[English] 日本語
Yorodumi
- PDB-3p4n: Crystal Structure of H2-Kb in complex with the NP205-PV epitope Y... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3p4n
TitleCrystal Structure of H2-Kb in complex with the NP205-PV epitope YTVKFPNM, an 8-mer peptide from PV
Components
  • Beta-2-microglobulin
  • H-2 class I histocompatibility antigen, K-B alpha chain
  • NP205-PV epitope, YTVKFPNM
KeywordsIMMUNE SYSTEM / H2-Kb / PV / LCMV / TCR / T cell / MHC / viral escape
Function / homology
Function and homology information


symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IKBKE activity / RNA-templated viral transcription / negative stranded viral RNA replication / Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / helical viral capsid ...symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IKBKE activity / RNA-templated viral transcription / negative stranded viral RNA replication / Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / helical viral capsid / antigen processing and presentation of exogenous peptide antigen via MHC class I / inner ear development / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / cellular defense response / Neutrophil degranulation / lumenal side of endoplasmic reticulum membrane / cellular response to iron(III) ion / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / iron ion transport / 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 / T cell mediated cytotoxicity / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / MHC class I protein complex / 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 / phagocytic vesicle membrane / negative regulation of epithelial cell proliferation / sensory perception of smell / positive regulation of cellular senescence / T cell differentiation in thymus / negative regulation of neuron projection development / protein refolding / viral nucleocapsid / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / host cell cytoplasm / learning or memory / hydrolase activity / defense response to bacterium / ribonucleoprotein complex / external side of plasma membrane / structural molecule activity / Golgi apparatus / protein homodimerization activity / extracellular space / RNA binding / metal ion binding / cytosol
Similarity search - Function
Nucleocapsid protein, arenaviridae / Nucleocapsid, N-terminal, Arenaviridae / Nucleocapsid, C-terminal, Arenaviridae / Nucleocapsid, C-terminal superfamily / Arenavirus nucleocapsid N-terminal domain / Arenavirus nucleocapsid C-terminal domain / 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 ...Nucleocapsid protein, arenaviridae / Nucleocapsid, N-terminal, Arenaviridae / Nucleocapsid, C-terminal, Arenaviridae / Nucleocapsid, C-terminal superfamily / Arenavirus nucleocapsid N-terminal domain / Arenavirus nucleocapsid C-terminal domain / 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
ACETYL GROUP / Beta-2-microglobulin / H-2 class I histocompatibility antigen, K-B alpha chain / Nucleoprotein
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsGras, S. / Guillonneau, C. / Rossjohn, J.
CitationJournal: To be Published
Title: Crystal Structure of H2-Kb in complex with the NP205-PV epitope YTVKFPNM, an 8-mer peptide from PV
Authors: Gras, S. / Guillonneau, C. / Rossjohn, J.
History
DepositionOct 6, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 12, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: H-2 class I histocompatibility antigen, K-B alpha chain
B: Beta-2-microglobulin
C: NP205-PV epitope, YTVKFPNM
D: H-2 class I histocompatibility antigen, K-B alpha chain
E: Beta-2-microglobulin
F: NP205-PV epitope, YTVKFPNM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,7038
Polymers89,6156
Non-polymers882
Water3,423190
1
A: H-2 class I histocompatibility antigen, K-B alpha chain
B: Beta-2-microglobulin
F: NP205-PV epitope, YTVKFPNM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,8514
Polymers44,8073
Non-polymers441
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4240 Å2
ΔGint-19 kcal/mol
Surface area19440 Å2
MethodPISA
2
C: NP205-PV epitope, YTVKFPNM
D: H-2 class I histocompatibility antigen, K-B alpha chain
E: Beta-2-microglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,8514
Polymers44,8073
Non-polymers441
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4180 Å2
ΔGint-18 kcal/mol
Surface area19390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.190, 90.600, 89.160
Angle α, β, γ (deg.)90.000, 111.110, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein H-2 class I histocompatibility antigen, K-B alpha chain / H-2K(B)


Mass: 32102.855 Da / Num. of mol.: 2 / Fragment: Extracellular domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-K1, H2-K / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P01901
#2: Protein Beta-2-microglobulin


Mass: 11704.359 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: B2m / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P01887
#3: Protein/peptide NP205-PV epitope, YTVKFPNM


Mass: 1000.191 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Synthetic peptide / References: UniProt: P03541
#4: Chemical ChemComp-ACE / ACETYL GROUP


Mass: 44.053 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 190 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.78 Å3/Da / Density % sol: 55.8 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2M ammonium acetate, 16-24% PEG 3350, 0.1M Na-cacodylate, pH 6.5, vapor diffusion, hanging drop, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jul 20, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.5→100 Å / Num. obs: 32752 / % possible obs: 95.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 30.537 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 10.76
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.5-2.60.3560.2223.66656376236470.29696.9
2.6-2.70.3180.194.35638322531140.25396.6
2.7-2.80.3130.1744.74931278526900.23296.6
2.8-2.90.2830.1475.44227242923430.19796.5
2.9-30.2430.1296.53673209820100.17395.8
3-40.110.06611.42003411400109860.08896.4
4-60.0470.03619.610527592756790.04895.8
6-100.0420.0320.63482198018450.0493.2
100.0240.02128.48255614380.02778.1

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
PHENIX1.6.1_357refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1vac

1vac


Resolution: 2.5→19.917 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.44 / σ(F): 0.03 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.3077 3166 9.97 %
Rwork0.2428 --
obs0.2493 31750 93.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 22.379 Å2 / ksol: 0.322 e/Å3
Displacement parametersBiso max: 97.74 Å2 / Biso mean: 27.3663 Å2 / Biso min: 8.29 Å2
Baniso -1Baniso -2Baniso -3
1--7.6989 Å20 Å2-0.745 Å2
2--13.9897 Å20 Å2
3----6.2908 Å2
Refinement stepCycle: LAST / Resolution: 2.5→19.917 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6298 0 6 190 6494
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086490
X-RAY DIFFRACTIONf_angle_d1.178804
X-RAY DIFFRACTIONf_chiral_restr0.078903
X-RAY DIFFRACTIONf_plane_restr0.0051147
X-RAY DIFFRACTIONf_dihedral_angle_d16.5172414
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5-2.58920.39833160.31262837315393
2.5892-2.69260.38323010.28942784308592
2.6926-2.81480.3523300.27832764309491
2.8148-2.96280.35242840.27162759304390
2.9628-3.14770.34773010.26332758305990
3.1477-3.38970.3213270.26242852317994
3.3897-3.72880.30713250.23573000332597
3.7288-4.26380.26223370.20572940327796
4.2638-5.35450.23253230.18012973329696
5.3545-19.91710.24983220.19922917323993

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more