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- PDB-3ln5: Crystal structure of HLA-B*4104 in complex with a 11mer self-pept... -

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Basic information

Entry
Database: PDB / ID: 3ln5
TitleCrystal structure of HLA-B*4104 in complex with a 11mer self-peptide derived from S-methyl-5-thioadenosine phosphorylase
Components
  • 11-mer peptide from S-methyl-5'-thioadenosine phosphorylase
  • 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


Methionine salvage pathway / 1,4-alpha-oligoglucan phosphorylase activity / S-methyl-5'-thioadenosine phosphorylase / S-methyl-5-thioadenosine phosphorylase activity / L-methionine salvage from methylthioadenosine / regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / regulation of interleukin-6 production / nucleobase-containing compound metabolic process ...Methionine salvage pathway / 1,4-alpha-oligoglucan phosphorylase activity / S-methyl-5'-thioadenosine phosphorylase / S-methyl-5-thioadenosine phosphorylase activity / L-methionine salvage from methylthioadenosine / regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / regulation of interleukin-6 production / nucleobase-containing compound metabolic process / purine ribonucleoside salvage / response to testosterone / 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 / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / 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 / negative regulation of neuron projection development / protein-folding chaperone binding / ER-Phagosome pathway / protein refolding / early endosome membrane / protein homotetramerization / methylation / adaptive immune response / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / 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 / nucleoplasm
Similarity search - Function
Methylthioadenosine phosphorylase (MTAP) / Purine phosphorylase, family 2, conserved site / Purine and other phosphorylases family 2 signature. / Nucleoside phosphorylase domain / Phosphorylase superfamily / Nucleoside phosphorylase 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 ...Methylthioadenosine phosphorylase (MTAP) / Purine phosphorylase, family 2, conserved site / Purine and other phosphorylases family 2 signature. / Nucleoside phosphorylase domain / Phosphorylase superfamily / Nucleoside phosphorylase 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 / S-methyl-5'-thioadenosine phosphorylase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 2, 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 / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Nov 6, 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-41 alpha chain
B: Beta-2-microglobulin
C: 11-mer peptide from S-methyl-5'-thioadenosine phosphorylase


Theoretical massNumber of molelcules
Total (without water)44,7763
Polymers44,7763
Non-polymers00
Water4,071226
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4380 Å2
ΔGint-15 kcal/mol
Surface area18910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.950, 82.120, 110.210
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: 31771.967 Da / Num. of mol.: 1 / Fragment: extracellular domains, UNP residues 25-298'
Source method: isolated from a genetically manipulated source
Details: B*4104 allele (W95L/R97S/V103L/N114D 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 11-mer peptide from S-methyl-5'-thioadenosine phosphorylase


Mass: 1255.377 Da / Num. of mol.: 1 / Fragment: UNP residues 227-237 / Source method: obtained synthetically / Details: Fmoc peptide synthesis / Source: (synth.) Homo sapiens (human) / References: UniProt: Q13126
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 226 / 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: 2.57 Å3/Da / Density % sol: 52.23 %
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: SSRL / Beamline: BL9-2 / Wavelength: 0.98133 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 22, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98133 Å / Relative weight: 1
ReflectionResolution: 1.9→55.1 Å / Num. all: 35909 / Num. obs: 35909 / % possible obs: 96.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 17.48 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 16.79
Reflection shellResolution: 1.9→2 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.455 / Mean I/σ(I) obs: 4.26 / Num. unique all: 4620 / % possible all: 88.9

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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: 1.9→34.044 Å / Occupancy max: 1 / Occupancy min: 0.01 / FOM work R set: 0.853 / SU ML: 0.25 / σ(F): 0.02 / Phase error: 21.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.241 3580 9.97 %RANDOM
Rwork0.1908 32322 --
obs0.1957 35902 96.53 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 27.162 Å2 / ksol: 0.325 e/Å3
Displacement parametersBiso max: 89.45 Å2 / Biso mean: 21.237 Å2 / Biso min: 5.35 Å2
Baniso -1Baniso -2Baniso -3
1--2.973 Å2-0 Å20 Å2
2---4.189 Å2-0 Å2
3---7.162 Å2
Refinement stepCycle: LAST / Resolution: 1.9→34.044 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3158 0 0 226 3384
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063300
X-RAY DIFFRACTIONf_angle_d1.0044485
X-RAY DIFFRACTIONf_dihedral_angle_d15.8231214
X-RAY DIFFRACTIONf_chiral_restr0.075459
X-RAY DIFFRACTIONf_plane_restr0.004595
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.9250.29681360.21051077X-RAY DIFFRACTION87
1.925-1.95140.25081390.20381116X-RAY DIFFRACTION89
1.9514-1.97930.27711130.20511144X-RAY DIFFRACTION89
1.9793-2.00880.28031440.19981122X-RAY DIFFRACTION92
2.0088-2.04020.24121220.19271240X-RAY DIFFRACTION95
2.0402-2.07360.25391410.18611198X-RAY DIFFRACTION97
2.0736-2.10940.24861380.18881248X-RAY DIFFRACTION97
2.1094-2.14770.22131210.19151272X-RAY DIFFRACTION98
2.1477-2.1890.26871380.17831240X-RAY DIFFRACTION98
2.189-2.23370.28181350.1921252X-RAY DIFFRACTION99
2.2337-2.28230.24431300.1861268X-RAY DIFFRACTION99
2.2823-2.33540.26231380.18631286X-RAY DIFFRACTION99
2.3354-2.39370.26591400.19861237X-RAY DIFFRACTION99
2.3937-2.45840.28511330.19251277X-RAY DIFFRACTION99
2.4584-2.53080.26181530.19341261X-RAY DIFFRACTION99
2.5308-2.61240.23641230.20061278X-RAY DIFFRACTION99
2.6124-2.70580.25041540.20321259X-RAY DIFFRACTION98
2.7058-2.8140.26481400.19831267X-RAY DIFFRACTION99
2.814-2.9420.27521290.2071270X-RAY DIFFRACTION98
2.942-3.09710.23361380.21031264X-RAY DIFFRACTION98
3.0971-3.2910.21911410.19371288X-RAY DIFFRACTION99
3.291-3.54480.22481380.18271279X-RAY DIFFRACTION99
3.5448-3.90110.23071530.16471294X-RAY DIFFRACTION98
3.9011-4.46450.17521380.13951277X-RAY DIFFRACTION97
4.4645-5.62070.16651610.14171282X-RAY DIFFRACTION97
5.6207-34.04920.21531440.20711326X-RAY DIFFRACTION93

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