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- PDB-6ilg: CRYSTAL STRUCTURE OF BAT MHC CLASS I PTAL-N*01:01 FOR 2.6 ANGSTROM -

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Basic information

Entry
Database: PDB / ID: 6ilg
TitleCRYSTAL STRUCTURE OF BAT MHC CLASS I PTAL-N*01:01 FOR 2.6 ANGSTROM
Components
  • Beta-2-microglobulin
  • HEV-1-P8L
  • MHC class I antigen
KeywordsIMMUNE SYSTEM / IMMUNOLOGY / VIRUS
Function / homology
Function and homology information


antigen processing and presentation of peptide antigen via MHC class I / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / lumenal side of endoplasmic reticulum membrane / MHC class I protein complex / positive regulation of T cell mediated cytotoxicity / phagocytic vesicle membrane / peptide antigen binding / disordered domain specific binding / amyloid fibril formation ...antigen processing and presentation of peptide antigen via MHC class I / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / lumenal side of endoplasmic reticulum membrane / MHC class I protein complex / positive regulation of T cell mediated cytotoxicity / phagocytic vesicle membrane / peptide antigen binding / disordered domain specific binding / amyloid fibril formation / immune response / external side of plasma membrane / signaling receptor binding / protein-containing complex / extracellular space / extracellular region
Similarity search - Function
Phosphoprotein P region PNT disordered / Phosphoprotein P region PNT disordered / Paramyxovirus structural protein P/V, N-terminal domain / Paramyxovirus structural protein V/P N-terminus / Phosphoprotein P soyouz module / N-terminal region of Paramyxovirinae phosphoprotein (P) / P/V phosphoprotein, paramyxoviral / Paramyxovirus P/V phosphoprotein C-terminal / MHC class I, alpha chain, C-terminal / MHC_I C-terminus ...Phosphoprotein P region PNT disordered / Phosphoprotein P region PNT disordered / Paramyxovirus structural protein P/V, N-terminal domain / Paramyxovirus structural protein V/P N-terminus / Phosphoprotein P soyouz module / N-terminal region of Paramyxovirinae phosphoprotein (P) / P/V phosphoprotein, paramyxoviral / Paramyxovirus P/V phosphoprotein C-terminal / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / 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 / Nucleic acid-binding, OB-fold / 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 / Phosphoprotein
Similarity search - Component
Biological speciesPteropus alecto (black flying fox)
Hendra virus
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsQu, Z.H. / Zhang, N.Z. / Xia, C.
CitationJournal: J Immunol. / Year: 2019
Title: Structure and Peptidome of the Bat MHC Class I Molecule Reveal a Novel Mechanism Leading to High-Affinity Peptide Binding.
Authors: Qu, Z. / Li, Z. / Ma, L. / Wei, X. / Zhang, L. / Liang, R. / Meng, G. / Zhang, N. / Xia, C.
History
DepositionOct 18, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 24, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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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: HEV-1-P8L


Theoretical massNumber of molelcules
Total (without water)44,7603
Polymers44,7603
Non-polymers00
Water2,090116
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4310 Å2
ΔGint-14 kcal/mol
Surface area19080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.876, 86.440, 135.121
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-121-

HOH

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Components

#1: Protein MHC class I antigen


Mass: 32345.482 Da / Num. of mol.: 1 / Fragment: UNP residues 25-303
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pteropus alecto (black flying fox) / Gene: Ptal-N / Production host: Escherichia coli (E. coli) / References: UniProt: A0A125R585
#2: Protein Beta-2-microglobulin


Mass: 11474.836 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pteropus alecto (black flying fox) / Gene: PAL_GLEAN10023531 / Production host: Escherichia coli (E. coli) / References: UniProt: L5K3Y9*PLUS
#3: Protein/peptide HEV-1-P8L


Mass: 940.051 Da / Num. of mol.: 1 / Mutation: P8L / Source method: obtained synthetically / Source: (synth.) Hendra virus / References: UniProt: O55778*PLUS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsNCBI Reference Sequence for Beta-2-microglobulin is XP_006920478.1.

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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: 2.38 Å3/Da / Density % sol: 48.26 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.2M Lithium sulfate monohydrate, 0.1M BIS-TRIS pH 6.5, 25%(w/v) Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 0.97915 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jun 20, 2017
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.93→135.12 Å / Num. obs: 14539 / % possible obs: 100 % / Redundancy: 2 % / Rmerge(I) obs: 0.285 / Net I/σ(I): 19
Reflection shellResolution: 2.54→2.6 Å / Rmerge(I) obs: 0.628 / Num. unique obs: 1065

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Processing

Software
NameVersionClassification
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
PHENIX(1.12_2829: ???)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→67.561 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.34
RfactorNum. reflection% reflection
Rfree0.2764 654 4.85 %
Rwork0.2135 --
obs0.2166 13475 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.6→67.561 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3159 0 0 116 3275
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033256
X-RAY DIFFRACTIONf_angle_d0.6444434
X-RAY DIFFRACTIONf_dihedral_angle_d11.3061914
X-RAY DIFFRACTIONf_chiral_restr0.04444
X-RAY DIFFRACTIONf_plane_restr0.005592
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.80080.37021080.25292546X-RAY DIFFRACTION100
2.8008-3.08260.33011320.25412514X-RAY DIFFRACTION100
3.0826-3.52870.26511340.23282544X-RAY DIFFRACTION100
3.5287-4.44560.27971250.1852567X-RAY DIFFRACTION100
4.4456-67.58330.23141550.19092650X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 82.9174 Å / Origin y: 28.6756 Å / Origin z: 17.829 Å
111213212223313233
T-0.1286 Å2-0.189 Å2-0.0283 Å2--0.241 Å2-0.2028 Å2---0.0669 Å2
L0.2975 °2-0.0586 °2-0.1846 °2-0.1935 °2-0.2038 °2--0.3107 °2
S0.2639 Å °-0.1537 Å °-0.0729 Å °0.2918 Å °-0.2787 Å °-0.0803 Å °-0.4915 Å °0.5206 Å °0.1541 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND ( RESID 1:279 OR RESID 301:386 ) ) OR ( CHAIN C AND ( RESID 1:8 OR RESID 101:107 ) ) OR ( CHAIN B AND ( RESID 1:98 OR RESID 101:123 ) )A1 - 279
2X-RAY DIFFRACTION1( CHAIN A AND ( RESID 1:279 OR RESID 301:386 ) ) OR ( CHAIN C AND ( RESID 1:8 OR RESID 101:107 ) ) OR ( CHAIN B AND ( RESID 1:98 OR RESID 101:123 ) )A301 - 386
3X-RAY DIFFRACTION1( CHAIN A AND ( RESID 1:279 OR RESID 301:386 ) ) OR ( CHAIN C AND ( RESID 1:8 OR RESID 101:107 ) ) OR ( CHAIN B AND ( RESID 1:98 OR RESID 101:123 ) )C1 - 8
4X-RAY DIFFRACTION1( CHAIN A AND ( RESID 1:279 OR RESID 301:386 ) ) OR ( CHAIN C AND ( RESID 1:8 OR RESID 101:107 ) ) OR ( CHAIN B AND ( RESID 1:98 OR RESID 101:123 ) )C101 - 107
5X-RAY DIFFRACTION1( CHAIN A AND ( RESID 1:279 OR RESID 301:386 ) ) OR ( CHAIN C AND ( RESID 1:8 OR RESID 101:107 ) ) OR ( CHAIN B AND ( RESID 1:98 OR RESID 101:123 ) )B1 - 98
6X-RAY DIFFRACTION1( CHAIN A AND ( RESID 1:279 OR RESID 301:386 ) ) OR ( CHAIN C AND ( RESID 1:8 OR RESID 101:107 ) ) OR ( CHAIN B AND ( RESID 1:98 OR RESID 101:123 ) )B101 - 123

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