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- PDB-5ocy: Crystal structure of ACPA E4 in complex with CII-C-48-CIT -

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Basic information

Entry
Database: PDB / ID: 5ocy
TitleCrystal structure of ACPA E4 in complex with CII-C-48-CIT
Components
  • ACPA E4 Fab fragment - heavy chain
  • ACPA E4 Fab fragment - light chain
  • CII-C-48-CIT
KeywordsIMMUNE SYSTEM / anti-citrullinated protein antibody Fab fragment / citrullinated collagen type II epitope
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 organization / notochord development ...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 organization / notochord development / limb bud formation / cartilage development involved in endochondral bone morphogenesis / extracellular matrix structural constituent conferring tensile strength / Collagen biosynthesis and modifying enzymes / 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 / Assembly of collagen fibrils and other multimeric structures / MET activates PTK2 signaling / cartilage condensation / inner ear morphogenesis / 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 / skeletal system development / central nervous 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: 2.6 Å
AuthorsDobritzsch, D. / Ge, C. / Holmdahl, R.
Funding support Sweden, 2items
OrganizationGrant numberCountry
Knut and Alice Wallenberg FoundationKAW 2010.0148 Sweden
Swedish Research Council2015-02662 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 / 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 / _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
H: ACPA E4 Fab fragment - heavy chain
L: ACPA E4 Fab fragment - light chain
C: CII-C-48-CIT


Theoretical massNumber of molelcules
Total (without water)48,4503
Polymers48,4503
Non-polymers00
Water1,856103
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5080 Å2
ΔGint-23 kcal/mol
Surface area19050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.130, 99.048, 100.330
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody ACPA E4 Fab fragment - heavy chain


Mass: 23357.219 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 / Plasmid: pCEP4 / Cell line (production host): Expi293F (TM) / Production host: Homo sapiens (human)
#2: Antibody ACPA E4 Fab fragment - light chain


Mass: 23261.754 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 / Plasmid: pCEP4 / Cell line (production host): Expi293F (TM) / Production host: Homo sapiens (human)
#3: Protein/peptide CII-C-48-CIT


Mass: 1831.021 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: part of the sequence occurs naturally in human collagen type II
Source: (synth.) Homo sapiens (human) / References: UniProt: P02458*PLUS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / 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: 2.42 Å3/Da / Density % sol: 48.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 15% (w/v) PEG 6000, 0.1 M Tris pH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 7, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.6→49.53 Å / Num. obs: 14679 / % possible obs: 99.6 % / Redundancy: 7.2 % / Biso Wilson estimate: 47.9 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.14 / Rpim(I) all: 0.081 / Net I/σ(I): 10.9
Reflection shellResolution: 2.6→2.72 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.621 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 1763 / CC1/2: 0.828 / Rpim(I) all: 0.367 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ocx (early model)

5ocx


Resolution: 2.6→49.53 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.899 / SU B: 11.408 / SU ML: 0.242 / Cross valid method: THROUGHOUT / ESU R: 1.473 / ESU R Free: 0.32 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24499 759 5.2 %RANDOM
Rwork0.18714 ---
obs0.19028 13887 99.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 36.939 Å2
Baniso -1Baniso -2Baniso -3
1--2.22 Å20 Å2-0 Å2
2--3.64 Å20 Å2
3----1.42 Å2
Refinement stepCycle: 1 / Resolution: 2.6→49.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3273 0 0 103 3376
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.023362
X-RAY DIFFRACTIONr_bond_other_d0.0020.023004
X-RAY DIFFRACTIONr_angle_refined_deg1.4091.9524592
X-RAY DIFFRACTIONr_angle_other_deg1.7942.9997009
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8935429
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.16923.333120
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.34215509
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.5451516
X-RAY DIFFRACTIONr_chiral_restr0.080.2524
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213697
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02663
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_it2.0233.7041731
X-RAY DIFFRACTIONr_mcbond_other2.0113.7031730
X-RAY DIFFRACTIONr_mcangle_it3.3635.5352155
X-RAY DIFFRACTIONr_mcangle_other3.3655.5362156
X-RAY DIFFRACTIONr_scbond_it2.0143.8671631
X-RAY DIFFRACTIONr_scbond_other2.0133.8681632
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.2015.7222438
X-RAY DIFFRACTIONr_long_range_B_refined5.30541.5213457
X-RAY DIFFRACTIONr_long_range_B_other5.29241.5353447
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 46 -
Rwork0.228 1002 -
obs--99.81 %

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