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- PDB-7apz: CLIP peptide bound to chicken MHC class II molecule (BL-2) from B... -

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Basic information

Entry
Database: PDB / ID: 7apz
TitleCLIP peptide bound to chicken MHC class II molecule (BL-2) from B2 haplotype with a decamer mode of binding
Components(MHC class II ...) x 2
KeywordsIMMUNE SYSTEM / CLIP / MHC classII / BLA / BLB2 / antigen presentation
Function / homology
Function and homology information


antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / antigen processing and presentation / MHC class II protein complex / adaptive immune response / immune response / metal ion binding
Similarity search - Function
MHC class II, beta chain, N-terminal / Class II histocompatibility antigen, beta domain / Class II histocompatibility antigen, beta domain / MHC class II, alpha chain, N-terminal / Class II histocompatibility antigen, alpha domain / Class II histocompatibility antigen, alpha domain / MHC class II, alpha/beta chain, N-terminal / MHC classes I/II-like antigen recognition protein / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. ...MHC class II, beta chain, N-terminal / Class II histocompatibility antigen, beta domain / Class II histocompatibility antigen, beta domain / MHC class II, alpha chain, N-terminal / Class II histocompatibility antigen, alpha domain / Class II histocompatibility antigen, alpha domain / MHC class II, alpha/beta chain, N-terminal / 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
Similarity search - Domain/homology
ACETYL GROUP / IMIDAZOLE / NICKEL (II) ION / DI(HYDROXYETHYL)ETHER / MHC class II beta chain 2 / MHC class II alpha chain
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.97 Å
AuthorsHalabi, S. / Kaufman, J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust110106/Z/15/Z United Kingdom
CitationJournal: To Be Published
Title: CLIP peptide bound to chicken MHC class II molecule (BL-2) from B2 haplotype with a decamer mode of binding
Authors: Halabi, S. / Kaufman, J.
History
DepositionOct 20, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 3, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / diffrn_source / pdbx_initial_refinement_model
Item: _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MHC class II alpha chain
B: MHC class II beta chain 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,08428
Polymers46,2442
Non-polymers1,84026
Water2,270126
1
A: MHC class II alpha chain
B: MHC class II beta chain 2
hetero molecules

A: MHC class II alpha chain
B: MHC class II beta chain 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,16856
Polymers92,4884
Non-polymers3,68052
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/61
Unit cell
Length a, b, c (Å)82.803, 82.803, 263.071
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-210-

ZN

21A-328-

HOH

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Components

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MHC class II ... , 2 types, 2 molecules AB

#1: Protein MHC class II alpha chain / MHC class II antigen alpha / MHC class II antigen alpha chain


Mass: 21234.750 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: B-LA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q4U5Z6
#2: Protein MHC class II beta chain 2


Mass: 25009.047 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: BLB2 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: B5BSA0

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Sugars , 1 types, 2 molecules

#7: 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

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Non-polymers , 6 types, 150 molecules

#3: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5N2
#4: Chemical
ChemComp-ACE / ACETYL GROUP


Mass: 44.053 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H4O
#5: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Zn
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#8: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 126 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.81 Å3/Da / Density % sol: 56.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M Zinc Acetate (Salt) 0.1 M Imidazole pH 6.5 (Buffer) 10 %w/v PEG 8000 (Precipitant)

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9786 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 3, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.97→71.71 Å / Num. obs: 38197 / % possible obs: 98.8 % / Redundancy: 35.8 % / CC1/2: 0.996 / Rmerge(I) obs: 0.527 / Rpim(I) all: 0.089 / Rrim(I) all: 0.535 / Net I/σ(I): 10.8 / Num. measured all: 1367042 / Scaling rejects: 50
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.97-2.0835.75.85719643854970.4170.9915.9411.4100
6.24-71.7126.80.0993884514520.9940.0190.10134.199.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0258refinement
XDSdata reduction
Aimless0.7.3data scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6T3Y

6t3y


Resolution: 1.97→69.28 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.92 / SU B: 4.677 / SU ML: 0.126 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.162 / ESU R Free: 0.157 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2549 1913 5 %RANDOM
Rwork0.2099 ---
obs0.2122 36174 98.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 121.29 Å2 / Biso mean: 32.208 Å2 / Biso min: 9.57 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å20.09 Å20 Å2
2--0.18 Å2-0 Å2
3----0.6 Å2
Refinement stepCycle: final / Resolution: 1.97→69.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3139 0 87 126 3352
Biso mean--68.07 35.91 -
Num. residues----390
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0133293
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172917
X-RAY DIFFRACTIONr_angle_refined_deg1.6441.6564450
X-RAY DIFFRACTIONr_angle_other_deg1.2651.5826737
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4025386
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.82621.818198
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.85415503
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1571526
X-RAY DIFFRACTIONr_chiral_restr0.0690.2395
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023755
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02778
LS refinement shellResolution: 1.975→2.026 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 152 -
Rwork0.318 2630 -
all-2782 -
obs--100 %

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