[English] 日本語
Yorodumi
- PDB-6atz: HLA-DRB1*1402 in complex with citrullinated fibrinogen peptide -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6atz
TitleHLA-DRB1*1402 in complex with citrullinated fibrinogen peptide
Components
  • Fibrinogen beta chain
  • HLA class II histocompatibility antigen, DR alpha chain
  • MHC class II antigen
KeywordsIMMUNE SYSTEM / HLA / MHC / citrulline / Rheumatoid Arthritis
Function / homology
Function and homology information


induction of bacterial agglutination / 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 / fibrinogen complex / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / MHC class II receptor activity / positive regulation of CD4-positive, alpha-beta T cell activation / platelet alpha granule ...induction of bacterial agglutination / 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 / fibrinogen complex / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / MHC class II receptor activity / positive regulation of CD4-positive, alpha-beta T cell activation / platelet alpha granule / Regulation of TLR by endogenous ligand / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / positive regulation of memory T cell differentiation / blood coagulation, fibrin clot formation / cellular response to leptin stimulus / MyD88 deficiency (TLR2/4) / positive regulation of heterotypic cell-cell adhesion / IRAK4 deficiency (TLR2/4) / extracellular matrix structural constituent / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / plasminogen activation / transport vesicle membrane / p130Cas linkage to MAPK signaling for integrins / positive regulation of peptide hormone secretion / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / positive regulation of vasoconstriction / polysaccharide binding / GRB2:SOS provides linkage to MAPK signaling for Integrins / Generation of second messenger molecules / immunological synapse / positive regulation of exocytosis / Co-inhibition by PD-1 / protein polymerization / cellular response to interleukin-1 / Integrin cell surface interactions / Common Pathway of Fibrin Clot Formation / negative regulation of endothelial cell apoptotic process / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / T cell receptor binding / fibrinolysis / Integrin signaling / positive regulation of substrate adhesion-dependent cell spreading / MHC class II antigen presentation / platelet alpha granule lumen / cell-matrix adhesion / trans-Golgi network membrane / positive regulation of protein secretion / 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 / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / response to calcium ion / 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 / positive regulation of T cell mediated cytotoxicity / platelet aggregation / cognition / Interferon gamma signaling / MHC class II protein complex binding / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / endocytic vesicle membrane / late endosome membrane / Signaling by BRAF and RAF1 fusions / Downstream TCR signaling / Platelet degranulation / extracellular vesicle / protein-folding chaperone binding / : / ER-Phagosome pathway / protein-containing complex assembly / early endosome membrane / cell cortex / blood microparticle / adaptive immune response / positive regulation of ERK1 and ERK2 cascade / lysosome / endosome membrane / immune response / signaling receptor binding / Golgi membrane / lysosomal membrane / innate immune response / external side of plasma membrane / synapse / structural molecule activity / cell surface / endoplasmic reticulum / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Fibrinogen, alpha/beta/gamma chain, coiled coil domain / Fibrinogen alpha/beta chain family / Fibrinogen alpha/beta chain family / Fibrinogen alpha chain / Fibrinogen, conserved site / Fibrinogen C-terminal domain signature. / Fibrinogen-related domains (FReDs) / Fibrinogen beta and gamma chains, C-terminal globular domain / Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 1 / Fibrinogen, alpha/beta/gamma chain, C-terminal globular domain ...Fibrinogen, alpha/beta/gamma chain, coiled coil domain / Fibrinogen alpha/beta chain family / Fibrinogen alpha/beta chain family / Fibrinogen alpha chain / Fibrinogen, conserved site / Fibrinogen C-terminal domain signature. / Fibrinogen-related domains (FReDs) / Fibrinogen beta and gamma chains, C-terminal globular domain / Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 1 / Fibrinogen, alpha/beta/gamma chain, C-terminal globular domain / Fibrinogen-like, C-terminal / Fibrinogen C-terminal domain profile. / 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 beta chain / HLA class II histocompatibility antigen, DR alpha chain / Fibrinogen beta chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsTing, Y.T. / Scally, S.W. / Rossjohn, J.
CitationJournal: Ann. Rheum. Dis. / Year: 2017
Title: Molecular basis for increased susceptibility of Indigenous North Americans to seropositive rheumatoid arthritis.
Authors: Scally, S.W. / Law, S.C. / Ting, Y.T. / Heemst, J.V. / Sokolove, J. / Deutsch, A.J. / Bridie Clemens, E. / Moustakas, A.K. / Papadopoulos, G.K. / Woude, D.V. / Smolik, I. / Hitchon, C.A. / ...Authors: Scally, S.W. / Law, S.C. / Ting, Y.T. / Heemst, J.V. / Sokolove, J. / Deutsch, A.J. / Bridie Clemens, E. / Moustakas, A.K. / Papadopoulos, G.K. / Woude, D.V. / Smolik, I. / Hitchon, C.A. / Robinson, D.B. / Ferucci, E.D. / Bernstein, C.N. / Meng, X. / Anaparti, V. / Huizinga, T. / Kedzierska, K. / Reid, H.H. / Raychaudhuri, S. / Toes, R.E. / Rossjohn, J. / El-Gabalawy, H. / Thomas, R.
History
DepositionAug 29, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 20, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jul 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 1.3Oct 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 / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
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.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_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 2.1Nov 6, 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: HLA class II histocompatibility antigen, DR alpha chain
D: MHC class II antigen
E: Fibrinogen beta chain
F: Fibrinogen beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,70911
Polymers87,5426
Non-polymers1,1675
Water2,018112
1
A: HLA class II histocompatibility antigen, DR alpha chain
B: MHC class II antigen
E: Fibrinogen beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,4966
Polymers43,7713
Non-polymers7253
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7450 Å2
ΔGint-21 kcal/mol
Surface area17870 Å2
MethodPISA
2
C: HLA class II histocompatibility antigen, DR alpha chain
D: MHC class II antigen
F: Fibrinogen beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,2135
Polymers43,7713
Non-polymers4422
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7780 Å2
ΔGint-20 kcal/mol
Surface area17720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.881, 72.885, 95.316
Angle α, β, γ (deg.)90.000, 107.400, 90.000
Int Tables number4
Space group name H-MP1211
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain B and (resid 3 through 21 or (resid 22...
21(chain D and (resid 3 through 51 or resid 53...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRTHRTHR(chain B and (resid 3 through 21 or (resid 22...BB3 - 211 - 19
12GLUGLUARGARG(chain B and (resid 3 through 21 or (resid 22...BB22 - 2320 - 21
13THRTHRALAALA(chain B and (resid 3 through 21 or (resid 22...BB3 - 1901 - 188
14THRTHRALAALA(chain B and (resid 3 through 21 or (resid 22...BB3 - 1901 - 188
15THRTHRALAALA(chain B and (resid 3 through 21 or (resid 22...BB3 - 1901 - 188
16THRTHRALAALA(chain B and (resid 3 through 21 or (resid 22...BB3 - 1901 - 188
21THRTHRTHRTHR(chain D and (resid 3 through 51 or resid 53...DD3 - 511 - 49
22LEULEUPROPRO(chain D and (resid 3 through 51 or resid 53...DD53 - 9751 - 95
23VALVALLEULEU(chain D and (resid 3 through 51 or resid 53...DD99 - 16197 - 159
24THRTHRTRPTRP(chain D and (resid 3 through 51 or resid 53...DD163 - 188161 - 186
25ARGARGALAALA(chain D and (resid 3 through 51 or resid 53...DD189 - 190187 - 188
26THRTHRALAALA(chain D and (resid 3 through 51 or resid 53...DD3 - 1901 - 188
27THRTHRALAALA(chain D and (resid 3 through 51 or resid 53...DD3 - 1901 - 188
28THRTHRALAALA(chain D and (resid 3 through 51 or resid 53...DD3 - 1901 - 188
29THRTHRALAALA(chain D and (resid 3 through 51 or resid 53...DD3 - 1901 - 188

-
Components

-
Protein , 2 types, 4 molecules ACBD

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


Mass: 20598.287 Da / Num. of mol.: 2 / Fragment: UNP residues 29-205
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DRA, HLA-DRA1
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P01903
#2: Protein MHC class II antigen


Mass: 21951.359 Da / Num. of mol.: 2 / Fragment: UNP residues 32-219
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DRB1
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A0A1I7H6

-
Protein/peptide / Sugars , 2 types, 6 molecules EF

#3: Protein/peptide Fibrinogen beta chain / Fibrinogen beta- 74Cit69-81


Mass: 1221.367 Da / Num. of mol.: 2 / Fragment: residues 69-81 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P02675*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.: 4
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

-
Non-polymers , 2 types, 113 molecules

#5: Chemical ChemComp-B3P / 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL


Mass: 282.334 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C11H26N2O6 / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.53 Å3/Da / Density % sol: 51.46 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.3
Details: 30% PEG3350, 0.2 M potassium nitrate, 0.1 M Bis-Tris propane, pH 7.3

-
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: Apr 28, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.7→47.06 Å / Num. obs: 24028 / % possible obs: 99.2 % / Redundancy: 3 % / Biso Wilson estimate: 39.6 Å2 / CC1/2: 0.981 / Rmerge(I) obs: 0.128 / Rpim(I) all: 0.089 / Rrim(I) all: 0.157 / Net I/σ(I): 6.1 / Num. measured all: 71175 / Scaling rejects: 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
2.7-2.8330.481958631460.7540.3280.5842.398.8
8.95-47.062.70.06318557000.9910.0440.07710.399.1

-
Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4MCY

4mcy


Resolution: 2.7→45.478 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2403 1106 4.61 %
Rwork0.2012 22901 -
obs0.203 24007 99.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 100.85 Å2 / Biso mean: 40.8262 Å2 / Biso min: 21.3 Å2
Refinement stepCycle: final / Resolution: 2.7→45.478 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6051 0 153 112 6316
Biso mean--59.2 33.73 -
Num. residues----753
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026322
X-RAY DIFFRACTIONf_angle_d0.5728608
X-RAY DIFFRACTIONf_chiral_restr0.044934
X-RAY DIFFRACTIONf_plane_restr0.0031115
X-RAY DIFFRACTIONf_dihedral_angle_d14.5823656
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11B2247X-RAY DIFFRACTION7.14TORSIONAL
12D2247X-RAY DIFFRACTION7.14TORSIONAL
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 (%)
2.7001-2.8230.33081140.25472845295999
2.823-2.97180.37151400.26142833297399
2.9718-3.15790.3221370.23422847298499
3.1579-3.40170.25451150.22142863297899
3.4017-3.74380.25931250.19382858298399
3.7438-4.28520.21351480.17152868301699
4.2852-5.39750.18591570.160228593016100
5.3975-45.48460.21681700.21312928309899

+
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