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- PDB-5gjy: Crystal structure of DUCK MHC CLASS I for 1.71 angstrom -

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Basic information

Entry
Database: PDB / ID: 5gjy
TitleCrystal structure of DUCK MHC CLASS I for 1.71 angstrom
Components
  • Beta-2-microglobulin
  • MET-VAL-MET-GLU-LEU-ILE-ARG-MET-ILE
  • MHC class I antigen
KeywordsIMMUNE SYSTEM / MHC / IMMUNOLOGY
Function / homology
Function and homology information


antigen processing and presentation of peptide antigen via MHC class I / helical viral capsid / lumenal side of endoplasmic reticulum membrane / MHC class I protein complex / viral penetration into host nucleus / phagocytic vesicle membrane / host cell / viral nucleocapsid / symbiont entry into host cell / ribonucleoprotein complex ...antigen processing and presentation of peptide antigen via MHC class I / helical viral capsid / lumenal side of endoplasmic reticulum membrane / MHC class I protein complex / viral penetration into host nucleus / phagocytic vesicle membrane / host cell / viral nucleocapsid / symbiont entry into host cell / ribonucleoprotein complex / host cell nucleus / structural molecule activity / RNA binding / extracellular region
Similarity search - Function
Influenza virus nucleoprotein (NP) / Influenza virus nucleoprotein / 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 / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein ...Influenza virus nucleoprotein (NP) / Influenza virus nucleoprotein / 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 / : / 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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Beta-2-microglobulin / MHC class I antigen / Nucleoprotein
Similarity search - Component
Biological speciesAnas platyrhynchos (mallard)
unidentified influenza virus
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.71 Å
AuthorsWu, Y. / Xia, C.
Funding support China, 2items
OrganizationGrant numberCountry
National Key Basic Research Program of ChinaNo.2013CB835302 China
National Natural Science Foundation of ChinaNo. 31572493 China
CitationJournal: To Be Published
Title: Structural Definition Of Duck MHC Class I Explains the Resistance to Influenza A virus
Authors: Wu, Y. / Xia, C.
History
DepositionJul 2, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 10, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 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
Revision 1.2Nov 20, 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: MET-VAL-MET-GLU-LEU-ILE-ARG-MET-ILE


Theoretical massNumber of molelcules
Total (without water)44,6843
Polymers44,6843
Non-polymers00
Water5,170287
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4730 Å2
ΔGint-21 kcal/mol
Surface area18280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.270, 64.390, 77.920
Angle α, β, γ (deg.)90.00, 105.74, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein MHC class I antigen


Mass: 31553.037 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 22-291
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anas platyrhynchos (mallard) / Gene: Du5MHC I / Production host: Escherichia coli (E. coli) / References: UniProt: Q6I7L2
#2: Protein Beta-2-microglobulin


Mass: 11994.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anas platyrhynchos (mallard) / Gene: b2m / Production host: Escherichia coli (E. coli) / References: UniProt: Q14U75
#3: Protein/peptide MET-VAL-MET-GLU-LEU-ILE-ARG-MET-ILE


Mass: 1136.514 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) unidentified influenza virus / References: UniProt: Q9Q0U8*PLUS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 287 / 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: 2.5 Å3/Da / Density % sol: 50.81 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 8% w/v Polyethylene glycol 1000, 8% w/v Polyethylene glycol 8000, 20% v/v Glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 0.97892 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 16, 2013
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97892 Å / Relative weight: 1
ReflectionResolution: 1.71→50 Å / Num. obs: 41752 / % possible obs: 96.2 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.063 / Rsym value: 0.063 / Net I/σ(I): 20.759
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.542 / Mean I/σ(I) obs: 2.667 / % possible all: 98.2

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Processing

Software
NameVersionClassification
PHENIX1.5_2refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
REFMAC5.8.0073refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4E0R

4e0r


Resolution: 1.71→50 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.951 / SU B: 4.119 / SU ML: 0.059 / Cross valid method: THROUGHOUT / ESU R: 0.157 / ESU R Free: 0.102
RfactorNum. reflection% reflectionSelection details
Rfree0.19739 2100 4.9 %RANDOM
Rwork0.1568 ---
obs0.15878 40154 89.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 33.273 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å2-0 Å2-0.81 Å2
2--0.23 Å2-0 Å2
3---0.17 Å2
Refinement stepCycle: 1 / Resolution: 1.71→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3034 0 0 287 3321
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0193119
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9311.9314233
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.655368
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.11823.558163
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.58815507
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6091526
X-RAY DIFFRACTIONr_chiral_restr0.1570.2437
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212435
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_it6.3322.9081487
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it7.1934.3511850
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it9.1253.3881632
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined9.55925.3795057
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr11.61833119
X-RAY DIFFRACTIONr_sphericity_free32.179596
X-RAY DIFFRACTIONr_sphericity_bonded25.71253225
LS refinement shellResolution: 1.71→1.754 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 108 -
Rwork0.282 2268 -
obs--68.04 %

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