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- PDB-6zwa: CLIP peptide bound to chicken MHC class II molecule (BL-2) from B... -

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Basic information

Entry
Database: PDB / ID: 6zwa
TitleCLIP peptide bound to chicken MHC class II molecule (BL-2) from B19 haplotype
Components
  • Invariant chain isoform p41,MHC class II beta chain 2
  • MHC class II alpha chain
KeywordsIMMUNE SYSTEM / CLIP / MHC classII / BLA / BLB2
Function / homology
Function and homology information


MHC protein complex / Phosphorylation of CD3 and TCR zeta chains / Translocation of ZAP-70 to Immunological synapse / Generation of second messenger molecules / Cell surface interactions at the vascular wall / MHC class II antigen presentation / PD-1 signaling / negative regulation of peptide secretion / macrophage migration inhibitory factor signaling pathway / NOS2-CD74 complex ...MHC protein complex / Phosphorylation of CD3 and TCR zeta chains / Translocation of ZAP-70 to Immunological synapse / Generation of second messenger molecules / Cell surface interactions at the vascular wall / MHC class II antigen presentation / PD-1 signaling / negative regulation of peptide secretion / macrophage migration inhibitory factor signaling pathway / NOS2-CD74 complex / MHC class II protein binding, via antigen binding groove / positive regulation of dendritic cell antigen processing and presentation / negative regulation of T cell differentiation / macrophage migration inhibitory factor binding / positive regulation of macrophage migration inhibitory factor signaling pathway / protein trimerization / macrophage migration inhibitory factor receptor complex / positive regulation of cytokine-mediated signaling pathway / T cell activation involved in immune response / positive regulation of type 2 immune response / negative thymic T cell selection / positive regulation of prostaglandin biosynthetic process / MHC class II protein binding / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / negative regulation of mature B cell apoptotic process / positive thymic T cell selection / positive regulation of monocyte differentiation / CD4 receptor binding / positive regulation of kinase activity / positive regulation of neutrophil chemotaxis / positive regulation of chemokine (C-X-C motif) ligand 2 production / positive regulation of macrophage cytokine production / prostaglandin biosynthetic process / positive regulation of T cell differentiation / cytokine receptor activity / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / response to type II interferon / nitric-oxide synthase binding / MHC class I protein binding / chaperone cofactor-dependent protein refolding / negative regulation of DNA damage response, signal transduction by p53 class mediator / antigen processing and presentation / immunoglobulin mediated immune response / protein folding chaperone / positive regulation of B cell proliferation / multivesicular body / negative regulation of cell migration / positive regulation of interleukin-8 production / intracellular protein transport / MHC class II protein complex / positive regulation of interleukin-6 production / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of peptidyl-tyrosine phosphorylation / positive regulation of fibroblast proliferation / amyloid-beta binding / positive regulation of canonical NF-kappaB signal transduction / adaptive immune response / membrane => GO:0016020 / positive regulation of viral entry into host cell / lysosome / positive regulation of ERK1 and ERK2 cascade / immune response / external side of plasma membrane / positive regulation of DNA-templated transcription / Golgi apparatus / cell surface / endoplasmic reticulum / nucleus / cytoplasm
Similarity search - Function
MHC class II-associated invariant chain, trimerisation / MHC class II-associated invariant chain/CLIP, MHC II-interacting / MHC class II-associated invariant chain / MHC class II-associated invariant chain, trimerisation domain superfamily / HLA class II histocompatibility antigen, gamma subunit / Class II MHC-associated invariant chain trimerisation domain / CLIP, MHC2 interacting / Thyroglobulin type-1 / Thyroglobulin type-1 superfamily / Thyroglobulin type-1 repeat ...MHC class II-associated invariant chain, trimerisation / MHC class II-associated invariant chain/CLIP, MHC II-interacting / MHC class II-associated invariant chain / MHC class II-associated invariant chain, trimerisation domain superfamily / HLA class II histocompatibility antigen, gamma subunit / Class II MHC-associated invariant chain trimerisation domain / CLIP, MHC2 interacting / Thyroglobulin type-1 / Thyroglobulin type-1 superfamily / Thyroglobulin type-1 repeat / Thyroglobulin type-1 domain profile. / Thyroglobulin type I repeats. / 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
DI(HYDROXYETHYL)ETHER / MHC class II beta chain 2 / MHC class II alpha chain / Invariant chain isoform p41
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.68 Å
AuthorsHalabi, S. / Brear, P. / 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 BL-2 from B19 haplotype
Authors: Halabi, S. / Kaufman, J.
History
DepositionJul 28, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 11, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MHC class II alpha chain
B: Invariant chain isoform p41,MHC class II beta chain 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,7613
Polymers45,6552
Non-polymers1061
Water2,324129
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6120 Å2
ΔGint-37 kcal/mol
Surface area18400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)151.863, 60.536, 53.855
Angle α, β, γ (deg.)90.000, 107.880, 90.000
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 21119.664 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 Invariant chain isoform p41,MHC class II beta chain 2


Mass: 24535.354 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: Ii, CD74, BLB2 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q6J613, UniProt: A5HUL4
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 129 / Source method: isolated from a natural source / Formula: H2O
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: 2.58 Å3/Da / Density % sol: 52.33 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1 M TRIS pH 8.5, 20.0% w/v PEG 4000, 200mM CaCl2

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 12, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 1.68→55.9 Å / Num. obs: 50834 / % possible obs: 95 % / Redundancy: 6.5 % / CC1/2: 0.997 / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.042 / Rrim(I) all: 0.106 / Net I/σ(I): 9.2
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
1.68-1.776.71.9725168677370.5410.8172.1381.199.7
5.3-55.845.70.062987917310.9950.0280.06822.398.7

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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: 1.68→55.8 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.945 / SU B: 3.79 / SU ML: 0.113 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.113 / ESU R Free: 0.113 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2519 2441 4.8 %RANDOM
Rwork0.2164 ---
obs0.2182 48269 94.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 105.17 Å2 / Biso mean: 35.048 Å2 / Biso min: 13.39 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å2-0 Å20.02 Å2
2---0.15 Å20 Å2
3---0.09 Å2
Refinement stepCycle: final / Resolution: 1.68→55.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3064 0 7 129 3200
Biso mean--65.47 35.57 -
Num. residues----376
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0133171
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172770
X-RAY DIFFRACTIONr_angle_refined_deg1.551.6454301
X-RAY DIFFRACTIONr_angle_other_deg1.3371.5696409
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0195373
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.01621.683202
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.04415494
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.151527
X-RAY DIFFRACTIONr_chiral_restr0.0730.2374
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023605
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02756
LS refinement shellResolution: 1.68→1.719 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.421 195 -
Rwork0.431 3642 -
obs--97.63 %

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