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- PDB-5h5z: Crystal structure of bony fish MHC class I, peptide and B2m II -

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Basic information

Entry
Database: PDB / ID: 5h5z
TitleCrystal structure of bony fish MHC class I, peptide and B2m II
Components
  • Beta-2-microglobulinBeta-2 microglobulin
  • MHC class I antigen
  • peptide chain
KeywordsPEPTIDE BINDING PROTEIN/IMMUNE SYSTEM / MHC / IMMUNOLOGY / IMMUNE SYSTEM-TRANSRERASE COMPLEX / PEPTIDE BINDING PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


NNS virus cap methyltransferase / GDP polyribonucleotidyltransferase / negative stranded viral RNA replication / antigen processing and presentation of peptide antigen via MHC class I / 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 ...NNS virus cap methyltransferase / GDP polyribonucleotidyltransferase / negative stranded viral RNA replication / antigen processing and presentation of peptide antigen via MHC class I / 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 / RNA-dependent RNA polymerase activity / GTPase activity / extracellular region / ATP binding / membrane
Similarity search - Function
: / Virus-capping methyltransferase, connector domain / RNA-directed RNA polymerase, rhabdovirus / 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 ...: / Virus-capping methyltransferase, connector domain / RNA-directed RNA polymerase, rhabdovirus / 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 / MOLECULAR REPLACEMENT / Resolution: 1.74 Å
AuthorsChen, Z. / Zhang, N. / Qi, J. / Li, X. / Chen, R. / Wang, Z. / Gao, F.G. / Xia, C.
Funding support China, 2items
OrganizationGrant numberCountry
the State Key Program of the National Natural Science Foundation of China31230074 China
the 973 Project of the China Ministry of Science and Technology2013CB835302 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 10, 2016Deposition site: PDBJ / Processing site: PDBJ
SupersessionNov 22, 2017ID: 5CNZ
Revision 1.0Nov 22, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 4, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 8, 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 chain


Theoretical massNumber of molelcules
Total (without water)43,8553
Polymers43,8553
Non-polymers00
Water6,323351
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5230 Å2
ΔGint-34 kcal/mol
Surface area18350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.350, 50.650, 90.310
Angle α, β, γ (deg.)90.00, 129.37, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein MHC class I antigen


Mass: 31449.723 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 17-291 / Mutation: E45K
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 / Beta-2 microglobulin


Mass: 11315.831 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: Q6L7B0
#3: Protein/peptide peptide chain


Mass: 1089.393 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Spring viraemia of carp virus / References: UniProt: Q91DR9*PLUS
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 351 / 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: 2.41 Å3/Da / Density % sol: 48.88 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Sodium citrate tribasic dihydrate, 20% w/v Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 0.9792 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jan 1, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.74→50 Å / Num. obs: 42201 / % possible obs: 98.5 % / Redundancy: 3.6 % / Net I/σ(I): 17.5
Reflection shellResolution: 1.74→1.79 Å / Mean I/σ(I) obs: 3 / % possible all: 98.3

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
REFMAC5.8.0071refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4E0R

4e0r


Resolution: 1.74→50 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.949 / SU B: 6.272 / SU ML: 0.088 / Cross valid method: NONE / ESU R: 0.186 / ESU R Free: 0.106
RfactorNum. reflection% reflectionSelection details
Rfree0.20449 2140 5 %RANDOM
Rwork0.17101 ---
obs0.17266 40283 98.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 32.855 Å2
Baniso -1Baniso -2Baniso -3
1-1.28 Å20 Å21.16 Å2
2---6.58 Å2-0 Å2
3---1.45 Å2
Refinement stepCycle: 1 / Resolution: 1.74→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3083 0 0 351 3434
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0193185
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0481.9284324
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6165387
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.60625.404161
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.615543
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.829159
X-RAY DIFFRACTIONr_chiral_restr0.0770.2455
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0212465
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.2932.6831539
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.3134.0231923
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.2813.0721645
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined5.48224.3575250
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr1.8533184
X-RAY DIFFRACTIONr_sphericity_free23.329592
X-RAY DIFFRACTIONr_sphericity_bonded30.54153360
LS refinement shellResolution: 1.74→1.785 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 168 -
Rwork0.242 2945 -
obs--98.29 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.12360.01250.03310.00770.00140.03780.0062-0.0005-0.00040.0029-0.005-0.00020.0047-0.0108-0.00120.0247-0.0014-0.00810.0448-0.00070.004823.31641.217712.2796
20.40830.18820.33980.17010.21810.36630.00130.00270.0226-0.0081-0.02120.0118-0.0185-0.05980.020.02230.0055-0.00550.07070.00330.00328.024914.121223.42
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 276
2X-RAY DIFFRACTION2B1 - 98

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