[English] 日本語
Yorodumi
- PDB-4z7w: T316 complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4z7w
TitleT316 complex
Components
  • (MHC class II HLA-DQ- ...) x 2
  • (T-CELL RECEPTOR, T316 ...) x 2
  • DQ8-glia-alpha1
KeywordsIMMUNE SYSTEM / IMMUNE RECEPTOR-LIGAND COMPLEX
Function / homology
Function and homology information


nutrient reservoir activity / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / MHC class II protein complex / adaptive immune response / endosome membrane / lysosomal membrane
Similarity search - Function
Gliadin/LMW glutenin / Cys-rich Gliadin N-terminal / Plant lipid transfer protein / seed storage protein / trypsin-alpha amylase inhibitor domain family / Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain / Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain superfamily / Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / MHC class II, beta chain, N-terminal / Class II histocompatibility antigen, beta domain / Class II histocompatibility antigen, beta domain ...Gliadin/LMW glutenin / Cys-rich Gliadin N-terminal / Plant lipid transfer protein / seed storage protein / trypsin-alpha amylase inhibitor domain family / Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain / Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain superfamily / Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / 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 / Immunoglobulins / Roll / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
MHC class II HLA-DQ-beta-1 / Alpha/beta-gliadin MM1 / MHC class II HLA-DQ-alpha chain
Similarity search - Component
Biological speciesHomo sapiens (human)
Triticum aestivum (bread wheat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.89 Å
AuthorsPetersen, J. / Rossjohn, J. / Reid, H.H. / Koning, F.
CitationJournal: J Immunol. / Year: 2015
Title: Determinants of Gliadin-Specific T Cell Selection in Celiac Disease.
Authors: Petersen, J. / van Bergen, J. / Loh, K.L. / Kooy-Winkelaar, Y. / Beringer, D.X. / Thompson, A. / Bakker, S.F. / Mulder, C.J. / Ladell, K. / McLaren, J.E. / Price, D.A. / Rossjohn, J. / Reid, H.H. / Koning, F.
History
DepositionApr 8, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 3, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 17, 2015Group: Database references
Revision 1.2Aug 23, 2017Group: Data collection / Derived calculations / Source and taxonomy
Category: diffrn_detector / diffrn_source ...diffrn_detector / diffrn_source / entity_src_gen / pdbx_struct_oper_list
Item: _diffrn_detector.detector / _diffrn_source.pdbx_synchrotron_site ..._diffrn_detector.detector / _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: MHC class II HLA-DQ-alpha chain
B: MHC class II HLA-DQ-beta-1
C: MHC class II HLA-DQ-alpha chain
D: MHC class II HLA-DQ-beta-1
E: T-CELL RECEPTOR, T316 ALPHA CHAIN
F: T-CELL RECEPTOR, T316 BETA CHAIN
G: T-CELL RECEPTOR, T316 ALPHA CHAIN
H: T-CELL RECEPTOR, T316 BETA CHAIN
I: DQ8-glia-alpha1
J: DQ8-glia-alpha1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)199,55015
Polymers196,93010
Non-polymers2,6205
Water1,856103
1
A: MHC class II HLA-DQ-alpha chain
B: MHC class II HLA-DQ-beta-1
G: T-CELL RECEPTOR, T316 ALPHA CHAIN
H: T-CELL RECEPTOR, T316 BETA CHAIN
J: DQ8-glia-alpha1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,7277
Polymers98,4655
Non-polymers1,2622
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: MHC class II HLA-DQ-alpha chain
D: MHC class II HLA-DQ-beta-1
E: T-CELL RECEPTOR, T316 ALPHA CHAIN
F: T-CELL RECEPTOR, T316 BETA CHAIN
I: DQ8-glia-alpha1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,8238
Polymers98,4655
Non-polymers1,3583
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.623, 200.518, 87.183
Angle α, β, γ (deg.)90.00, 100.63, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
MHC class II HLA-DQ- ... , 2 types, 4 molecules ACBD

#1: Protein MHC class II HLA-DQ-alpha chain


Mass: 21882.221 Da / Num. of mol.: 2 / Fragment: UNP residues 1-184
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DQA1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q30069
#2: Protein MHC class II HLA-DQ-beta-1


Mass: 24484.211 Da / Num. of mol.: 2 / Fragment: UNP residues 1-192
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DQB1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: O19707

-
T-CELL RECEPTOR, T316 ... , 2 types, 4 molecules EGFH

#3: Protein T-CELL RECEPTOR, T316 ALPHA CHAIN /


Mass: 22918.309 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
#4: Protein T-CELL RECEPTOR, T316 BETA CHAIN /


Mass: 27376.443 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21

-
Protein/peptide , 1 types, 2 molecules IJ

#5: Protein/peptide DQ8-glia-alpha1


Mass: 1803.795 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Triticum aestivum (bread wheat) / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P18573*PLUS

-
Sugars , 2 types, 4 molecules

#6: Polysaccharide alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1040.964 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpa1-3DGlcpNAcb1-4[LFucpa1-3][LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5][a1122h-1a_1-5]/1-2-1-3-3-2/a3-b1_a4-c1_a6-f1_c3-d1_d6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-GlcpNAc]{[(3+1)][a-D-Manp]{[(6+1)][a-D-Manp]{}}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#7: 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 / N-Acetylglucosamine


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

-
Non-polymers , 2 types, 104 molecules

#8: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 103 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.91 Å3/Da / Density % sol: 57.71 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: 0.32 M (NH4)2SO4, 0.1 M HEPES pH 7.8, 20% PEG3350 / PH range: 7.8

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 4, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.89→85.69 Å / Num. obs: 45344 / % possible obs: 99.59 % / Redundancy: 4.1 % / Biso Wilson estimate: 58.59 Å2 / Rmerge(I) obs: 0.117 / Net I/σ(I): 11.13
Reflection shellResolution: 2.89→3 Å / Redundancy: 4 % / Rmerge(I) obs: 0.421 / Mean I/σ(I) obs: 3.34 / % possible all: 79.16

-
Processing

Software
NameVersionClassification
BUSTER2.10.1refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GG8

4gg8


Resolution: 2.89→85.69 Å / Cor.coef. Fo:Fc: 0.8476 / Cor.coef. Fo:Fc free: 0.8333 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.378
RfactorNum. reflection% reflectionSelection details
Rfree0.2473 2286 5.04 %RANDOM
Rwork0.2279 ---
obs0.2289 45340 90.31 %-
Displacement parametersBiso mean: 59.64 Å2
Baniso -1Baniso -2Baniso -3
1--6.8535 Å20 Å29.61 Å2
2---0.2016 Å20 Å2
3---7.0551 Å2
Refine analyzeLuzzati coordinate error obs: 0.493 Å
Refinement stepCycle: LAST / Resolution: 2.89→85.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12708 0 173 103 12984
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00713252HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.8518123HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d5868SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes334HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1930HARMONIC5
X-RAY DIFFRACTIONt_it13252HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion1.71
X-RAY DIFFRACTIONt_other_torsion3
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1768SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact13560SEMIHARMONIC4
LS refinement shellResolution: 2.89→2.96 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3091 137 4.96 %
Rwork0.2646 2625 -
all0.2669 2762 -
obs--90.31 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.77680.4130.28681.8551-0.03210.83550.0079-0.13510.1765-0.05310.07060.27720.0697-0.2436-0.0785-0.0027-0.07210.0007-0.1410.04890.04511.6972-33.1137.6251
22.21411.81641.21882.57970.86181.68350.03250.02580.0122-0.41030.1624-0.02080.2940.0077-0.1950.1186-0.1065-0.0468-0.24330.0928-0.04477.5571-47.2856-0.7407
30.97240.2926-0.70642.42530.36582.1686-0.091-0.1752-0.12470.1735-0.01480.06760.0589-0.21250.1059-0.01490.06730.0277-0.0802-0.0206-0.080920.33166.490237.095
40.852-0.2240.28622.95611.89953.6741-0.2050.02880.19430.12950.1333-0.2994-0.12350.0090.0716-0.03790.0715-0.0049-0.237-0.0236-0.019430.744620.430135.9213
51.0188-0.5291.89270.177-0.85613.840.04880.17240.01750.0201-0.06140.0689-0.1999-0.03250.01260.13790.15370.06060.0121-0.0478-0.145711.073818.5966-18.7823
60.6692-0.43730.89641.15840.46192.45880.0779-0.0054-0.356-0.0221-0.12020.2862-0.0464-0.3440.0423-0.1579-0.02470.02560.0134-0.1593-0.01191.69271.9727-14.4923
72.7514-1.61443.10140.022-1.46672.8337-0.0127-0.1582-0.0673-0.03660.05110.02060.10070.1953-0.0384-0.0234-0.108-0.1851-0.07460.08690.115945.3534-46.239441.9223
80.73810.53051.34480.48120.9792.86070.0603-0.2976-0.06040.10220.0660.12020.04030.0049-0.12630.1034-0.14560.0382-0.0158-0.0482-0.171437.9947-28.057648.1583
91.02271.1497-0.65350.744-2.20132.39750.0014-0.0101-0.0140.0066-0.0129-0.0032-0.00820.00470.01160.04140.0510.0222-0.0495-0.0128-0.025922.05429.033615.2024
101.5625-1.3984-0.58880.60781.77932.2395-0.0022-0.01250.00720.01610.00220.00360.0070.0020.00010.0079-0.12710.0305-0.08060.02740.032422.1566-35.64916.6881
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }
5X-RAY DIFFRACTION5{ E|* }
6X-RAY DIFFRACTION6{ F|* }
7X-RAY DIFFRACTION7{ G|* }
8X-RAY DIFFRACTION8{ H|* }
9X-RAY DIFFRACTION9{ I|* }
10X-RAY DIFFRACTION10{ J|* }

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more