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- PDB-5ujt: Crystal structure of human HLA-DQ8 in complex with insulin mimoto... -

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Basic information

Entry
Database: PDB / ID: 5ujt
TitleCrystal structure of human HLA-DQ8 in complex with insulin mimotope binding in register 3
Components
  • (MHC class II ...) x 2
  • insulin mimotope
KeywordsIMMUNE SYSTEM / INSULIN / TYPE I DIABETES / T CELL / AUTOIMMUNE DISEASE
Function / homology
Function and homology information


antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / MHC class II protein complex / adaptive immune response / membrane => GO:0016020 / endosome membrane / lysosomal membrane
Similarity search - Function
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 ...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 / HLA class II histocompatibility antigen DQ alpha chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsWang, Y. / Dai, S.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: C-terminal modification of the insulin B:11-23 peptide creates superagonists in mouse and human type 1 diabetes.
Authors: Wang, Y. / Sosinowski, T. / Novikov, A. / Crawford, F. / Neau, D.B. / Yang, J. / Kwok, W.W. / Marrack, P. / Kappler, J.W. / Dai, S.
History
DepositionJan 18, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 20, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 3, 2018Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 10, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / 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 / pdbx_validate_close_contact / 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_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 4, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MHC class II antigen
B: MHC class II HLA-DQ-beta-1
C: insulin mimotope
D: MHC class II antigen
E: MHC class II HLA-DQ-beta-1
F: insulin mimotope
G: MHC class II antigen
H: MHC class II HLA-DQ-beta-1
I: insulin mimotope
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,19013
Polymers134,8999
Non-polymers1,2914
Water11,620645
1
A: MHC class II antigen
B: MHC class II HLA-DQ-beta-1
C: insulin mimotope
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,8155
Polymers44,9663
Non-polymers8492
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8260 Å2
ΔGint-22 kcal/mol
Surface area18770 Å2
MethodPISA
2
D: MHC class II antigen
E: MHC class II HLA-DQ-beta-1
F: insulin mimotope
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1874
Polymers44,9663
Non-polymers2211
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7660 Å2
ΔGint-32 kcal/mol
Surface area18080 Å2
MethodPISA
3
G: MHC class II antigen
H: MHC class II HLA-DQ-beta-1
I: insulin mimotope
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1874
Polymers44,9663
Non-polymers2211
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7710 Å2
ΔGint-29 kcal/mol
Surface area17870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.038, 138.767, 159.735
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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MHC class II ... , 2 types, 6 molecules ADGBEH

#1: Protein MHC class II antigen


Mass: 21138.500 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DQA1 / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): Hi5 / References: UniProt: Q5Y7C3
#2: Protein MHC class II HLA-DQ-beta-1


Mass: 22246.021 Da / Num. of mol.: 3
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

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Protein/peptide / Non-polymers , 2 types, 648 molecules CFI

#3: Protein/peptide insulin mimotope


Mass: 1581.701 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Trichoplusia ni (cabbage looper)
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 645 / Source method: isolated from a natural source / Formula: H2O

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Sugars , 2 types, 4 molecules

#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 627.594 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-3[DGlcpNAcb1-4]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a2122h-1b_1-5_2*NCC/3=O]/1-1-1/a3-b1_a4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(3+1)][b-D-GlcpNAc]{}[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
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

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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: 2.97 Å3/Da / Density % sol: 58.59 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 4.5 / Details: 15% PEG3350, 100mM Tacsimate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 6, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.94→79.868 Å / Num. obs: 118542 / % possible obs: 99.6 % / Redundancy: 2 % / Net I/σ(I): 50

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JK8

1jk8


Resolution: 1.94→79.87 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.62
RfactorNum. reflection% reflection
Rfree0.238 5832 4.92 %
Rwork0.209 --
obs0.21 118542 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.94→79.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9301 0 84 645 10030
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0089632
X-RAY DIFFRACTIONf_angle_d1.09813147
X-RAY DIFFRACTIONf_dihedral_angle_d17.2025701
X-RAY DIFFRACTIONf_chiral_restr0.0671456
X-RAY DIFFRACTIONf_plane_restr0.0061698
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.94-1.9620.36732140.3133629X-RAY DIFFRACTION98
1.962-1.98510.31781900.30483657X-RAY DIFFRACTION98
1.9851-2.00930.31941880.29333714X-RAY DIFFRACTION99
2.0093-2.03480.34531860.29493692X-RAY DIFFRACTION100
2.0348-2.06160.32422100.28323715X-RAY DIFFRACTION100
2.0616-2.08980.31111800.27523706X-RAY DIFFRACTION100
2.0898-2.11970.31142060.26783710X-RAY DIFFRACTION99
2.1197-2.15130.29911960.27493726X-RAY DIFFRACTION100
2.1513-2.18490.32961730.2633738X-RAY DIFFRACTION100
2.1849-2.22070.28482040.26613714X-RAY DIFFRACTION100
2.2207-2.2590.27192250.25843714X-RAY DIFFRACTION100
2.259-2.30010.27531900.24243714X-RAY DIFFRACTION100
2.3001-2.34440.27841780.24963745X-RAY DIFFRACTION100
2.3444-2.39220.30821850.26253738X-RAY DIFFRACTION99
2.3922-2.44420.28512030.25473730X-RAY DIFFRACTION100
2.4442-2.50110.27122000.2213748X-RAY DIFFRACTION100
2.5011-2.56360.24681810.2193782X-RAY DIFFRACTION100
2.5636-2.6330.26311880.21653721X-RAY DIFFRACTION100
2.633-2.71040.26731780.20943768X-RAY DIFFRACTION100
2.7104-2.79790.22692010.20023776X-RAY DIFFRACTION100
2.7979-2.89790.25271850.20283804X-RAY DIFFRACTION100
2.8979-3.0140.22571880.2043780X-RAY DIFFRACTION100
3.014-3.15120.22341900.19823755X-RAY DIFFRACTION100
3.1512-3.31730.20422000.18453787X-RAY DIFFRACTION100
3.3173-3.52510.20771830.1853748X-RAY DIFFRACTION99
3.5251-3.79730.17632050.17893816X-RAY DIFFRACTION100
3.7973-4.17940.19531840.16773829X-RAY DIFFRACTION100
4.1794-4.78410.17352010.1473857X-RAY DIFFRACTION100
4.7841-6.02720.21882170.18163882X-RAY DIFFRACTION100
6.0272-79.93520.23242030.22214015X-RAY DIFFRACTION99

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