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- PDB-8w86: HLA-DQ2.5-B/C hordein peptide in complex with DQN0385AE02 -

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Basic information

Entry
Database: PDB / ID: 8w86
TitleHLA-DQ2.5-B/C hordein peptide in complex with DQN0385AE02
Components
  • (DQN0385AE02 Fab ...) x 2
  • HLA class II histocompatibility antigen, DQ alpha 1 chain
  • MHC class II HLA-DQ-beta-1 - B/C hordein 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 / PD-1 signaling / 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 / PD-1 signaling / MHC class II antigen presentation / trans-Golgi network membrane / lumenal side of endoplasmic reticulum membrane / clathrin-coated endocytic vesicle membrane / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / endocytic vesicle membrane / Interferon gamma signaling / positive regulation of immune response / Downstream TCR signaling / positive regulation of T cell activation / MHC class II protein complex binding / late endosome membrane / adaptive immune response / endosome membrane / immune response / lysosomal membrane / Golgi 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 / 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
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: 2.236 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DQN0385AE02 Fab heavy chain
B: DQN0385AE02 Fab light chain
C: HLA class II histocompatibility antigen, DQ alpha 1 chain
D: MHC class II HLA-DQ-beta-1 - B/C hordein peptide chimeric protein
E: DQN0385AE02 Fab heavy chain
F: DQN0385AE02 Fab light chain
G: HLA class II histocompatibility antigen, DQ alpha 1 chain
H: MHC class II HLA-DQ-beta-1 - B/C hordein peptide chimeric protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)190,32210
Polymers189,8808
Non-polymers4422
Water6,341352
1
A: DQN0385AE02 Fab heavy chain
B: DQN0385AE02 Fab light chain
C: HLA class II histocompatibility antigen, DQ alpha 1 chain
D: MHC class II HLA-DQ-beta-1 - B/C hordein peptide chimeric protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,1615
Polymers94,9404
Non-polymers2211
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: DQN0385AE02 Fab heavy chain
F: DQN0385AE02 Fab light chain
G: HLA class II histocompatibility antigen, DQ alpha 1 chain
H: MHC class II HLA-DQ-beta-1 - B/C hordein peptide chimeric protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,1615
Polymers94,9404
Non-polymers2211
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.701, 127.187, 130.365
Angle α, β, γ (deg.)90, 104.45, 90
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 4 molecules CGDH

#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 - B/C hordein peptide chimeric protein


Mass: 26299.449 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

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Antibody , 2 types, 4 molecules AEBF

#1: Antibody DQN0385AE02 Fab heavy chain


Mass: 23846.578 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 DQN0385AE02 Fab light chain


Mass: 23397.072 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)

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Sugars / Non-polymers , 2 types, 354 molecules

#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
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 352 / 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: 3.12 Å3/Da / Density % sol: 60.53 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1 M MES monohydrate (pH5.5), 12.0 %w/v Polyethylene glycol 8,000, 0.1 M Calcium acetate hydrate, and 30 %v/v Ethylene glycol as cryoprotectant

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.236→126.22 Å / Num. obs: 77604 / % possible obs: 93.6 % / Redundancy: 5.32 % / CC1/2: 0.998 / CC1/2 anomalous: -0.073 / Rmerge(I) obs: 0.1016 / Rpim(I) all: 0.048 / Rrim(I) all: 0.1127 / AbsDiff over sigma anomalous: 0.789 / Baniso tensor eigenvalue 1: 74.5 Å2 / Baniso tensor eigenvalue 2: 48.3 Å2 / Baniso tensor eigenvalue 3: 46 Å2 / Baniso tensor eigenvector 1 ortho1: 0.9129 / Baniso tensor eigenvector 1 ortho2: 0 / Baniso tensor eigenvector 1 ortho3: 0.4083 / Baniso tensor eigenvector 2 ortho1: 0 / Baniso tensor eigenvector 2 ortho2: 1 / Baniso tensor eigenvector 2 ortho3: 0 / Baniso tensor eigenvector 3 ortho1: -0.4083 / Baniso tensor eigenvector 3 ortho2: 0 / Baniso tensor eigenvector 3 ortho3: 0.9129 / Aniso diffraction limit 1: 2.849 Å / Aniso diffraction limit 2: 2.235 Å / Aniso diffraction limit 3: 2.394 Å / Aniso diffraction limit axis 1 ortho1: 0.96158 / Aniso diffraction limit axis 1 ortho2: 0 / Aniso diffraction limit axis 1 ortho3: 0.27449 / 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: -0.27449 / Aniso diffraction limit axis 3 ortho2: 0 / Aniso diffraction limit axis 3 ortho3: 0.96158 / Net I/σ(I): 10.72 / Num. measured all: 412512 / Orthogonalization convention: pdb / % possible anomalous: 92.1 / % possible ellipsoidal: 93.6 / % possible ellipsoidal anomalous: 92.1 / % possible spherical: 69.1 / % possible spherical anomalous: 68 / Redundancy anomalous: 2.72
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
6.921-126.225.360.033829.042079220792387938790.998-0.160.01590.03750.6299.799.799.799.799.72.7999.7
5.481-6.9215.480.052423.842127721277388138810.997-0.1220.02430.05790.78299.999.999.999.999.92.8199.9
4.775-5.4814.450.047522.331725517255388038800.997-0.1070.02430.05360.74195.598.695.598.695.52.3398.6
4.329-4.7754.450.049221.851724917249388038800.997-0.1340.02530.05560.75795.398.895.398.895.32.3198.8
4.02-4.3294.810.062219.751867718677388038800.996-0.0390.03110.06980.7919799.49799.4972.4799.4
3.781-4.024.980.078317.141931419314388138810.995-0.0830.03810.08740.839799.89799.8972.5699.8
3.591-3.7815.070.092615.381965819658388038800.993-0.0640.04460.10310.83497.899.797.899.797.82.5999.7
3.434-3.5915.20.116812.662017020170388038800.991-0.0370.05530.12970.85397.899.897.899.897.82.6799.8
3.302-3.4345.320.147810.882064320643388138810.986-0.0370.0690.16360.84698.499.798.499.798.42.7299.7
3.187-3.3025.380.20198.422086420864387938790.977-0.0610.09370.22320.82398.499.898.499.898.42.7499.8
3.087-3.1875.40.26336.632094520945388138810.96-0.0210.12190.2910.8189899.79899.7982.7699.7
2.998-3.0875.440.3375.282111921119388038800.94-0.0230.15530.37210.79498.999.698.999.698.92.7799.6
2.919-2.9985.450.4224.252115621156388038800.912-0.0350.19390.46570.79398.699.898.699.898.62.7899.8
2.847-2.9195.510.47043.762139921399388138810.904-0.0030.21510.51850.78597.898.597.898.597.82.898.5
2.776-2.8475.650.57943.212192821928388138810.860.0240.26210.63740.79894.695.194.691.2912.8695.1
2.704-2.7765.780.7242.632241122411387938790.778-0.0160.32420.7950.78491.392.191.381.2812.9392.1
2.63-2.7045.520.83962.212140521405388138810.6970.0050.39080.9280.7838888.7887170.82.7988.7
2.549-2.635.340.89621.942071720717387938790.663-0.0030.42580.99430.78582.483.482.457.457.12.7183.4
2.457-2.5495.741.06581.692229522295388138810.564-0.0040.4811.17170.76577.978.677.944.144.12.9178.6
2.236-2.4575.991.22921.562323823238388038800.5110.020.53841.3440.7860.261.460.214143.0461.4

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Processing

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

7vg1
PDB Unreleased entry


Resolution: 2.236→126.22 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.889 / SU R Cruickshank DPI: 0.355 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.341 / SU Rfree Blow DPI: 0.261 / SU Rfree Cruickshank DPI: 0.269
RfactorNum. reflection% reflectionSelection details
Rfree0.2804 4001 -RANDOM
Rwork0.241 ---
obs0.243 77604 69.1 %-
Displacement parametersBiso mean: 54.72 Å2
Baniso -1Baniso -2Baniso -3
1-0.3778 Å20 Å2-0.0732 Å2
2---0.4886 Å20 Å2
3---0.1108 Å2
Refine analyzeLuzzati coordinate error obs: 0.37 Å
Refinement stepCycle: LAST / Resolution: 2.236→126.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10808 0 28 352 11188
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00811127HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0315202HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3606SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes1870HARMONIC5
X-RAY DIFFRACTIONt_it11127HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion1478SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact8226SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.33
X-RAY DIFFRACTIONt_other_torsion18.31
LS refinement shellResolution: 2.24→2.38 Å
RfactorNum. reflection% reflection
Rfree0.3472 97 -
Rwork0.3085 --
obs0.3108 1553 8.3 %

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