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- PDB-8gm8: Crystal structure of shark nonclassical MHC CLASS I, UFA -

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Basic information

Entry
Database: PDB / ID: 8gm8
TitleCrystal structure of shark nonclassical MHC CLASS I, UFA
Components
  • Beta-2-microglobulin
  • MHC class I protein
KeywordsIMMUNE SYSTEM / MHC / class I / shark / nurse shark / B2m / beta-2-microglobulin
Function / homology
Function and homology information


antigen processing and presentation of peptide antigen via MHC class I / MHC class I protein complex / extracellular region
Similarity search - Function
: / 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
Similarity search - Domain/homology
Beta-2-microglobulin
Similarity search - Component
Biological speciesGinglymostoma cirratum (nurse shark)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.83 Å
AuthorsCastro, C.D. / Adams, E.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1R01AI170844-01 United States
CitationJournal: To Be Published
Title: Characterization of Shark CD1 Establishes Its Presence in the Primordial MHC
Authors: Castro, C.D. / Adams, E.J.
History
DepositionMar 24, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MHC class I protein
B: Beta-2-microglobulin
C: MHC class I protein
D: Beta-2-microglobulin
E: MHC class I protein
F: Beta-2-microglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,9538
Polymers123,5106
Non-polymers4422
Water00
1
A: MHC class I protein
B: Beta-2-microglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,3913
Polymers41,1702
Non-polymers2211
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2440 Å2
ΔGint-13 kcal/mol
Surface area17440 Å2
MethodPISA
2
C: MHC class I protein
D: Beta-2-microglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,3913
Polymers41,1702
Non-polymers2211
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2470 Å2
ΔGint-15 kcal/mol
Surface area17900 Å2
MethodPISA
3
E: MHC class I protein
F: Beta-2-microglobulin


Theoretical massNumber of molelcules
Total (without water)41,1702
Polymers41,1702
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1680 Å2
ΔGint-12 kcal/mol
Surface area14810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.065, 89.865, 90.080
Angle α, β, γ (deg.)63.570, 78.250, 80.350
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein MHC class I protein


Mass: 30321.963 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ginglymostoma cirratum (nurse shark) / Gene: Gici-UFA, UFA / Production host: Trichoplusia ni (cabbage looper)
#2: Protein Beta-2-microglobulin


Mass: 10848.119 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ginglymostoma cirratum (nurse shark) / Gene: B2M / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: F4ZE04
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
Has ligand of interestN
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: 3.39 Å3/Da / Density % sol: 63.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 16% w/v PEG 4000, 0.1 M Tris pH 8.5, and 0.2 M lithium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Sep 26, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.83→79.8 Å / Num. obs: 36200 / % possible obs: 94 % / Redundancy: 3.7 % / Biso Wilson estimate: 96.52 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.055 / Net I/σ(I): 12
Reflection shellResolution: 2.83→2.96 Å / Redundancy: 3.7 % / Rmerge(I) obs: 1.036 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 4278 / CC1/2: 0.674 / % possible all: 90.9

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX1.20.1-4487refinement
Aimlessdata scaling
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.83→79.8 Å / SU ML: 0.4273 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 36.1873
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.274 1637 4.53 %
Rwork0.2287 34523 -
obs0.2306 36160 93.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 130.24 Å2
Refinement stepCycle: LAST / Resolution: 2.83→79.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7636 0 28 0 7664
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01297834
X-RAY DIFFRACTIONf_angle_d1.546210643
X-RAY DIFFRACTIONf_chiral_restr0.07991225
X-RAY DIFFRACTIONf_plane_restr0.01111358
X-RAY DIFFRACTIONf_dihedral_angle_d19.59172900
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.83-2.910.43571470.42672667X-RAY DIFFRACTION88.05
2.91-3.010.37711580.37482906X-RAY DIFFRACTION95.78
3.01-3.120.38481460.34392911X-RAY DIFFRACTION94.82
3.12-3.240.36111490.3352831X-RAY DIFFRACTION92.58
3.24-3.390.33631180.28662819X-RAY DIFFRACTION92.71
3.39-3.570.32881490.28132955X-RAY DIFFRACTION96.43
3.57-3.790.33541460.26782965X-RAY DIFFRACTION96.44
3.79-4.080.31291200.23952958X-RAY DIFFRACTION95.77
4.08-4.490.27241290.20192922X-RAY DIFFRACTION94.63
4.49-5.140.22751210.18712787X-RAY DIFFRACTION91.53
5.14-6.480.25031180.22433012X-RAY DIFFRACTION96.63
6.48-79.80.21661360.1872790X-RAY DIFFRACTION91.52

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