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- PDB-8w85: HLA-DQ2.5-gamma2 gliadin peptide in complex with DQN0385AE01 -

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Basic information

Entry
Database: PDB / ID: 8w85
TitleHLA-DQ2.5-gamma2 gliadin peptide in complex with DQN0385AE01
Components
  • DQN0385AE01 Fab heavy chain
  • DQN0385AE01 Fab light chain
  • HLA class II histocompatibility antigen, DQ alpha 1 chain
  • MHC class II HLA-DQ-beta-1 - gamma2 gliadin peptide chimeric protein
KeywordsIMMUNE SYSTEM / CELIAC DISEASE / ANTIBODY
Function / homology
Function and homology information


MHC class II receptor activity / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / transport vesicle membrane / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / Generation of second messenger molecules / Co-inhibition by PD-1 / MHC class II antigen presentation / trans-Golgi network membrane / lumenal side of endoplasmic reticulum membrane ...MHC class II receptor activity / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / transport vesicle membrane / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / Generation of second messenger molecules / Co-inhibition by PD-1 / MHC class II antigen presentation / trans-Golgi network membrane / lumenal side of endoplasmic reticulum membrane / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / clathrin-coated endocytic vesicle membrane / ER to Golgi transport vesicle membrane / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / peptide antigen binding / positive regulation of T cell activation / Interferon gamma signaling / MHC class II protein complex binding / endocytic vesicle membrane / late endosome membrane / Downstream TCR signaling / adaptive immune response / endosome membrane / immune response / Golgi membrane / lysosomal membrane / membrane / plasma membrane
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 ...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
MHC class II HLA-DQ-beta-1 / HLA class II histocompatibility antigen, DQ alpha 1 chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.769 Å
AuthorsIrie, M. / Tsushima, T. / Teranishi-Ikawa, Y. / Takahashi, N. / Ishii, S. / Okura, Y. / Fukami, T.A. / Torizawa, T.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2023
Title: Characterizations of a neutralizing antibody broadly reactive to multiple gluten peptide:HLA-DQ2.5 complexes in the context of celiac disease.
Authors: Okura, Y. / Ikawa-Teranishi, Y. / Mizoroki, A. / Takahashi, N. / Tsushima, T. / Irie, M. / Harfuddin, Z. / Miura-Okuda, M. / Ito, S. / Nakamura, G. / Takesue, H. / Ozono, Y. / Nishihara, M. ...Authors: Okura, Y. / Ikawa-Teranishi, Y. / Mizoroki, A. / Takahashi, N. / Tsushima, T. / Irie, M. / Harfuddin, Z. / Miura-Okuda, M. / Ito, S. / Nakamura, G. / Takesue, H. / Ozono, Y. / Nishihara, M. / Yamada, K. / Gan, S.W. / Hayasaka, A. / Ishii, S. / Wakabayashi, T. / Muraoka, M. / Nagaya, N. / Hino, H. / Nemoto, T. / Kuramochi, T. / Torizawa, T. / Shimada, H. / Kitazawa, T. / Okazaki, M. / Nezu, J. / Sollid, L.M. / Igawa, T.
History
DepositionAug 31, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 8, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2May 8, 2024Group: Database references / Category: citation
Item: _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _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: DQN0385AE01 Fab heavy chain
B: DQN0385AE01 Fab light chain
C: HLA class II histocompatibility antigen, DQ alpha 1 chain
D: MHC class II HLA-DQ-beta-1 - gamma2 gliadin peptide chimeric protein
E: DQN0385AE01 Fab heavy chain
F: DQN0385AE01 Fab light chain
G: HLA class II histocompatibility antigen, DQ alpha 1 chain
H: MHC class II HLA-DQ-beta-1 - gamma2 gliadin peptide chimeric protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)188,17110
Polymers187,7288
Non-polymers4422
Water00
1
A: DQN0385AE01 Fab heavy chain
B: DQN0385AE01 Fab light chain
C: HLA class II histocompatibility antigen, DQ alpha 1 chain
D: MHC class II HLA-DQ-beta-1 - gamma2 gliadin peptide chimeric protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,0855
Polymers93,8644
Non-polymers2211
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: DQN0385AE01 Fab heavy chain
F: DQN0385AE01 Fab light chain
G: HLA class II histocompatibility antigen, DQ alpha 1 chain
H: MHC class II HLA-DQ-beta-1 - gamma2 gliadin peptide chimeric protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,0855
Polymers93,8644
Non-polymers2211
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)150.525, 243.913, 136.081
Angle α, β, γ (deg.)90, 90, 90
Int Tables number21
Space group name H-MC222

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Components

#1: Antibody DQN0385AE01 Fab heavy chain


Mass: 23810.703 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): Expi293 / Production host: Homo sapiens (human)
#2: Antibody DQN0385AE01 Fab light chain


Mass: 23269.846 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): Expi293 / Production host: Homo sapiens (human)
#3: Protein HLA class II histocompatibility antigen, DQ alpha 1 chain / DC-1 alpha chain / DC-alpha / HLA-DCA / MHC class II DQA1


Mass: 21396.939 Da / Num. of mol.: 2 / Mutation: C47S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DQA1 / Cell line (production host): FreeStyle 293-F cells / Production host: Homo sapiens (human) / References: UniProt: P01909
#4: Protein MHC class II HLA-DQ-beta-1 - gamma2 gliadin peptide chimeric protein


Mass: 25386.594 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DQB1 / Cell line (production host): FreeStyle 293-F cells / Production host: Homo sapiens (human) / References: UniProt: O19712
#5: 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: 3.33 Å3/Da / Density % sol: 63.03 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Ammonium sulfate, 10.0 %w/v Polyethylene glycol 3,350, and 30 %v/v Ethylene glycol as cryoprotectant

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Dec 5, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.769→136.081 Å / Num. obs: 41787 / % possible obs: 94 % / Redundancy: 13.67 % / CC1/2: 0.999 / CC1/2 anomalous: -0.036 / Rmerge(I) obs: 0.1197 / Rpim(I) all: 0.0337 / Rrim(I) all: 0.1244 / AbsDiff over sigma anomalous: 0.776 / Baniso tensor eigenvalue 1: 138.1 Å2 / Baniso tensor eigenvalue 2: 100.1 Å2 / Baniso tensor eigenvalue 3: 76.8 Å2 / Baniso tensor eigenvector 1 ortho1: 1 / Baniso tensor eigenvector 1 ortho2: 0 / Baniso tensor eigenvector 1 ortho3: 0 / Baniso tensor eigenvector 2 ortho1: 0 / Baniso tensor eigenvector 2 ortho2: 1 / Baniso tensor eigenvector 2 ortho3: 0 / Baniso tensor eigenvector 3 ortho1: 0 / Baniso tensor eigenvector 3 ortho2: 0 / Baniso tensor eigenvector 3 ortho3: 1 / Aniso diffraction limit 1: 3.51 Å / Aniso diffraction limit 2: 3.193 Å / Aniso diffraction limit 3: 2.751 Å / Aniso diffraction limit axis 1 ortho1: 1 / Aniso diffraction limit axis 1 ortho2: 0 / Aniso diffraction limit axis 1 ortho3: 0 / Aniso diffraction limit axis 2 ortho1: 0 / Aniso diffraction limit axis 2 ortho2: 1 / Aniso diffraction limit axis 2 ortho3: 0 / Aniso diffraction limit axis 3 ortho1: 0 / Aniso diffraction limit axis 3 ortho2: 0 / Aniso diffraction limit axis 3 ortho3: 1 / Net I/σ(I): 16.25 / Num. measured all: 571351 / Orthogonalization convention: pdb / % possible anomalous: 94 / % possible ellipsoidal: 94 / % possible ellipsoidal anomalous: 94 / % possible spherical: 65.3 / % possible spherical anomalous: 64.6 / Redundancy anomalous: 7.12
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. measured obsNum. unique allNum. unique obsCC1/2CC1/2 anomalousRpim(I) allRrim(I) allAbsDiff over sigma anomalous% possible anomalous% possible ellipsoidal% possible ellipsoidal anomalous% possible spherical% possible spherical anomalousRedundancy anomalous% possible all
8.886-136.08112.970.030252.892709127091208920890.999-0.030.0090.03160.67699.899.699.899.699.87.3299.6
7.005-8.88614.140.051540.192955129551209020900.999-0.0990.01410.05340.8071001001001001007.57100
6.095-7.00514.410.079729.73008130081208820880.998-0.0590.02170.08270.831001001001001007.63100
5.523-6.09514.580.091226.843045730457208920890.998-0.040.02470.09450.8261001001001001007.67100
5.117-5.52314.640.093826.433060330603209020900.998-0.0950.02530.09720.8061001001001001007.67100
4.808-5.11714.740.094125.943079130791208920890.998-0.0680.02530.09750.7931001001001001007.71100
4.565-4.80814.830.102523.813098730987208920890.998-0.0880.02760.10620.8241001001001001007.72100
4.361-4.56514.870.118420.813109431094209120910.998-0.0570.03170.12260.811001001001001007.73100
4.19-4.36114.740.1516.733077630776208820880.997-0.0390.04040.15540.7861001001001001007.66100
4.043-4.1913.240.192112.742769327693209120910.9940.0060.05470.19980.78699.910099.910099.96.87100
3.915-4.04312.580.242110.312628126281208920890.991-0.0170.07090.25240.7611001001001001006.51100
3.8-3.91512.580.32757.872626226262208820880.985-0.050.09610.34150.7651001001001001006.5100
3.699-3.811.920.37776.572491724917209120910.9840.0090.11410.39480.7791001001001001006.15100
3.607-3.69911.810.48365.392465424654208820880.97-0.0390.14690.50580.76199.899.799.899.799.86.199.7
3.519-3.60712.920.61534.642700027000208920890.953-0.0360.17780.64080.7529695.19695.1966.6595.1
3.432-3.51913.360.72014.122791627916209020900.940.0240.20420.74890.77190.59090.586.2876.8690
3.341-3.43213.670.86683.492855328553208920890.9170.0150.24260.90050.7688.287.788.274.575.5787.7
3.234-3.34113.841.04812.882890228902208920890.894-0.0370.29091.08820.73180.78080.756.657.47.0780
3.105-3.23413.841.3982.182894528945209120910.801-0.0010.38771.45130.75682.782.582.740.240.57.0882.5
2.769-3.10513.791.88341.572879728797208920890.684-0.0270.52381.95580.72663.664.863.611.310.97.1964.8

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Processing

Software
NameVersionClassification
BUSTER2.11.8refinement
autoPROCdata processing
XDSJan 31, 2020data reduction
Aimless0.7.7data scaling
STARANISO2.3.63data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7VG1

7vg1
PDB Unreleased entry


Resolution: 2.769→50.47 Å / Cor.coef. Fo:Fc: 0.893 / Cor.coef. Fo:Fc free: 0.857 / SU R Cruickshank DPI: 3.344 / Cross valid method: THROUGHOUT / SU R Blow DPI: 1.794 / SU Rfree Blow DPI: 0.458 / SU Rfree Cruickshank DPI: 0.474
RfactorNum. reflection% reflectionSelection details
Rfree0.2999 2093 -RANDOM
Rwork0.253 ---
obs0.2554 41778 65.3 %-
Displacement parametersBiso mean: 85.53 Å2
Baniso -1Baniso -2Baniso -3
1--1.3473 Å20 Å20 Å2
2--0.4404 Å20 Å2
3---0.9068 Å2
Refine analyzeLuzzati coordinate error obs: 0.48 Å
Refinement stepCycle: LAST / Resolution: 2.769→50.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10267 0 28 0 10295
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00810574HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0514511HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3251SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes1775HARMONIC5
X-RAY DIFFRACTIONt_it10574HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion1455SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact7484SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.99
X-RAY DIFFRACTIONt_other_torsion19.9
LS refinement shellResolution: 2.77→2.98 Å
RfactorNum. reflection% reflection
Rfree0.347 34 -
Rwork0.3355 --
obs0.336 836 6.57 %

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