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- PDB-9ch4: Crystal structure of shark nonclassical MHC CLASS I, UGA -

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Basic information

Entry
Database: PDB / ID: 9ch4
TitleCrystal structure of shark nonclassical MHC CLASS I, UGA
Components
  • Beta-2-microglobulin
  • Ig-like domain-containing 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
Chem-03F / Beta-2-microglobulin
Similarity search - Component
Biological speciesGinglymostoma cirratum (nurse shark)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.67 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)R01 AI170844 United States
CitationJournal: To Be Published
Title: CD1-like, lipid-presenting, nonclassical MHC molecules in shark
Authors: Castro, C.D. / Adams, E.J.
History
DepositionJul 1, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ig-like domain-containing protein
B: Beta-2-microglobulin
C: Ig-like domain-containing protein
D: Beta-2-microglobulin
E: Ig-like domain-containing protein
F: Beta-2-microglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,91519
Polymers124,9266
Non-polymers6,98913
Water1,72996
1
A: Ig-like domain-containing protein
B: Beta-2-microglobulin
hetero molecules

hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7008
Polymers41,6422
Non-polymers3,0586
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,y,-z1
Buried area4770 Å2
ΔGint23 kcal/mol
Surface area20160 Å2
MethodPISA
2
C: Ig-like domain-containing protein
D: Beta-2-microglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,0556
Polymers41,6422
Non-polymers2,4134
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4550 Å2
ΔGint20 kcal/mol
Surface area19360 Å2
MethodPISA
3
E: Ig-like domain-containing protein
F: Beta-2-microglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,5846
Polymers41,6422
Non-polymers1,9424
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3400 Å2
ΔGint-2 kcal/mol
Surface area18320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)165.773, 95.628, 112.372
Angle α, β, γ (deg.)90.00, 123.96, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 2 types, 6 molecules ACEBDF

#1: Protein Ig-like domain-containing protein


Mass: 30890.941 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ginglymostoma cirratum (nurse shark) / Gene: scyTo_0002318 / Production host: Trichoplusia ni (cabbage looper)
#2: Protein Beta-2-microglobulin


Mass: 10751.004 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ginglymostoma cirratum (nurse shark) / Gene: B2M, b2m / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: F4ZE04

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Sugars , 4 types, 10 molecules

#3: Polysaccharide alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1040.964 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpb1-4DGlcpNAcb1-4[LFucpa1-3][LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5][a1122h-1b_1-5][a1122h-1a_1-5]/1-2-1-3-4-2/a3-b1_a4-c1_a6-f1_c4-d1_d6-e1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{}}}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#4: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#5: Polysaccharide alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-6DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#6: 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.: 3
Source method: isolated from a genetically manipulated source
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

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Non-polymers , 2 types, 99 molecules

#7: Chemical ChemComp-03F / (9Z)-N-[(2S,3R,4E)-1-(beta-D-glucopyranosyloxy)-3-hydroxyoctadec-4-en-2-yl]octadec-9-enamide / N-(9Z-octadecenoyl)-1--glucosyl-sphing-4-enine


Mass: 726.079 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C42H79NO8 / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.92 Å3/Da / Density % sol: 57.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Morpheus H8: 37.5 % v/v Precipitant Mix 4 (25% v/v MPD; 25% PEG 1000; 25% w/v PEG 3350), 0.1 M Sodium HEPES; MOPS (acid) pH 7.5, 0.1 M Amino acids

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 11, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.67→93.2 Å / Num. obs: 41251 / % possible obs: 99.6 % / Redundancy: 7 % / CC1/2: 0.987 / Rmerge(I) obs: 0.291 / Rpim(I) all: 0.119 / Rrim(I) all: 0.314 / Net I/σ(I): 6.5 / Num. measured all: 288789
Reflection shellResolution: 2.67→2.78 Å / % possible obs: 99 % / Redundancy: 7 % / Rmerge(I) obs: 1.55 / Num. measured all: 32111 / Num. unique obs: 4586 / CC1/2: 0.522 / Rpim(I) all: 0.627 / Rrim(I) all: 1.674 / Net I/σ(I) obs: 1.3

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.67→93.2 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2617 1979 4.8 %
Rwork0.2394 --
obs0.2405 41199 99.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.67→93.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8956 0 290 96 9342
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012
X-RAY DIFFRACTIONf_angle_d1.625
X-RAY DIFFRACTIONf_dihedral_angle_d20.5373908
X-RAY DIFFRACTIONf_chiral_restr0.1011428
X-RAY DIFFRACTIONf_plane_restr0.0231590
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.67-2.740.3551290.3262767X-RAY DIFFRACTION98
2.74-2.810.34991460.31262787X-RAY DIFFRACTION99
2.81-2.890.3351510.30782738X-RAY DIFFRACTION99
2.89-2.990.32861280.29262782X-RAY DIFFRACTION99
2.99-3.090.32121490.28212777X-RAY DIFFRACTION100
3.09-3.220.33041320.28532813X-RAY DIFFRACTION100
3.22-3.370.2841660.25832751X-RAY DIFFRACTION100
3.37-3.540.2781490.24812827X-RAY DIFFRACTION100
3.54-3.760.24971250.22032805X-RAY DIFFRACTION100
3.76-4.060.23511510.21672791X-RAY DIFFRACTION100
4.06-4.460.17991370.19972816X-RAY DIFFRACTION99
4.46-5.110.21071520.19772828X-RAY DIFFRACTION100
5.11-6.440.25771470.24362831X-RAY DIFFRACTION100
6.44-93.20.29781170.23292907X-RAY DIFFRACTION99

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