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- PDB-8w84: HLA-DQ2.5-alpha2 gliadin peptide in complex with DQN0344AE02 -

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Basic information

Entry
Database: PDB / ID: 8w84
TitleHLA-DQ2.5-alpha2 gliadin peptide in complex with DQN0344AE02
Components
  • (DQN0344AE02 Fab ...) x 2
  • HLA class II histocompatibility antigen, DQ alpha 1 chain
  • MHC class II HLA-DQ-beta-1 - alpha2 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 / positive regulation of T cell activation / peptide antigen binding / 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: 2.105 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 1.3Oct 9, 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: DQN0344AE02 Fab heavy chain
B: DQN0344AE02 Fab light chain
C: HLA class II histocompatibility antigen, DQ alpha 1 chain
D: MHC class II HLA-DQ-beta-1 - alpha2 gliadin peptide chimeric protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,7326
Polymers95,2904
Non-polymers4422
Water3,009167
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12500 Å2
ΔGint-63 kcal/mol
Surface area35250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.86, 138.707, 201.928
Angle α, β, γ (deg.)90, 90, 90
Int Tables number24
Space group name H-MI212121

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Components

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Protein , 2 types, 2 molecules CD

#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.: 1 / Mutation: C47S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DQA1 / Cell line (production host): Expi293 / Production host: Homo sapiens (human) / References: UniProt: P01909
#4: Protein MHC class II HLA-DQ-beta-1 - alpha2 gliadin peptide chimeric protein


Mass: 25836.053 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DQB1 / Cell line (production host): Expi293 / Production host: Homo sapiens (human) / References: UniProt: O19712

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Antibody , 2 types, 2 molecules AB

#1: Antibody DQN0344AE02 Fab heavy chain


Mass: 24573.516 Da / Num. of mol.: 1
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 DQN0344AE02 Fab light chain


Mass: 23483.055 Da / Num. of mol.: 1
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, 169 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.: 167 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.04 Å3/Da / Density % sol: 59.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 80 mM di-Sodium malonate (pH4.0), 9.6 %w/v Polyethylene glycol 3,350, and 25 %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: Apr 8, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.105→114.332 Å / Num. obs: 39315 / % possible obs: 93.4 % / Redundancy: 9.02 % / CC1/2: 0.999 / CC1/2 anomalous: -0.156 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.0277 / Rrim(I) all: 0.0829 / AbsDiff over sigma anomalous: 0.765 / Baniso tensor eigenvalue 1: 47.8 Å2 / Baniso tensor eigenvalue 2: 43.1 Å2 / Baniso tensor eigenvalue 3: 142.7 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: 2.105 Å / Aniso diffraction limit 2: 2.126 Å / Aniso diffraction limit 3: 3.384 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): 17.13 / Num. measured all: 354515 / Orthogonalization convention: pdb / % possible anomalous: 93.3 / % possible ellipsoidal: 93.4 / % possible ellipsoidal anomalous: 93.3 / % possible spherical: 58.1 / % possible spherical anomalous: 57.5 / Redundancy anomalous: 4.7
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
7.046-114.3328.660.029652.711702517025196519651-0.4020.0110.03170.73399.999.899.999.899.94.8899.8
5.544-7.0469.650.042940.631897818978196619660.999-0.0930.01480.04550.7931001001001001005.18100
4.822-5.5449.710.042339.731907419074196519650.999-0.1130.01460.04480.7671001001001001005.16100
4.368-4.8229.260.044437.041822418224196719670.9990.0510.01590.04730.7951001001001001004.88100
4.05-4.3689.090.053231.131787117871196619660.9990.0010.01920.05670.7741001001001001004.78100
3.805-4.059.770.070125.621919919199196519650.999-0.1160.02430.07430.7910099.910099.91005.1199.9
3.611-3.805100.087621.391964519645196519650.999-0.030.02960.09260.77899.910099.910099.95.23100
3.451-3.61110.130.106218.361992819928196719670.9980.0380.03540.11210.8161001001001001005.28100
3.313-3.45110.220.142715.222008320083196619660.9970.0070.04710.15050.7899.899.899.899.199.25.399.8
3.191-3.3139.270.177712.021821618216196519650.996-0.0250.06170.18830.7899.899.899.893.594.54.8199.8
3.075-3.1919.330.22319.961833218332196519650.994-0.010.07710.23630.7799.799.799.787.188.14.8299.7
2.967-3.0758.720.27088.171713517135196619660.991-0.0160.09710.2880.78698.398.298.379.980.74.598.2
2.862-2.9678.650.31157.021700617006196719670.985-0.0040.11190.33140.75495.595.495.57272.94.4795.4
2.761-2.8628.610.38995.591692216922196619660.979-0.0080.14080.41490.73592.992.892.964.765.44.4492.8
2.667-2.7618.430.45354.651657216572196519650.96-00.16590.48330.7619392.99359.660.14.3492.9
2.576-2.6678.360.5443.911643416434196519650.925-0.010.19990.580.75192.692.592.654.254.84.3192.5
2.483-2.5768.250.6813.131622716227196719670.8980.020.25260.7270.74487.98887.946.146.24.2588
2.389-2.4837.980.78492.661569315693196619660.8440.0060.29710.840.74885.385.585.339394.1185.5
2.29-2.3897.90.9782.041552615526196519650.78-0.020.3721.04740.70683.583.983.531.931.64.0883.9
2.105-2.298.351.42121.531642516425196619660.5520.0070.52271.51570.73361.761.461.713.212.94.3361.4

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Processing

Software
NameVersionClassification
BUSTER2.11.8refinement
autoPROCdata processing
XDSJan 31, 2020data reduction
Aimless0.7.4data scaling
STARANISO2.3.63data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7VG1

7vg1
PDB Unreleased entry


Resolution: 2.105→114.33 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.854 / SU R Cruickshank DPI: 0.449 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.441 / SU Rfree Blow DPI: 0.324 / SU Rfree Cruickshank DPI: 0.331
RfactorNum. reflection% reflectionSelection details
Rfree0.3251 1916 -RANDOM
Rwork0.2603 ---
obs0.2634 39315 58.1 %-
Displacement parametersBiso mean: 52.44 Å2
Baniso -1Baniso -2Baniso -3
1--1.5194 Å20 Å20 Å2
2---1.1718 Å20 Å2
3---2.6912 Å2
Refine analyzeLuzzati coordinate error obs: 0.41 Å
Refinement stepCycle: LAST / Resolution: 2.105→114.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6220 0 28 167 6415
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0086420HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.018788HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2052SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes1080HARMONIC5
X-RAY DIFFRACTIONt_it6420HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion862SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact4656SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.23
X-RAY DIFFRACTIONt_other_torsion18.7
LS refinement shellResolution: 2.105→2.22 Å
RfactorNum. reflection% reflection
Rfree0.3824 48 -
Rwork0.3084 --
obs--8.11 %

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