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- PDB-6lbe: Crystal structure of bony fish MHC class I binding beta2M-2 for 2... -

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Basic information

Entry
Database: PDB / ID: 6lbe
TitleCrystal structure of bony fish MHC class I binding beta2M-2 for 2.6 angstrom
Components
  • 9-mer peptide from RNA-DIRECTED RNA POLYMERASE L
  • Beta-2-microglobulin
  • MHC class I antigen
KeywordsIMMUNE SYSTEM / Immunoglobulin-like / MHC class I / Peptide-binding protein / Antigen presentation
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 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 / : / Prokaryotic membrane lipoprotein lipid attachment site profile. / 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
Similarity search - Domain/homology
Beta-2-microglobulin / MHC class I antigen / RNA-directed RNA polymerase L
Similarity search - Component
Biological speciesCtenopharyngodon idella (grass carp)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsLi, Z.B. / Xia, C.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of ChinaGrant 31572653 China
CitationJournal: Iscience / Year: 2020
Title: The Mechanism of beta 2m Molecule-Induced Changes in the Peptide Presentation Profile in a Bony Fish.
Authors: Li, Z. / Zhang, N. / Ma, L. / Zhang, L. / Meng, G. / Xia, C.
History
DepositionNov 14, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 4, 2020Provider: 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 1.2Oct 9, 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: MHC class I antigen
B: Beta-2-microglobulin
C: MHC class I antigen
D: Beta-2-microglobulin
E: 9-mer peptide from RNA-DIRECTED RNA POLYMERASE L
F: 9-mer peptide from RNA-DIRECTED RNA POLYMERASE L


Theoretical massNumber of molelcules
Total (without water)87,8706
Polymers87,8706
Non-polymers00
Water3,045169
1
A: MHC class I antigen
B: Beta-2-microglobulin
E: 9-mer peptide from RNA-DIRECTED RNA POLYMERASE L


Theoretical massNumber of molelcules
Total (without water)43,9353
Polymers43,9353
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5200 Å2
ΔGint-32 kcal/mol
Surface area17910 Å2
MethodPISA
2
C: MHC class I antigen
D: Beta-2-microglobulin
F: 9-mer peptide from RNA-DIRECTED RNA POLYMERASE L


Theoretical massNumber of molelcules
Total (without water)43,9353
Polymers43,9353
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5020 Å2
ΔGint-32 kcal/mol
Surface area18030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.190, 65.270, 69.710
Angle α, β, γ (deg.)64.94, 75.67, 73.61
Int Tables number1
Space group name H-MP1

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Components

#1: Protein MHC class I antigen


Mass: 31449.723 Da / Num. of mol.: 2
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: 11395.793 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ctenopharyngodon idella (grass carp) / Gene: b2m-b / Production host: Escherichia coli (E. coli) / References: UniProt: A0A3G2VUI3
#3: Protein/peptide 9-mer peptide from RNA-DIRECTED RNA POLYMERASE L


Mass: 1089.393 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: UniProt: Q91DR9*PLUS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 169 / 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: 2.39 Å3/Da / Density % sol: 48.46 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M Ammonium sulfate, 0.1 M BIS-TRIS pH 6.5, 25% Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97892 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 24, 2018
RadiationMonochromator: LN2-cooled DCM with Si(111) crystals / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97892 Å / Relative weight: 1
ReflectionResolution: 2.03→62.459 Å / Num. obs: 20364 / % possible obs: 82.09 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.0134 / Rsym value: 0.08 / Net I/σ(I): 17.177
Reflection shellResolution: 2.03→2.03 Å / Num. unique obs: 20364 / CC1/2: 0.08

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5Y91

5y91


Resolution: 2.6→62.459 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 27.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2543 933 4.58 %
Rwork0.1692 --
obs0.1731 20356 82.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.6→62.459 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6104 0 0 169 6273
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086268
X-RAY DIFFRACTIONf_angle_d0.9338510
X-RAY DIFFRACTIONf_dihedral_angle_d9.0263681
X-RAY DIFFRACTIONf_chiral_restr0.051893
X-RAY DIFFRACTIONf_plane_restr0.0061109
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.73710.32661410.19852733X-RAY DIFFRACTION81
2.7371-2.90860.3231380.20762629X-RAY DIFFRACTION78
2.9086-3.13310.34261190.20062880X-RAY DIFFRACTION85
3.1331-3.44840.28391110.18642874X-RAY DIFFRACTION85
3.4484-3.94730.22411260.16012737X-RAY DIFFRACTION81
3.9473-4.97290.2151500.13472872X-RAY DIFFRACTION85
4.9729-62.4590.21161480.15892698X-RAY DIFFRACTION81

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