[English] 日本語
Yorodumi
- PDB-5y91: The structure of the MHC class I molecule of bony fishes provides... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5y91
TitleThe structure of the MHC class I molecule of bony fishes provides insights into the conserved nature of the antigen-presenting system
Components
  • Beta-2-microglobulin
  • MHC class I antigen
  • PEPTIDE PHE-ALA-ASN-PHE-CYS-LEU-MET-MET-ILE
KeywordsIMMUNE SYSTEM / Fish / MHC class I / Evolution
Function / homology
Function and homology information


NNS virus cap methyltransferase / GDP polyribonucleotidyltransferase / negative stranded viral RNA replication / viral transcription / antigen processing and presentation of peptide antigen via MHC class I / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / MHC class I protein complex / virion component / host cell cytoplasm / mRNA 5'-cap (guanine-N7-)-methyltransferase activity ...NNS virus cap methyltransferase / GDP polyribonucleotidyltransferase / negative stranded viral RNA replication / viral transcription / antigen processing and presentation of peptide antigen via MHC class I / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / MHC class I protein complex / virion component / host cell cytoplasm / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / immune response / external side of plasma membrane / RNA-directed RNA polymerase / RNA-directed RNA polymerase activity / GTPase activity / extracellular space / extracellular region / ATP binding
Similarity search - Function
RNA-directed RNA polymerase, rhabdovirus / : / Virus-capping methyltransferase, connector domain / RNA-directed RNA polymerase L methyltransferase domain, rhabdovirus / Virus-capping methyltransferase, MT domain / Mononegavirus L protein 2-O-ribose methyltransferase / RNA-directed RNA polymerase L, C-terminal / Mononegavirus L protein 2'-O-ribose methyltransferase domain profile. / Mononegavirales RNA-directed RNA polymerase catalytic domain / Mononegavirales mRNA-capping domain V ...RNA-directed RNA polymerase, rhabdovirus / : / Virus-capping methyltransferase, connector domain / RNA-directed RNA polymerase L methyltransferase domain, rhabdovirus / Virus-capping methyltransferase, MT domain / Mononegavirus L protein 2-O-ribose methyltransferase / RNA-directed RNA polymerase L, C-terminal / Mononegavirus L protein 2'-O-ribose methyltransferase domain profile. / Mononegavirales RNA-directed RNA polymerase catalytic domain / Mononegavirales mRNA-capping domain V / Mononegavirales RNA dependent RNA polymerase / Mononegavirales mRNA-capping region V / RdRp of negative ssRNA viruses with non-segmented genomes catalytic domain profile. / 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 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
MHC class I antigen / Beta-2-microglobulin / RNA-directed RNA polymerase L
Similarity search - Component
Biological speciesCtenopharyngodon idella (grass carp)
Spring viraemia of carp virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.901 Å
AuthorsZhaosan, C. / Nianzhi, Z. / Chun, X.
CitationJournal: To Be Published
Title: Crystal structure of bony fish MHC class I complex at 1.9 Angstroms resolution.
Authors: Zhaosan, C. / Nianzhi, Z. / Chun, X.
History
DepositionAug 22, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 20, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: MHC class I antigen
B: Beta-2-microglobulin
C: PEPTIDE PHE-ALA-ASN-PHE-CYS-LEU-MET-MET-ILE


Theoretical massNumber of molelcules
Total (without water)45,7543
Polymers45,7543
Non-polymers00
Water6,161342
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5240 Å2
ΔGint-31 kcal/mol
Surface area18160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.280, 50.413, 86.077
Angle α, β, γ (deg.)90.00, 124.08, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-173-

HOH

-
Components

#1: Protein MHC class I antigen


Mass: 31449.723 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 17-291
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ctenopharyngodon idella (grass carp) / Gene: UAA106 / Production host: Escherichia coli (E. coli) / References: UniProt: Q65XY8
#2: Protein Beta-2-microglobulin


Mass: 13215.154 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ctenopharyngodon idella (grass carp) / Gene: B2m / Production host: Escherichia coli (E. coli) / References: UniProt: Q65XZ7
#3: Protein/peptide PEPTIDE PHE-ALA-ASN-PHE-CYS-LEU-MET-MET-ILE


Mass: 1089.393 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Spring viraemia of carp virus / Production host: Escherichia coli (E. coli) / References: UniProt: Q91DR9*PLUS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 342 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.34 Å3/Da / Density % sol: 47.49 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2 M ammonium citrate tribasic, pH 7.0 and 20% w/v polyethylene glycol 3,350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97931 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 19, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 31840 / % possible obs: 99 % / Redundancy: 3.2 % / Net I/σ(I): 17.711

-
Processing

Software
NameVersionClassification
PHENIX1.5_2refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2YEZ

2yez


Resolution: 1.901→32.883 Å / SU ML: 0.25 / Cross valid method: NONE / σ(F): 0.1 / Phase error: 21.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2235 1622 5.09 %
Rwork0.1902 --
obs0.1918 31840 94.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.917 Å2 / ksol: 0.35 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.142 Å20 Å2-0.6788 Å2
2--4.0645 Å2-0 Å2
3----2.9225 Å2
Refinement stepCycle: LAST / Resolution: 1.901→32.883 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3053 0 0 342 3395
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033140
X-RAY DIFFRACTIONf_angle_d0.7654252
X-RAY DIFFRACTIONf_dihedral_angle_d17.9661122
X-RAY DIFFRACTIONf_chiral_restr0.059448
X-RAY DIFFRACTIONf_plane_restr0.003552
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9005-1.95640.29921180.23492137X-RAY DIFFRACTION81
1.9564-2.01960.27461290.20512339X-RAY DIFFRACTION89
2.0196-2.09170.23841250.20392434X-RAY DIFFRACTION92
2.0917-2.17550.24441300.1942467X-RAY DIFFRACTION94
2.1755-2.27450.24811400.19652485X-RAY DIFFRACTION95
2.2745-2.39430.24221350.20632575X-RAY DIFFRACTION96
2.3943-2.54430.26891450.20572525X-RAY DIFFRACTION96
2.5443-2.74070.25871360.20512583X-RAY DIFFRACTION97
2.7407-3.01630.24181330.20662615X-RAY DIFFRACTION98
3.0163-3.45230.23511450.19712650X-RAY DIFFRACTION99
3.4523-4.3480.1871410.15732676X-RAY DIFFRACTION99
4.348-32.88790.16831450.17262732X-RAY DIFFRACTION99

+
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