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- PDB-6atz: HLA-DRB1*1402 in complex with citrullinated fibrinogen peptide -

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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 / Regulation of TLR by endogenous ligand / positive regulation of CD4-positive, alpha-beta T cell activation ...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 / Regulation of TLR by endogenous ligand / positive regulation of CD4-positive, alpha-beta T cell activation / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / blood coagulation, fibrin clot formation / platelet alpha granule / positive regulation of memory T cell differentiation / cellular response to leptin stimulus / MyD88 deficiency (TLR2/4) / positive regulation of heterotypic cell-cell adhesion / IRAK4 deficiency (TLR2/4) / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / transport vesicle membrane / extracellular matrix structural constituent / polysaccharide binding / plasminogen activation / p130Cas linkage to MAPK signaling for integrins / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / positive regulation of peptide hormone secretion / positive regulation of exocytosis / GRB2:SOS provides linkage to MAPK signaling for Integrins / Generation of second messenger molecules / immunological synapse / protein polymerization / PD-1 signaling / cellular response to interleukin-1 / Integrin cell surface interactions / negative regulation of endothelial cell apoptotic process / Common Pathway of Fibrin Clot Formation / positive regulation of substrate adhesion-dependent cell spreading / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / positive regulation of vasoconstriction / fibrinolysis / MHC class II antigen presentation / T cell receptor binding / cell-matrix adhesion / Integrin signaling / trans-Golgi network membrane / platelet alpha granule lumen / lumenal side of endoplasmic reticulum membrane / positive regulation of protein secretion / clathrin-coated endocytic vesicle membrane / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / ER to Golgi transport vesicle membrane / platelet aggregation / cognition / positive regulation of T cell mediated cytotoxicity / peptide antigen assembly with MHC class II protein complex / response to calcium ion / MHC class II protein complex / peptide antigen binding / endocytic vesicle membrane / extracellular vesicle / 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 / antigen processing and presentation of exogenous peptide antigen via MHC class II / Interferon gamma signaling / positive regulation of immune response / positive regulation of T cell activation / Signaling by BRAF and RAF1 fusions / Downstream TCR signaling / Platelet degranulation / MHC class II protein complex binding / late endosome membrane / cell cortex / ER-Phagosome pathway / protein-folding chaperone binding / early endosome membrane / collagen-containing extracellular matrix / protein-containing complex assembly / blood microparticle / adaptive immune response / lysosome / positive regulation of ERK1 and ERK2 cascade / endosome membrane / immune response / lysosomal membrane / external side of plasma membrane / Golgi membrane / signaling receptor binding / innate immune response / 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 chain / Fibrinogen alpha/beta chain family / Fibrinogen alpha/beta chain family / Fibrinogen, conserved site / Fibrinogen C-terminal domain signature. / Fibrinogen-related domains (FReDs) / Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 1 / Fibrinogen beta and gamma chains, C-terminal globular domain / Fibrinogen, alpha/beta/gamma chain, C-terminal globular domain ...Fibrinogen, alpha/beta/gamma chain, coiled coil domain / Fibrinogen alpha chain / Fibrinogen alpha/beta chain family / Fibrinogen alpha/beta chain family / Fibrinogen, conserved site / Fibrinogen C-terminal domain signature. / Fibrinogen-related domains (FReDs) / Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 1 / Fibrinogen beta and gamma chains, C-terminal globular domain / 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 / Immunoglobulins / Roll / Immunoglobulin-like fold / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
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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

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Components

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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

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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 / N-Acetylglucosamine


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

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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 / Bis-tris propane


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 / Water


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

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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: 2.53 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

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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

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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

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