / poly(U) RNA binding / nucleosomal DNA binding / negative regulation of telomere maintenance via telomerase / TAP binding / Processing of Capped Intron-Containing Pre-mRNA / 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 / RHOBTB2 GTPase cycle / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / RNA splicing / 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 / mRNA 3'-UTR binding / 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 / spliceosomal 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 / mRNA splicing, via spliceosome / 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 / osteoblast differentiation / 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 / actin cytoskeleton / 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 / immune response / chromatin remodeling / 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
Similarity search - Function
Heterogeneous nuclear ribonucleoprotein C / : / 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 / RNA recognition motif / RNA recognition motif ...Heterogeneous nuclear ribonucleoprotein C / : / 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 / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / RNA-binding domain 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 / Nucleotide-binding alpha-beta plait domain superfamily / 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 / Heterogeneous nuclear ribonucleoproteins C1/C2 / 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: 1.296 Å
AuthorsTheodossis, A. / Gras, S. / Rossjohn, J.
CitationJournal: Haematologica / Year: 2011
Title: The impact of human leukocyte antigen (HLA) micropolymorphism on ligand specificity within the HLA-B*41 allotypic family
Authors: Bade-Doding, C. / Theodossis, A. / Gras, S. / Kjer-Nielsen, L. / Eiz-Vesper, B. / Seltsam, A. / Huyton, T. / Rossjohn, J. / McCluskey, J. / Blasczyk, R.
History
DepositionFeb 1, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 20, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HLA class I histocompatibility antigen, B-41 alpha chain
B: Beta-2-microglobulin
C: 16-mer peptide from Heterogeneous nuclear ribonucleoproteins C1/C2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3965
Polymers45,2783
Non-polymers1182
Water10,881604
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3950 Å2
ΔGint-17 kcal/mol
Surface area19270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.777, 81.992, 109.810
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein HLA class I histocompatibility antigen, B-41 alpha chain / HLA class I histocompatibility antigen / B*4103 alpha chain / MHC class I antigen B*41 / Bw-41


Mass: 31827.072 Da / Num. of mol.: 1 / Fragment: extracellular domains, UNP residues 25-298
Source method: isolated from a genetically manipulated source
Details: B*4103 allele (W95L polymorphic variant) / Source: (gene. exp.) Homo sapiens (human) / Plasmid: pcRT7 / Production host: Escherichia coli (E. coli) / References: UniProt: P30479, 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) / Plasmid: pcRT7 / Production host: Escherichia coli (E. coli) / References: UniProt: P61769
#3: Protein/peptide 16-mer peptide from Heterogeneous nuclear ribonucleoproteins C1/C2


Mass: 1702.859 Da / Num. of mol.: 1 / Fragment: UNP residues 102-117 / Source method: obtained synthetically / Details: Fmoc peptide synthesis / Source: (synth.) Homo sapiens (human) / References: UniProt: P07910
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 604 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsCYS A 101 AND 164 IN ALTERNATIVE CONFORMATION B & C ARE IN REDUCED FORM.

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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: 2.52 Å3/Da / Density % sol: 51.27 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.1M citrate pH 5.6, 14-20% PEG 4000, 0.2M NH4OAc, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97934 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 13, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.296→65.6 Å / Num. all: 110817 / Num. obs: 110817 / % possible obs: 97.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 7.4 % / Biso Wilson estimate: 12.19 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 16.8
Reflection shellResolution: 1.296→1.35 Å / Redundancy: 5 % / Rmerge(I) obs: 0.364 / Mean I/σ(I) obs: 4.2 / Num. unique all: 9992 / % possible all: 88.6

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(phenix.refine)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1SYV

1syv


Resolution: 1.296→27.918 Å / Occupancy max: 1 / Occupancy min: 0.01 / FOM work R set: 0.92 / SU ML: 0.11 / σ(F): 1.33 / Phase error: 14.2 / Stereochemistry target values: ML
Details: REFINEMENT OF REDUCED CONFORMERS CARRIED OUT IN PHENIX USING THE THREE LETTER CODE CSH.
RfactorNum. reflection% reflectionSelection details
Rfree0.1766 1110 1 %RANDOM
Rwork0.1547 109572 --
obs0.1549 110682 96.87 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.643 Å2 / ksol: 0.349 e/Å3
Displacement parametersBiso max: 54.57 Å2 / Biso mean: 20.013 Å2 / Biso min: 4.61 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.296→27.918 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3137 0 8 604 3749
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063392
X-RAY DIFFRACTIONf_angle_d1.1014628
X-RAY DIFFRACTIONf_dihedral_angle_d15.4061263
X-RAY DIFFRACTIONf_chiral_restr0.08473
X-RAY DIFFRACTIONf_plane_restr0.005618
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2961-1.35510.18731080.171112312X-RAY DIFFRACTION88
1.3551-1.42650.20611280.151813647X-RAY DIFFRACTION98
1.4265-1.51590.17241600.124913763X-RAY DIFFRACTION98
1.5159-1.63290.15931410.10713923X-RAY DIFFRACTION99
1.6329-1.79720.13791520.110613940X-RAY DIFFRACTION99
1.7972-2.05720.14471390.115714094X-RAY DIFFRACTION100
2.0572-2.59160.15971440.146614164X-RAY DIFFRACTION100
2.5916-27.92480.19911380.187413729X-RAY DIFFRACTION94

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