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- PDB-5gjx: Crystal structure of DUCK MHC I for 2.06 angstrom -

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Basic information

Entry
Database: PDB / ID: 5gjx
TitleCrystal structure of DUCK MHC I for 2.06 angstrom
Components
  • ARG-LEU-ILE-GLN-ASN-SER-ILE-THR-ILE
  • Beta-2-microglobulin
  • MHC class I antigen
KeywordsIMMUNE SYSTEM / MHC / IMMUNOLOGY
Function / homology
Function and homology information


response to metal ion / helical viral capsid / antigen processing and presentation of peptide antigen via MHC class I / MHC class I protein complex / viral penetration into host nucleus / host cell / viral nucleocapsid / immune response / ribonucleoprotein complex / external side of plasma membrane ...response to metal ion / helical viral capsid / antigen processing and presentation of peptide antigen via MHC class I / MHC class I protein complex / viral penetration into host nucleus / host cell / viral nucleocapsid / immune response / ribonucleoprotein complex / external side of plasma membrane / symbiont entry into host cell / host cell nucleus / structural molecule activity / extracellular space / 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 / Immunoglobulin-like fold / Immunoglobulins / 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: 2.06 Å
AuthorsWu, Y. / Xia, C.
Funding support China, 2items
OrganizationGrant numberCountry
National Key Basic Research Program of China2013CB835302 China
National Natural Science Foundation of ChinaNo. 31572493 China
CitationJournal: To Be Published
Title: Structural Definition Of Duck MHC Class I For 2.06 Angstrom Explains its 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 1.2Oct 23, 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: ARG-LEU-ILE-GLN-ASN-SER-ILE-THR-ILE


Theoretical massNumber of molelcules
Total (without water)44,6063
Polymers44,6063
Non-polymers00
Water3,045169
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4910 Å2
ΔGint-20 kcal/mol
Surface area18420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.487, 63.538, 79.954
Angle α, β, γ (deg.)90.00, 106.10, 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 ARG-LEU-ILE-GLN-ASN-SER-ILE-THR-ILE


Mass: 1058.253 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.: 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: 2.54 Å3/Da / Density % sol: 51.64 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 24 % w/v Polyethylene glycol 1500, 20 % v/v Glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 0.9792 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: 2.05→50 Å / Num. obs: 27433 / % possible obs: 99.8 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.092 / Rsym value: 0.092 / Net I/σ(I): 24.1
Reflection shellResolution: 2.05→2.09 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.568 / Mean I/σ(I) obs: 3.691 / % possible all: 99.9

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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: 2.06→50 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.919 / SU B: 10.629 / SU ML: 0.149 / Cross valid method: THROUGHOUT / ESU R: 0.218 / ESU R Free: 0.188
RfactorNum. reflection% reflectionSelection details
Rfree0.25334 1296 4.7 %RANDOM
Rwork0.20795 ---
obs0.21014 26122 98.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 33.681 Å2
Baniso -1Baniso -2Baniso -3
1-0.26 Å2-0 Å2-1.07 Å2
2--0.31 Å20 Å2
3---0.04 Å2
Refinement stepCycle: 1 / Resolution: 2.06→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3081 0 0 169 3250
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0193168
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0571.9294301
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5445375
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.01323.653167
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.53715513
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3711526
X-RAY DIFFRACTIONr_chiral_restr0.080.2443
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212482
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_it0.9992.4511512
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.6993.6651883
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.3532.6061656
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined4.69720.7214920
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.063→2.117 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 69 -
Rwork0.306 1744 -
obs--87.88 %
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)
10.2161-0.16530.04220.64130.28710.42240.0363-0.11520.02430.0292-0.0048-0.00680.0560.0021-0.03150.0133-0.02470.00240.1129-0.02660.01964.0146-11.048520.2796
20.3812-0.50190.41213.01091.37572.0573-0.04750.0233-0.05230.0866-0.0320.2817-0.07650.1060.07950.0417-0.0760.04360.1529-0.0760.0611-4.94934.625418.3315
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 273
2X-RAY DIFFRACTION2B1 - 104

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