[English] 日本語
Yorodumi
- PDB-6bir: HLA-DRB1 in complex with citrullinated Vimentin peptide -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6bir
TitleHLA-DRB1 in complex with citrullinated Vimentin peptide
Components
  • HLA class II histocompatibility antigen, DR alpha chain
  • MHC class II antigen
  • Vimentin 424Cit419-431
KeywordsIMMUNE SYSTEM / HLA / MHC / citrulline / Rheumatoid Arthritis
Function / homology
Function and homology information


keratin filament binding / lens fiber cell development / regulation of interleukin-4 production / intermediate filament organization / regulation of interleukin-10 production / myeloid dendritic cell antigen processing and presentation / antigen processing and presentation of endogenous peptide antigen via MHC class II / autolysosome membrane / regulation of T-helper cell differentiation / cellular response to muramyl dipeptide ...keratin filament binding / lens fiber cell development / regulation of interleukin-4 production / intermediate filament organization / regulation of interleukin-10 production / myeloid dendritic cell antigen processing and presentation / antigen processing and presentation of endogenous peptide antigen via MHC class II / autolysosome membrane / regulation of T-helper cell differentiation / cellular response to muramyl dipeptide / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / structural constituent of eye lens / MHC class II receptor activity / positive regulation of CD4-positive, alpha-beta T cell activation / astrocyte development / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / positive regulation of T cell mediated immune response to tumor cell / positive regulation of kinase activity / positive regulation of memory T cell differentiation / CD4 receptor binding / positive regulation of monocyte differentiation / inflammatory response to antigenic stimulus / intermediate filament cytoskeleton / Striated Muscle Contraction / RHOBTB1 GTPase cycle / intermediate filament / T-helper 1 type immune response / transport vesicle membrane / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / cell leading edge / microtubule organizing center / Bergmann glial cell differentiation / polysaccharide binding / negative regulation of type II interferon production / humoral immune response / macrophage differentiation / positive regulation of insulin secretion involved in cellular response to glucose stimulus / Generation of second messenger molecules / positive regulation of collagen biosynthetic process / immunological synapse / Co-inhibition by PD-1 / epidermis development / Caspase-mediated cleavage of cytoskeletal proteins / detection of bacterium / T cell receptor binding / phagocytic vesicle / negative regulation of T cell proliferation / regulation of mRNA stability / MHC class II antigen presentation / trans-Golgi network membrane / lumenal side of endoplasmic reticulum membrane / protein tetramerization / peptide antigen assembly with MHC class II protein complex / negative regulation of inflammatory response to antigenic stimulus / MHC class II protein complex / clathrin-coated endocytic vesicle membrane / ER to Golgi transport vesicle membrane / Late endosomal microautophagy / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / peptide antigen binding / structural constituent of cytoskeleton / positive regulation of T cell mediated cytotoxicity / cellular response to type II interferon / positive regulation of T cell activation / cognition / nuclear matrix / Chaperone Mediated Autophagy / Interferon gamma signaling / Aggrephagy / neuron projection development / MHC class II protein complex binding / endocytic vesicle membrane / late endosome membrane / peroxisome / Downstream TCR signaling / double-stranded RNA binding / T cell receptor signaling pathway / positive regulation of protein phosphorylation / negative regulation of neuron projection development / cellular response to lipopolysaccharide / early endosome membrane / scaffold protein binding / Interleukin-4 and Interleukin-13 signaling / molecular adaptor activity / adaptive immune response / positive regulation of canonical NF-kappaB signal transduction / cytoskeleton / positive regulation of viral entry into host cell / lysosome / positive regulation of ERK1 and ERK2 cascade / positive regulation of MAPK cascade / endosome membrane / immune response / protein domain specific binding / axon / Golgi membrane / external side of plasma membrane / lysosomal membrane
Similarity search - Function
Intermediate filament head, DNA-binding domain / : / Intermediate filament head (DNA binding) region / Intermediate filament protein, conserved site / Intermediate filament protein / Intermediate filament (IF) rod domain signature. / Intermediate filament, rod domain / Intermediate filament (IF) rod domain profile. / Intermediate filament protein / Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 ...Intermediate filament head, DNA-binding domain / : / Intermediate filament head (DNA binding) region / Intermediate filament protein, conserved site / Intermediate filament protein / Intermediate filament (IF) rod domain signature. / Intermediate filament, rod domain / Intermediate filament (IF) rod domain profile. / Intermediate filament 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 / Roll / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
HLA class II histocompatibility antigen, DR alpha chain / HLA class II histocompatibility antigen, DRB1 beta chain / Vimentin / MHC class II antigen
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsTing, Y.T. / Scally, S.W. / Rossjohn, J.
CitationJournal: J. Biol. Chem. / Year: 2018
Title: The interplay between citrullination and HLA-DRB1 polymorphism in shaping peptide binding hierarchies in rheumatoid arthritis.
Authors: Ting, Y.T. / Petersen, J. / Ramarathinam, S.H. / Scally, S.W. / Loh, K.L. / Thomas, R. / Suri, A. / Baker, D.G. / Purcell, A.W. / Reid, H.H. / Rossjohn, J.
History
DepositionNov 2, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 17, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / entity / struct
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _entity.pdbx_description / _struct.title
Revision 1.2Mar 14, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_validate_main_chain_plane / pdbx_validate_rmsd_angle / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id
Revision 2.1Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: HLA class II histocompatibility antigen, DR alpha chain
B: MHC class II antigen
C: Vimentin 424Cit419-431
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,0495
Polymers46,6073
Non-polymers4422
Water2,648147
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7980 Å2
ΔGint-17 kcal/mol
Surface area17470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.460, 183.010, 77.080
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein HLA class II histocompatibility antigen, DR alpha chain / MHC class II antigen DRA


Mass: 21919.594 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DRA, HLA-DRA1 / Cell line (production host): HEK293S GnTI- / Production host: Homo sapiens (human) / References: UniProt: P01903
#2: Protein MHC class II antigen


Mass: 23224.621 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DR-beta 1 / Cell line (production host): HEK293S GnTI- / Production host: Homo sapiens (human) / References: UniProt: P79552, UniProt: P01911*PLUS
#3: Protein/peptide Vimentin 424Cit419-431


Mass: 1462.562 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P08670*PLUS
#4: 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: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 147 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.69 Å3/Da / Density % sol: 54.2 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Imidazole/MES pH 6.5, 0.01 M ammonium sulfate, 0.01 M di-sodium hydrogen phosphate, 0.01 M sodium nitrate, 12.5% 2-methyl-2,4-pentanediol (MPD), 14% PEG3350, 12.5% PEG1000

-
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: Feb 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.3→39.345 Å / Num. obs: 21534 / % possible obs: 99.6 % / Redundancy: 6.8 % / Biso Wilson estimate: 25.61 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.176 / Rpim(I) all: 0.072 / Rrim(I) all: 0.19 / Net I/σ(I): 9.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.3-2.386.30.8261290220410.7920.3450.8982.498
8.91-39.345.70.05724064220.9980.0250.06319.398.5

-
Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
Aimless0.2.7data scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MDI

4mdi


Resolution: 2.3→39.344 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.08
RfactorNum. reflection% reflection
Rfree0.2371 1102 5.12 %
Rwork0.1854 --
obs0.1881 21511 99.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 76.28 Å2 / Biso mean: 25.5611 Å2 / Biso min: 9.51 Å2
Refinement stepCycle: final / Resolution: 2.3→39.344 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3046 0 28 147 3221
Biso mean--51.89 27.03 -
Num. residues----376
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073169
X-RAY DIFFRACTIONf_angle_d0.9224313
X-RAY DIFFRACTIONf_chiral_restr0.053471
X-RAY DIFFRACTIONf_plane_restr0.005558
X-RAY DIFFRACTIONf_dihedral_angle_d14.7771859
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3001-2.40480.27151220.2312486260898
2.4048-2.53150.28541330.22312501263499
2.5315-2.69010.28131310.2222532266399
2.6901-2.89770.26631460.207225192665100
2.8977-3.18920.30561580.202925322690100
3.1892-3.65040.22871380.174425552693100
3.6504-4.5980.20551300.147125932723100
4.598-39.34930.17751440.17382691283599

+
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