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- PDB-4o2c: An Nt-acetylated peptide complexed with HLA-B*3901 -

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Basic information

Entry
Database: PDB / ID: 4o2c
TitleAn Nt-acetylated peptide complexed with HLA-B*3901
Components
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, B-39 alpha chain
  • Peptide from ATP-dependent RNA helicase DDX3X
KeywordsIMMUNE SYSTEM / Ig-like
Function / homology
Function and homology information


CTPase activity / positive regulation of toll-like receptor 8 signaling pathway / positive regulation of toll-like receptor 7 signaling pathway / positive regulation of translation in response to endoplasmic reticulum stress / protein localization to cytoplasmic stress granule / eukaryotic initiation factor 4E binding / RNA strand annealing activity / positive regulation of chemokine (C-C motif) ligand 5 production / positive regulation of mitochondrial translation / gamete generation ...CTPase activity / positive regulation of toll-like receptor 8 signaling pathway / positive regulation of toll-like receptor 7 signaling pathway / positive regulation of translation in response to endoplasmic reticulum stress / protein localization to cytoplasmic stress granule / eukaryotic initiation factor 4E binding / RNA strand annealing activity / positive regulation of chemokine (C-C motif) ligand 5 production / positive regulation of mitochondrial translation / gamete generation / positive regulation of protein K63-linked ubiquitination / NLRP3 inflammasome complex / cellular response to arsenic-containing substance / poly(A) binding / regulation of interleukin-12 production / regulation of dendritic cell differentiation / gamma-tubulin binding / regulation of T cell anergy / P granule / cellular response to osmotic stress / regulation of interleukin-6 production / negative regulation of non-canonical NF-kappaB signal transduction / cytoplasmic pattern recognition receptor signaling pathway / transcription factor binding / positive regulation of NLRP3 inflammasome complex assembly / negative regulation of intrinsic apoptotic signaling pathway / lipid homeostasis / cell leading edge / TAP binding / positive regulation of interferon-alpha production / protection from natural killer cell mediated cytotoxicity / positive regulation of translational initiation / ribosomal small subunit binding / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / extrinsic apoptotic signaling pathway via death domain receptors / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / positive regulation of type I interferon production / positive regulation of G1/S transition of mitotic cell cycle / detection of bacterium / negative regulation of protein-containing complex assembly / positive regulation of viral genome replication / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / translation initiation factor binding / signaling adaptor activity / stress granule assembly / intrinsic apoptotic signaling pathway / DNA helicase activity / positive regulation of interferon-beta production / ribonucleoside triphosphate phosphatase activity / secretory granule membrane / negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / positive regulation of translation / DAP12 interactions / protein serine/threonine kinase activator activity / transferrin transport / cytosolic ribosome assembly / cellular response to iron ion / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / chromosome segregation / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide antigen assembly with MHC class II protein complex / translational initiation / 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 / positive regulation of non-canonical NF-kappaB signal transduction / HFE-transferrin receptor complex / response to molecule of bacterial origin / MHC class I peptide loading complex / defense response / negative regulation of cell growth / 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 / cellular response to virus / peptide antigen binding / mRNA 5'-UTR 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 / response to virus / RNA stem-loop binding / specific granule lumen / Wnt signaling pathway / phagocytic vesicle membrane / recycling endosome membrane
Similarity search - Function
DEAD-box subfamily ATP-dependent helicases signature. / ATP-dependent RNA helicase DEAD-box, conserved site / RNA helicase, DEAD-box type, Q motif / DEAD-box RNA helicase Q motif profile. / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 ...DEAD-box subfamily ATP-dependent helicases signature. / ATP-dependent RNA helicase DEAD-box, conserved site / RNA helicase, DEAD-box type, Q motif / DEAD-box RNA helicase Q motif profile. / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / 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 / Helicase conserved C-terminal domain / MHC classes I/II-like antigen recognition protein / : / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / helicase superfamily c-terminal domain / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ATP-dependent RNA helicase DDX3X / 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: 1.802 Å
AuthorsSun, M. / Liu, J. / Qi, J. / Tefsen, B. / Shi, Y. / Yan, J. / Gao, G.F.
CitationJournal: J.Immunol. / Year: 2014
Title: N alpha-terminal acetylation for T cell recognition: molecular basis of MHC class I-restricted n alpha-acetylpeptide presentation
Authors: Sun, M. / Liu, J. / Qi, J. / Tefsen, B. / Shi, Y. / Yan, J. / Gao, G.F.
History
DepositionDec 17, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 23, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.2Nov 20, 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-39 alpha chain
B: Beta-2-microglobulin
C: Peptide from ATP-dependent RNA helicase DDX3X


Theoretical massNumber of molelcules
Total (without water)44,4293
Polymers44,4293
Non-polymers00
Water8,917495
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4400 Å2
ΔGint-20 kcal/mol
Surface area18830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.845, 81.459, 110.958
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-39 alpha chain / MHC class I antigen B*39


Mass: 31714.873 Da / Num. of mol.: 1 / Fragment: UNP residues 25-298
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: P30475, 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
#3: Protein/peptide Peptide from ATP-dependent RNA helicase DDX3X / DEAD box protein 3 / X-chromosomal / DEAD box / X isoform / Helicase-like protein 2 / HLP2


Mass: 966.069 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: O00571
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 495 / 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: 2.59 Å3/Da / Density % sol: 52.43 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M ammonium acetate, 0.1M Bis-Tris (pH 6.5), 17% (w/v) PEG 10000, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97916 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 13, 2010
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97916 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 41844 / Num. obs: 41844 / % possible obs: 99.6 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Biso Wilson estimate: 12.72 Å2
Reflection shellResolution: 1.8→1.86 Å / % possible all: 99.2

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.5_2)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BST

2bst


Resolution: 1.802→30.559 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8914 / SU ML: 0.16 / σ(F): 0.1 / Phase error: 17.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2015 2108 5.04 %Random
Rwork0.1745 ---
obs0.1759 41844 96.52 %-
all-41844 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 31.197 Å2 / ksol: 0.36 e/Å3
Displacement parametersBiso max: 82.59 Å2 / Biso mean: 18.7783 Å2 / Biso min: 1.89 Å2
Baniso -1Baniso -2Baniso -3
1--1.8117 Å2-0 Å20 Å2
2---2.8194 Å2-0 Å2
3---4.6311 Å2
Refinement stepCycle: LAST / Resolution: 1.802→30.559 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3134 0 0 495 3629
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023221
X-RAY DIFFRACTIONf_angle_d0.7014369
X-RAY DIFFRACTIONf_dihedral_angle_d16.9651169
X-RAY DIFFRACTIONf_chiral_restr0.053450
X-RAY DIFFRACTIONf_plane_restr0.002578
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.802-1.84390.22411250.17922322244787
1.8439-1.890.211490.17362507265692
1.89-1.94110.17741310.17362490262192
1.9411-1.99820.21891430.172560270395
1.9982-2.06270.23771410.16792605274696
2.0627-2.13640.21631470.17192618276597
2.1364-2.22190.24731180.16722673279197
2.2219-2.3230.20861390.17212665280498
2.323-2.44540.19781440.1772665280998
2.4454-2.59850.21271310.18052688281998
2.5985-2.79910.18071350.18172716285199
2.7991-3.08050.19491380.18222745288399
3.0805-3.52570.20431570.163527542911100
3.5257-4.43980.17061620.153227912953100
4.4398-30.56310.18561480.18512937308599
Refinement TLS params.Method: refined / Origin x: 12.3268 Å / Origin y: 9.0104 Å / Origin z: 18.62 Å
111213212223313233
T0.0195 Å20.0011 Å2-0.0068 Å2-0.0045 Å20.0005 Å2--0.0158 Å2
L0.5318 °20.0435 °2-0.1374 °2-0.2733 °2-0.003 °2--0.3764 °2
S0.0005 Å °0.0103 Å °-0.0503 Å °-0.019 Å °-0.009 Å °0.0083 Å °0.0028 Å °0.0142 Å °-0 Å °
Refinement TLS groupSelection details: ALL

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