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- PDB-5ocx: Crystal structure of ACPA E4 in complex with CII-C-13-CIT -

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Entry
Database: PDB / ID: 5ocx
TitleCrystal structure of ACPA E4 in complex with CII-C-13-CIT
Components
  • CII-C-13-CIT
  • Fab fragment anti-citrullinated protein antibody E4 - light chain
  • Fab fragment of anti-citrullinated protein antibody E4 - heavy chain
KeywordsIMMUNE SYSTEM / anti-citrullinated protein antibody Fab fragment / collagen type II epitope IMMUNE SYSTEM
Function / homology
Function and homology information


collagen type II trimer / collagen type XI trimer / anterior head development / embryonic skeletal joint morphogenesis / otic vesicle development / Collagen chain trimerization / proteoglycan metabolic process / platelet-derived growth factor binding / extracellular matrix structural constituent conferring tensile strength / Extracellular matrix organization ...collagen type II trimer / collagen type XI trimer / anterior head development / embryonic skeletal joint morphogenesis / otic vesicle development / Collagen chain trimerization / proteoglycan metabolic process / platelet-derived growth factor binding / extracellular matrix structural constituent conferring tensile strength / Extracellular matrix organization / notochord development / limb bud formation / Collagen biosynthesis and modifying enzymes / cartilage development involved in endochondral bone morphogenesis / tissue homeostasis / MHC class II protein binding / cellular response to BMP stimulus / Signaling by PDGF / endochondral ossification / NCAM1 interactions / collagen fibril organization / cartilage development / proteoglycan binding / MET activates PTK2 signaling / Assembly of collagen fibrils and other multimeric structures / inner ear morphogenesis / cartilage condensation / roof of mouth development / Collagen degradation / Non-integrin membrane-ECM interactions / basement membrane / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / ECM proteoglycans / Integrin cell surface interactions / chondrocyte differentiation / heart morphogenesis / extrinsic apoptotic signaling pathway in absence of ligand / visual perception / central nervous system development / skeletal system development / sensory perception of sound / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / regulation of gene expression / collagen-containing extracellular matrix / endoplasmic reticulum lumen / protein homodimerization activity / extracellular space / extracellular region / metal ion binding
Similarity search - Function
Fibrillar collagen, C-terminal / Fibrillar collagen C-terminal domain / Fibrillar collagen C-terminal non-collagenous (NC1) domain profile. / Fibrillar collagens C-terminal domain / von Willebrand factor type C domain / VWFC domain signature. / VWFC domain profile. / von Willebrand factor (vWF) type C domain / VWFC domain / Collagen triple helix repeat ...Fibrillar collagen, C-terminal / Fibrillar collagen C-terminal domain / Fibrillar collagen C-terminal non-collagenous (NC1) domain profile. / Fibrillar collagens C-terminal domain / von Willebrand factor type C domain / VWFC domain signature. / VWFC domain profile. / von Willebrand factor (vWF) type C domain / VWFC domain / Collagen triple helix repeat / Collagen triple helix repeat (20 copies) / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Collagen alpha-1(II) chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsDobritzsch, D. / Ge, C. / Holmdahl, R.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Knut and Alice Wallenberg FoundationKAW 2010.0148 Sweden
CitationJournal: Arthritis Rheumatol / Year: 2019
Title: Structural Basis of Cross-Reactivity of Anti-Citrullinated Protein Antibodies.
Authors: Ge, C. / Xu, B. / Liang, B. / Lonnblom, E. / Lundstrom, S.L. / Zubarev, R.A. / Ayoglu, B. / Nilsson, P. / Skogh, T. / Kastbom, A. / Malmstrom, V. / Klareskog, L. / Toes, R.E.M. / Rispens, T. ...Authors: Ge, C. / Xu, B. / Liang, B. / Lonnblom, E. / Lundstrom, S.L. / Zubarev, R.A. / Ayoglu, B. / Nilsson, P. / Skogh, T. / Kastbom, A. / Malmstrom, V. / Klareskog, L. / Toes, R.E.M. / Rispens, T. / Dobritzsch, D. / Holmdahl, R.
History
DepositionJul 4, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 4, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 7, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 2.0Mar 11, 2020Group: Database references / Polymer sequence / Category: citation / entity_poly
Item: _citation.country / _citation.journal_id_ISSN / _entity_poly.pdbx_seq_one_letter_code_can
Revision 3.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id
Revision 3.1Jan 17, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: Fab fragment anti-citrullinated protein antibody E4 - light chain
H: Fab fragment of anti-citrullinated protein antibody E4 - heavy chain
A: CII-C-13-CIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8874
Polymers48,8253
Non-polymers621
Water7,206400
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5330 Å2
ΔGint-21 kcal/mol
Surface area18990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.716, 99.602, 51.877
Angle α, β, γ (deg.)90.00, 101.88, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody Fab fragment anti-citrullinated protein antibody E4 - light chain


Mass: 23622.998 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: B cell clone of a rheumatoid arthritis patient / Source: (gene. exp.) Homo sapiens (human) / Cell line: B cells / Cell (production host): Expi293F (TM) / Production host: Homo sapiens (human)
#2: Antibody Fab fragment of anti-citrullinated protein antibody E4 - heavy chain


Mass: 23454.334 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: B cell clone of a rheumatoid arthritis patient / Source: (gene. exp.) Homo sapiens (human) / Cell line: B cells / Cell (production host): Expi293F (TM) / Production host: Homo sapiens (human)
#3: Protein/peptide CII-C-13-CIT


Mass: 1747.909 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: citrullinated epitope derived from human collagen type II biotin and aminohexanoic acid attached at N-terminus circularized via disulfide bridge formation between the two cysteines ...Details: citrullinated epitope derived from human collagen type II biotin and aminohexanoic acid attached at N-terminus circularized via disulfide bridge formation between the two cysteines unmodelled residues not visible in electron density map
Source: (synth.) Homo sapiens (human) / References: UniProt: P02458*PLUS
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 400 / 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: 1.82 Å3/Da / Density % sol: 32.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20% (w/v) PEG3350, 0.2 M ammonium citrate dibasic

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jan 28, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.75→45.23 Å / Num. obs: 37660 / % possible obs: 97.3 % / Redundancy: 3.1 % / Biso Wilson estimate: 15.2 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.076 / Net I/σ(I): 7.5
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.584 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 1896 / CC1/2: 0.606 / Rpim(I) all: 0.539 / % possible all: 90

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4M1Q,3LMJ

4m1q

3lmj


Resolution: 1.75→45.23 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.945 / SU B: 3.629 / SU ML: 0.108 / Cross valid method: THROUGHOUT / ESU R: 0.137 / ESU R Free: 0.125 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21231 1948 5.2 %RANDOM
Rwork0.17623 ---
obs0.17812 35680 97.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 23.114 Å2
Baniso -1Baniso -2Baniso -3
1-0.19 Å20 Å21.04 Å2
2---2.03 Å20 Å2
3---1.3 Å2
Refinement stepCycle: 1 / Resolution: 1.75→45.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3356 0 4 400 3760
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.023509
X-RAY DIFFRACTIONr_bond_other_d0.0020.023113
X-RAY DIFFRACTIONr_angle_refined_deg1.4281.9484804
X-RAY DIFFRACTIONr_angle_other_deg1.5812.9997285
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6065467
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.37123.385130
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.68715540
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.5951518
X-RAY DIFFRACTIONr_chiral_restr0.080.2542
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213921
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02709
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3372.231802
X-RAY DIFFRACTIONr_mcbond_other1.3342.2281801
X-RAY DIFFRACTIONr_mcangle_it2.1933.3342252
X-RAY DIFFRACTIONr_mcangle_other2.1953.3352253
X-RAY DIFFRACTIONr_scbond_it1.5322.3381707
X-RAY DIFFRACTIONr_scbond_other1.5312.3381707
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.4433.4372540
X-RAY DIFFRACTIONr_long_range_B_refined4.62727.0673957
X-RAY DIFFRACTIONr_long_range_B_other4.62727.0693958
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 134 -
Rwork0.305 2445 -
obs--91.26 %

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