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- PDB-6kvm: Crystal structure of Chicken MHC Class II for 1.9 angstrom -

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Basic information

Entry
Database: PDB / ID: 6kvm
TitleCrystal structure of Chicken MHC Class II for 1.9 angstrom
Components
  • MHC class II alpha chain
  • MHC class II beta chain 2
  • peptide from 60S ribosomal protein L30
KeywordsIMMUNE SYSTEM / Complex crystal structure MHC class II chicken evolution
Function / homology
Function and homology information


: / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / antigen processing and presentation / MHC class II protein complex / antimicrobial humoral immune response mediated by antimicrobial peptide / defense response to Gram-negative bacterium / adaptive immune response / killing of cells of another organism / cytosolic large ribosomal subunit / membrane => GO:0016020 ...: / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / antigen processing and presentation / MHC class II protein complex / antimicrobial humoral immune response mediated by antimicrobial peptide / defense response to Gram-negative bacterium / adaptive immune response / killing of cells of another organism / cytosolic large ribosomal subunit / membrane => GO:0016020 / cytoplasmic translation / postsynaptic density / structural constituent of ribosome / immune response / RNA binding / nucleus / metal ion binding
Similarity search - Function
Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / MHC class II, beta chain, N-terminal / Class II histocompatibility antigen, beta domain / Class II histocompatibility antigen, beta domain / MHC class II, alpha chain, N-terminal / Class II histocompatibility antigen, alpha domain / Class II histocompatibility antigen, alpha domain / MHC class II, alpha/beta chain, N-terminal / Ribosomal protein L30e ...Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / MHC class II, beta chain, N-terminal / Class II histocompatibility antigen, beta domain / Class II histocompatibility antigen, beta domain / MHC class II, alpha chain, N-terminal / Class II histocompatibility antigen, alpha domain / Class II histocompatibility antigen, alpha domain / MHC class II, alpha/beta chain, N-terminal / Ribosomal protein L30e / Ribosomal protein L30e signature 1. / Ribosomal protein L30e signature 2. / Ribosomal protein L30e, conserved site / Ribosomal protein L30/YlxQ / Ribosomal protein L7Ae/L30e/S12e/Gadd45 / Ribosomal protein L7Ae/L30e/S12e/Gadd45 family / 50S ribosomal protein L30e-like / 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 / Immunoglobulins / Roll / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
60S ribosomal protein L30 / MHC class II alpha chain / MHC class II beta chain
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.897 Å
AuthorsZhang, L. / Xia, C.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)No.31972683 China
National Natural Science Foundation of China (NSFC)No.31572493 China
CitationJournal: J Immunol. / Year: 2020
Title: A Newly Recognized Pairing Mechanism of the alpha- and beta-Chains of the Chicken Peptide-MHC Class II Complex.
Authors: Zhang, L. / Li, X. / Ma, L. / Zhang, B. / Meng, G. / Xia, C.
History
DepositionSep 4, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 25, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 8, 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 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

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Assembly

Deposited unit
A: MHC class II alpha chain
B: MHC class II beta chain 2
C: peptide from 60S ribosomal protein L30
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2244
Polymers48,1313
Non-polymers921
Water3,783210
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation, gel filtration, native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7950 Å2
ΔGint-42 kcal/mol
Surface area18370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)152.397, 57.297, 58.057
Angle α, β, γ (deg.)90.000, 110.676, 90.000
Int Tables number5
Space group name H-MC121
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-305-

HOH

21B-256-

HOH

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Components

#1: Protein MHC class II alpha chain / MHC class II antigen alpha chain


Mass: 22125.748 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: B-LA / Production host: Escherichia coli (E. coli) / References: UniProt: Q4U5Z6
#2: Protein MHC class II beta chain 2


Mass: 24113.691 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: B-LB, BLB2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q4U600
#3: Protein/peptide peptide from 60S ribosomal protein L30


Mass: 1892.051 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: RPL30 / Production host: Escherichia coli (E. coli) / References: UniProt: P67883
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 210 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.58 Å3/Da / Density % sol: 52.28 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 30% PEG 4000, 100mM Tris base/Hydrochloric acid pH 8.5, 200mM Lithium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97915 Å
DetectorType: Nonius Kappa CCD / Detector: CCD / Date: Jun 20, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.897→71.29 Å / Num. obs: 37303 / % possible obs: 99.9 % / Redundancy: 7.4 % / CC1/2: 0.997 / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.042 / Rrim(I) all: 0.113 / Net I/σ(I): 15.1
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 7.1 % / Mean I/σ(I) obs: 3.5 / Num. unique all: 2737 / Rpim(I) all: 0.274 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AQD

1aqd


Resolution: 1.897→54.377 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.923 / SU ML: 0 / Cross valid method: THROUGHOUT / ESU R: 0.121 / ESU R Free: 0.135
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2274 1793 4.853 %RANDOM
Rwork0.2028 ---
all0.204 ---
obs-36949 99.072 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 29.683 Å2
Baniso -1Baniso -2Baniso -3
1-2.879 Å2-0 Å21.089 Å2
2---2.067 Å20 Å2
3----1.272 Å2
Refinement stepCycle: LAST / Resolution: 1.897→54.377 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3101 0 6 210 3317
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.897-1.9460.2651510.2532525X-RAY DIFFRACTION97.593
1.946-20.2511080.2312445X-RAY DIFFRACTION96.5948
2-2.0570.2681080.2342357X-RAY DIFFRACTION95.027
2.057-2.1210.2451180.2142409X-RAY DIFFRACTION99.4882
2.121-2.190.2371390.2052311X-RAY DIFFRACTION99.634
2.19-2.2670.2391440.2022217X-RAY DIFFRACTION99.7465
2.267-2.3520.244810.2062181X-RAY DIFFRACTION99.5599
2.352-2.4480.2481380.2132056X-RAY DIFFRACTION99.7726
2.448-2.5570.2581080.2132001X-RAY DIFFRACTION99.8107
2.557-2.6820.2351070.2151917X-RAY DIFFRACTION99.852
2.682-2.8270.25780.2121828X-RAY DIFFRACTION99.9476
2.827-2.9980.194480.1921781X-RAY DIFFRACTION99.7274
2.998-3.2040.248730.2041654X-RAY DIFFRACTION99.9421
3.204-3.4610.206620.1981539X-RAY DIFFRACTION100
3.461-3.790.233850.1831388X-RAY DIFFRACTION100
3.79-4.2360.189750.1731256X-RAY DIFFRACTION100
4.236-4.8880.161570.151136X-RAY DIFFRACTION100
4.888-5.980.234460.202961X-RAY DIFFRACTION100
5.98-8.4270.228360.226757X-RAY DIFFRACTION100

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