[English] 日本語
Yorodumi
- PDB-8jhv: The first crystal structure of a H-2Kb-restricted decapeptide fro... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8jhv
TitleThe first crystal structure of a H-2Kb-restricted decapeptide from Cryptosporidium parvum
Components
  • Beta-2-microglobulin
  • H-2 class I histocompatibility antigen, K-B alpha chain
  • VAL-THR-PHE-GLU-LYS-SER-TYR-ASN-THR-VAL
KeywordsIMMUNE SYSTEM / Cryptosporidium parvum / MHC I / T cell epitope / cell-mediated immunity
Function / homology
Function and homology information


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 / 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 ...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 / 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 / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / defense response to bacterium / external side of plasma membrane / structural molecule activity / Golgi apparatus / protein homodimerization activity / extracellular space / cytosol
Similarity search - Function
MHC class I, alpha chain, C-terminal / MHC_I C-terminus / 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 / : ...MHC class I, alpha chain, C-terminal / MHC_I C-terminus / 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
Similarity search - Domain/homology
Beta-2-microglobulin / H-2 class I histocompatibility antigen, K-B alpha chain
Similarity search - Component
Biological speciesMus musculus (house mouse)
Cryptosporidium parvum (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.47 Å
AuthorsFan, S. / Wang, Y. / Zhao, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)31702232 China
CitationJournal: To Be Published
Title: The first crystal structure of a H-2Kb-restricted decapeptide from Cryptosporidium parvum
Authors: Fan, S. / Wang, Y.
History
DepositionMay 25, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0May 29, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
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: VAL-THR-PHE-GLU-LYS-SER-TYR-ASN-THR-VAL
D: H-2 class I histocompatibility antigen, K-B alpha chain
E: Beta-2-microglobulin
F: VAL-THR-PHE-GLU-LYS-SER-TYR-ASN-THR-VAL


Theoretical massNumber of molelcules
Total (without water)89,5156
Polymers89,5156
Non-polymers00
Water00
1
A: H-2 class I histocompatibility antigen, K-B alpha chain
B: Beta-2-microglobulin
C: VAL-THR-PHE-GLU-LYS-SER-TYR-ASN-THR-VAL


Theoretical massNumber of molelcules
Total (without water)44,7573
Polymers44,7573
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4070 Å2
ΔGint-15 kcal/mol
Surface area20090 Å2
MethodPISA
2
D: H-2 class I histocompatibility antigen, K-B alpha chain
E: Beta-2-microglobulin
F: VAL-THR-PHE-GLU-LYS-SER-TYR-ASN-THR-VAL


Theoretical massNumber of molelcules
Total (without water)44,7573
Polymers44,7573
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4160 Å2
ΔGint-15 kcal/mol
Surface area19800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.380, 89.380, 296.370
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number153
Space group name H-MP3212

-
Components

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


Mass: 31777.438 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-K1, H2-K / Production host: Escherichia coli (E. coli) / References: UniProt: P01901
#2: Protein Beta-2-microglobulin


Mass: 11791.545 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: B2m / Production host: Escherichia coli (E. coli) / References: UniProt: P01887
#3: Protein/peptide VAL-THR-PHE-GLU-LYS-SER-TYR-ASN-THR-VAL


Mass: 1188.306 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cryptosporidium parvum (eukaryote) / Production host: Synthecium (invertebrata)
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.82 Å3/Da / Density % sol: 67.78 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 20%(w/v) Polyethylene glycol 3350; 0.2M Lithium acetate dihydrate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 20, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 3.47→47.16 Å / Num. obs: 18018 / % possible obs: 99.9 % / Redundancy: 20 % / CC1/2: 0.999 / Net I/σ(I): 11.3
Reflection shellResolution: 3.47→3.8 Å / Num. unique obs: 4242 / CC1/2: 0.875

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.47→47.105 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.854 / SU B: 1.7 / SU ML: 0 / Cross valid method: NONE / ESU R: 0.529 / ESU R Free: 0.659
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.29678 894 4.975 %
Rwork0.23039 17075 -
all0.25 --
obs-17969 99.889 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 42.986 Å2
Baniso -1Baniso -2Baniso -3
1-0.135 Å20.067 Å2-0 Å2
2--0.135 Å20 Å2
3----0.438 Å2
Refinement stepCycle: LAST / Resolution: 3.47→47.105 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6282 0 0 0 6282
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.47-3.560.32660.3141249X-RAY DIFFRACTION99.3953
3.56-3.6570.329410.3261220X-RAY DIFFRACTION100
3.657-3.7630.417550.3431203X-RAY DIFFRACTION100
3.763-3.8790.263550.251174X-RAY DIFFRACTION100
3.879-4.0060.241650.2021072X-RAY DIFFRACTION99.9121
4.006-4.1460.211580.1891090X-RAY DIFFRACTION99.8261
4.146-4.3020.205650.2041039X-RAY DIFFRACTION100
4.302-4.4780.214460.2121013X-RAY DIFFRACTION100
4.478-4.6770.215550.201961X-RAY DIFFRACTION100
4.677-4.9040.218640.213899X-RAY DIFFRACTION100
4.904-5.1690.31500.23879X-RAY DIFFRACTION100
5.169-5.4810.419480.254822X-RAY DIFFRACTION100
5.481-5.8590.503280.292798X-RAY DIFFRACTION100
5.859-6.3260.432350.298754X-RAY DIFFRACTION100
6.326-6.9270.348520.258661X-RAY DIFFRACTION100
6.927-7.740.32190.246636X-RAY DIFFRACTION100
7.74-7.9280.315320.21553X-RAY DIFFRACTION100
7.928-8.9280.238220.198466X-RAY DIFFRACTION100
7.991-9.8860.365180.221379X-RAY DIFFRACTION100
8-100.48200.478207X-RAY DIFFRACTION96.1864

+
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