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- PDB-5y91: The structure of the MHC class I molecule of bony fishes provides... -

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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 / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / virion component / MHC class I protein complex / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / host cell cytoplasm / immune response ...NNS virus cap methyltransferase / GDP polyribonucleotidyltransferase / negative stranded viral RNA replication / viral transcription / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / virion component / MHC class I protein complex / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / host cell cytoplasm / immune response / RNA-directed RNA polymerase / external side of plasma membrane / RNA-dependent 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 / Mononegavirales RNA-directed RNA polymerase catalytic domain / Mononegavirus L protein 2-O-ribose methyltransferase / Mononegavirales mRNA-capping domain V / RNA-directed RNA polymerase L, C-terminal / Mononegavirales RNA dependent RNA polymerase ...RNA-directed RNA polymerase, rhabdovirus / : / Virus-capping methyltransferase, connector domain / RNA-directed RNA polymerase L methyltransferase domain, rhabdovirus / Virus-capping methyltransferase, MT domain / Mononegavirales RNA-directed RNA polymerase catalytic domain / Mononegavirus L protein 2-O-ribose methyltransferase / Mononegavirales mRNA-capping domain V / RNA-directed RNA polymerase L, C-terminal / Mononegavirales RNA dependent RNA polymerase / Mononegavirales mRNA-capping region V / RdRp of negative ssRNA viruses with non-segmented genomes catalytic domain profile. / Mononegavirus L protein 2'-O-ribose methyltransferase 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 / Immunoglobulins / Immunoglobulin-like fold / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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

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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: 2.34 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

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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

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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

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