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- PDB-8w83: HLA-DQ2.5-alpha1 gliadin peptide in complex with DQN0344AE02 -

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Basic information

Entry
Database: PDB / ID: 8w83
TitleHLA-DQ2.5-alpha1 gliadin peptide in complex with DQN0344AE02
Components
  • DQN0344AE02 Fab heavy chain
  • DQN0344AE02 Fab light chain
  • HLA class II histocompatibility antigen, DQ alpha 1 chain
  • MHC class II HLA-DQ-beta-1 - alpha1 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 / 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 / positive regulation of immune response / Interferon gamma signaling / endocytic vesicle membrane / positive regulation of T cell activation / Downstream TCR signaling / MHC class II protein complex binding / late endosome membrane / 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: 2.818 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 13, 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 - alpha1 gliadin peptide chimeric protein
E: DQN0344AE02 Fab heavy chain
F: DQN0344AE02 Fab light chain
G: HLA class II histocompatibility antigen, DQ alpha 1 chain
H: MHC class II HLA-DQ-beta-1 - alpha1 gliadin peptide chimeric protein
I: DQN0344AE02 Fab heavy chain
J: DQN0344AE02 Fab light chain
K: HLA class II histocompatibility antigen, DQ alpha 1 chain
L: MHC class II HLA-DQ-beta-1 - alpha1 gliadin peptide chimeric protein
M: DQN0344AE02 Fab heavy chain
N: DQN0344AE02 Fab light chain
O: HLA class II histocompatibility antigen, DQ alpha 1 chain
P: MHC class II HLA-DQ-beta-1 - alpha1 gliadin peptide chimeric protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)382,10320
Polymers381,21816
Non-polymers8854
Water00
1
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 - alpha1 gliadin peptide chimeric protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,5265
Polymers95,3054
Non-polymers2211
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: DQN0344AE02 Fab heavy chain
F: DQN0344AE02 Fab light chain
G: HLA class II histocompatibility antigen, DQ alpha 1 chain
H: MHC class II HLA-DQ-beta-1 - alpha1 gliadin peptide chimeric protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,5265
Polymers95,3054
Non-polymers2211
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
I: DQN0344AE02 Fab heavy chain
J: DQN0344AE02 Fab light chain
K: HLA class II histocompatibility antigen, DQ alpha 1 chain
L: MHC class II HLA-DQ-beta-1 - alpha1 gliadin peptide chimeric protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,5265
Polymers95,3054
Non-polymers2211
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
M: DQN0344AE02 Fab heavy chain
N: DQN0344AE02 Fab light chain
O: HLA class II histocompatibility antigen, DQ alpha 1 chain
P: MHC class II HLA-DQ-beta-1 - alpha1 gliadin peptide chimeric protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,5265
Polymers95,3054
Non-polymers2211
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)87.488, 174.235, 129.656
Angle α, β, γ (deg.)90, 93.17, 90
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody
DQN0344AE02 Fab heavy chain


Mass: 24573.516 Da / Num. of mol.: 4
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.: 4
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.: 4 / Mutation: C47S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DQA1 / Cell line (production host): FreeStyle293-F / Production host: Homo sapiens (human) / References: UniProt: P01909
#4: Protein
MHC class II HLA-DQ-beta-1 - alpha1 gliadin peptide chimeric protein


Mass: 25851.066 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DQB1 / Cell line (production host): FreeStyle293-F / 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.: 4 / 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: 2.81 Å3/Da / Density % sol: 56.27 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M HEPES (pH7.5), 25.0 %w/v Polyethylene glycol 1,000, and 20 %v/v Glycerol as cryoprotectant

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 14, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.818→129.458 Å / Num. obs: 44543 / % possible obs: 92.7 % / Redundancy: 6.41 %
Details: Some remarks regarding the mmCIF items written, the PDB Exchange Dictionary (PDBx/mmCIF) Version 5.0 supporting the data files in the current PDB archive (dictionary version 5.325, last ...Details: Some remarks regarding the mmCIF items written, the PDB Exchange Dictionary (PDBx/mmCIF) Version 5.0 supporting the data files in the current PDB archive (dictionary version 5.325, last updated 2020-04-13: http://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Index/) and the actual quantities provided by MRFANA (https://github.com/githubgphl/MRFANA) from the autoPROC package (https://www.globalphasing.com/autoproc/). In general, the mmCIF categories here should provide items that are currently used in the PDB archive. If there are alternatives, the one recommended by the PDB developers has been selected. The distinction between *_all and *_obs quantities is not always clear: often only one version is actively used within the PDB archive (or is the one recommended by PDB developers). The intention of distinguishing between classes of reflections before and after some kind of observation criterion was applied, can in principle be useful - but such criteria change in various ways throughout the data processing steps (rejection of overloaded or too partial reflections, outlier/misfit rejections during scaling etc) and there is no retrospect computation of data scaling/merging statistics for the reflections used in the final refinement (where another observation criterion might have been applied). Typical data processing will usually only provide one version of statistics at various stages and these are given in the recommended item here, irrespective of the "_all" and "_obs" connotation, see e.g. the use of _reflns.pdbx_Rmerge_I_obs, _reflns.pdbx_Rrim_I_all and _reflns.pdbx_Rpim_I_all. Please note that all statistics related to "merged intensities" (or "merging") are based on inverse-variance weighting of the individual measurements making up a symmetry-unique reflection. This is standard for several decades now, even if some of the dictionary definitions seem to suggest that a simple "mean" or "average" intensity is being used instead. R-values are always given for all symmetry-equivalent reflections following Friedel's law, i.e. Bijvoet pairs are not treated separately (since we want to describe the overall mean intensity and not the mean I(+) and I(-) here). The Rrim metric is identical to the Rmeas R-value and only differs in name. _reflns.pdbx_number_measured_all is the number of measured intensities just before the final merging step (at which point no additional rejection takes place). _reflns.number_obs is the number of symmetry-unique observations, i.e. the result of merging those measurements via inverse-variance weighting. _reflns.pdbx_netI_over_sigmaI is based on the merged intensities (_reflns.number_obs) as expected. _reflns.pdbx_redundancy is synonymous with "multiplicity". The per-shell item _reflns_shell.number_measured_all corresponds to the overall value _reflns.pdbx_number_measured_all. The per-shell item _reflns_shell.number_unique_all corresponds to the overall value _reflns.number_obs. The per-shell item _reflns_shell.percent_possible_all corresponds to the overall value _reflns.percent_possible_obs. The per-shell item _reflns_shell.meanI_over_sigI_obs corresponds to the overall value given as _reflns.pdbx_netI_over_sigmaI. But be aware of the incorrect definition of the former in the current dictionary!
CC1/2: 0.9 / CC1/2 anomalous: 0.22 / Rmerge(I) obs: 0.5004 / Rpim(I) all: 0.2174 / Rrim(I) all: 0.5466 / AbsDiff over sigma anomalous: 0.843 / Baniso tensor eigenvalue 1: 93.6 Å2 / Baniso tensor eigenvalue 2: 55.4 Å2 / Baniso tensor eigenvalue 3: 27 Å2 / Baniso tensor eigenvector 1 ortho1: 0.7173 / Baniso tensor eigenvector 1 ortho2: 0 / Baniso tensor eigenvector 1 ortho3: 0.6968 / Baniso tensor eigenvector 2 ortho1: 0 / Baniso tensor eigenvector 2 ortho2: 1 / Baniso tensor eigenvector 2 ortho3: 0 / Baniso tensor eigenvector 3 ortho1: -0.6968 / Baniso tensor eigenvector 3 ortho2: 0 / Baniso tensor eigenvector 3 ortho3: 0.7173 / Aniso diffraction limit 1: 4.256 Å / Aniso diffraction limit 2: 3.653 Å / Aniso diffraction limit 3: 2.817 Å / Aniso diffraction limit axis 1 ortho1: 0.75744 / Aniso diffraction limit axis 1 ortho2: 0 / Aniso diffraction limit axis 1 ortho3: 0.65284 / 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: -0.65284 / Aniso diffraction limit axis 3 ortho2: 0 / Aniso diffraction limit axis 3 ortho3: 0.75744 / Net I/σ(I): 4.68 / Num. measured all: 285587 / Orthogonalization convention: pdb / % possible anomalous: 91.6 / % possible ellipsoidal: 92.7 / % possible ellipsoidal anomalous: 91.6 / % possible spherical: 47.7 / % possible spherical anomalous: 46.8 / Redundancy anomalous: 3.28
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
9.881-129.45860.0913.211337213372222722270.990.3820.040.09880.72598.399.798.399.798.33.1699.7
7.824-9.8816.790.129710.661510615106222622260.992-0.0420.05350.14050.75599.510099.510099.53.49100
6.826-7.8246.270.26286.041397213972222822280.9710.0150.11350.28670.79199.510099.510099.53.2100
6.192-6.8266.340.37024.791413314133222822280.9390.020.15860.40330.79999.710099.710099.73.23100
5.749-6.1926.750.40094.641501715017222622260.9390.0320.16540.43410.79399.910099.910099.93.43100
5.407-5.7496.860.39214.81527815278222722270.9510.0730.16040.4240.81899.910099.910099.93.49100
5.133-5.4076.970.35835.051553015530222822280.9640.0220.14540.3870.77999.910099.910099.93.54100
4.91-5.1336.540.34525.041454914549222622260.9560.0030.14580.37510.77399.710099.710099.73.32100
4.72-4.916.530.35894.921455714557222822280.9520.0030.15150.390.80299.610099.610099.63.32100
4.556-4.726.240.33334.991388213882222622260.955-0.0250.14480.3640.78799.710099.710099.73.16100
4.413-4.5566.590.38794.661467414674222822280.9550.0460.16310.42130.899.710099.710099.73.34100
4.286-4.4136.680.45594.21489214892222822280.9430.0460.18960.49430.82899.199.399.199.399.13.3999.3
4.163-4.2866.710.58693.631492714927222622260.9140.0390.24350.6360.81695.195.295.193.293.23.3995.2
4.044-4.1636.650.75713.241480414804222722270.8770.1030.31750.82180.84491.992.291.983.683.63.3792.2
3.922-4.0446.50.99962.771447014470222622260.8590.110.4271.08830.8668990.28973.973.23.3190.2
3.794-3.9226.051.31272.31348313483222922290.7150.4630.59241.44391.19681.185.281.161.758.93.1585.2
3.653-3.7946.071.19582.51353513535222822280.6950.3420.53751.31410.94176.879.976.848.246.53.1479.9
3.485-3.6535.991.35112.441334413344222722270.6410.1320.62281.49170.91878.681.178.634.433.33.0981.1
3.27-3.4855.811.61882.021293412934222622260.6110.2320.75311.79070.9877577.77521.320.43.0177.7
2.818-3.275.891.23711.671312813128222822280.5930.0970.55091.3580.84671.872.871.86.76.43.0272.8

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Processing

Software
NameVersionClassification
BUSTER2.11.8 (8-JUN-2022)refinement
autoPROCdata processing
XDSJan 31, 2020data reduction
Aimless0.7.4data scaling
STARANISO2.3.63data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1S9V

1s9v


Resolution: 2.818→54.86 Å / Cor.coef. Fo:Fc: 0.794 / Cor.coef. Fo:Fc free: 0.71 / Cross valid method: THROUGHOUT / SU Rfree Blow DPI: 0.802
RfactorNum. reflection% reflectionSelection details
Rfree0.3209 2141 -RANDOM
Rwork0.2779 ---
obs0.28 44529 47.7 %-
Displacement parametersBiso mean: 39.44 Å2
Baniso -1Baniso -2Baniso -3
1--5.4439 Å20 Å2-10.4007 Å2
2--5.7555 Å20 Å2
3----0.3116 Å2
Refine analyzeLuzzati coordinate error obs: 0.59 Å
Refinement stepCycle: LAST / Resolution: 2.818→54.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23587 0 56 0 23643
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00424274HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.5933249HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d7564SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes4090HARMONIC5
X-RAY DIFFRACTIONt_it24274HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion3278SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact14376SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion1.39
X-RAY DIFFRACTIONt_other_torsion17.51
LS refinement shellResolution: 2.82→3.1 Å
RfactorNum. reflection% reflection
Rfree0.4333 39 -
Rwork0.3551 --
obs0.3589 891 3.8 %

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