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- PDB-6yxk: Crystal structure of ACPA 3F3 in complex with cit-vimentin 59-74 -

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Basic information

Entry
Database: PDB / ID: 6yxk
TitleCrystal structure of ACPA 3F3 in complex with cit-vimentin 59-74
Components
  • ACPA 3F3 Fab fragment - heavy chain
  • ACPA 3F3 Fab fragment - light chain
  • Citrullinated Vimentin (59-74)
KeywordsIMMUNE SYSTEM / anti-citrullinated protein antibody Fab fragment / citrullinated vimentin
Function / homology
Function and homology information


keratin filament binding / lens fiber cell development / intermediate filament organization / cellular response to muramyl dipeptide / structural constituent of eye lens / astrocyte development / intermediate filament cytoskeleton / Striated Muscle Contraction / intermediate filament / RHOBTB1 GTPase cycle ...keratin filament binding / lens fiber cell development / intermediate filament organization / cellular response to muramyl dipeptide / structural constituent of eye lens / astrocyte development / intermediate filament cytoskeleton / Striated Muscle Contraction / intermediate filament / RHOBTB1 GTPase cycle / cell leading edge / Bergmann glial cell differentiation / microtubule organizing center / positive regulation of collagen biosynthetic process / Caspase-mediated cleavage of cytoskeletal proteins / phagocytic vesicle / regulation of mRNA stability / Late endosomal microautophagy / cellular response to type II interferon / structural constituent of cytoskeleton / nuclear matrix / Chaperone Mediated Autophagy / neuron projection development / Aggrephagy / peroxisome / double-stranded RNA binding / negative regulation of neuron projection development / cellular response to lipopolysaccharide / scaffold protein binding / Interleukin-4 and Interleukin-13 signaling / molecular adaptor activity / cytoskeleton / protein domain specific binding / axon / focal adhesion / positive regulation of gene expression / extracellular exosome / identical protein binding / plasma membrane / cytosol / cytoplasm
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 / Immunoglobulins ...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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsGe, C. / Holmdahl, R.
Funding support Sweden, 2items
OrganizationGrant numberCountry
Swedish Research Council Sweden
Knut and Alice Wallenberg Foundation Sweden
CitationJournal: Sci Adv / Year: 2022
Title: Surface Ig variable domain glycosylation affects autoantigen binding and acts as threshold for human autoreactive B cell activation.
Authors: Kissel, T. / Ge, C. / Hafkenscheid, L. / Kwekkeboom, J.C. / Slot, L.M. / Cavallari, M. / He, Y. / van Schie, K.A. / Vergroesen, R.D. / Kampstra, A.S.B. / Reijm, S. / Stoeken-Rijsbergen, G. / ...Authors: Kissel, T. / Ge, C. / Hafkenscheid, L. / Kwekkeboom, J.C. / Slot, L.M. / Cavallari, M. / He, Y. / van Schie, K.A. / Vergroesen, R.D. / Kampstra, A.S.B. / Reijm, S. / Stoeken-Rijsbergen, G. / Koeleman, C. / Voortman, L.M. / Heitman, L.H. / Xu, B. / Pruijn, G.J.M. / Wuhrer, M. / Rispens, T. / Huizinga, T.W.J. / Scherer, H.U. / Reth, M. / Holmdahl, R. / Toes, R.E.M.
History
DepositionMay 3, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 12, 2021Provider: repository / Type: Initial release
Revision 1.1May 25, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.0Nov 15, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / atom_type / chem_comp_atom / chem_comp_bond / pdbx_validate_close_contact / pdbx_validate_main_chain_plane / 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 / _atom_site.occupancy / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _pdbx_validate_close_contact.auth_atom_id_2 / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id
Revision 2.1Jan 24, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 2.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ACPA 3F3 Fab fragment - heavy chain
B: ACPA 3F3 Fab fragment - light chain
C: Citrullinated Vimentin (59-74)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,2696
Polymers49,6053
Non-polymers6643
Water5,459303
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5670 Å2
ΔGint-4 kcal/mol
Surface area20320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.379, 82.094, 135.613
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody ACPA 3F3 Fab fragment - heavy chain


Mass: 23772.783 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pCEP4 / Cell line (production host): Expi 293F(TM) / Production host: Homo sapiens (human)
#2: Antibody ACPA 3F3 Fab fragment - light chain


Mass: 24120.625 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pCEP4 / Cell line (production host): Expi 293F(TM) / Production host: Homo sapiens (human)
#3: Protein/peptide Citrullinated Vimentin (59-74)


Mass: 1711.897 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P08670
#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.: 3
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.: 303 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 3.03 Å3/Da / Density % sol: 59.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 20mM Tris pH 7.5, 20mM NaCl, 0.2M ammonium chloride pH 6.3, (20%) w/v PEG 3350)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.9184 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 9, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2→52.334 Å / Num. obs: 40933 / % possible obs: 99.5 % / Redundancy: 8 % / CC1/2: 0.996 / Rmerge(I) obs: 0.122 / Rpim(I) all: 0.067 / Rrim(I) all: 0.14 / Net I/σ(I): 9.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
8.94-52.286.90.0585420.9960.0320.066
2-2.058.20.93630180.6760.5111.069

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
REFMAC5.8.0258refinement
XDS0.7.4data reduction
Cootmodel building
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5OCX(early model)

5ocx


Resolution: 2→52.28 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.931 / SU B: 9.327 / SU ML: 0.125 / Cross valid method: FREE R-VALUE / ESU R: 0.17 / ESU R Free: 0.161
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2534 2026 4.953 %
Rwork0.2105 38876 -
all0.213 --
obs-40902 99.513 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 33.325 Å2
Baniso -1Baniso -2Baniso -3
1--0.926 Å20 Å2-0 Å2
2---1.275 Å20 Å2
3---2.201 Å2
Refinement stepCycle: LAST / Resolution: 2→52.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3395 0 64 303 3762
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0133546
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173151
X-RAY DIFFRACTIONr_angle_refined_deg2.2591.6654819
X-RAY DIFFRACTIONr_angle_other_deg1.4721.5977356
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.145439
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.06923.66153
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.78615546
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.9681511
X-RAY DIFFRACTIONr_chiral_restr0.0930.2469
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.023939
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02728
X-RAY DIFFRACTIONr_nbd_refined0.240.2631
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2110.23066
X-RAY DIFFRACTIONr_nbtor_refined0.1820.21711
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0980.21823
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1920.2289
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2530.214
X-RAY DIFFRACTIONr_nbd_other0.2720.239
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2050.29
X-RAY DIFFRACTIONr_mcbond_it1.3441.671774
X-RAY DIFFRACTIONr_mcbond_other1.3441.6691773
X-RAY DIFFRACTIONr_mcangle_it2.0512.492207
X-RAY DIFFRACTIONr_mcangle_other2.0512.4922208
X-RAY DIFFRACTIONr_scbond_it1.8421.8771772
X-RAY DIFFRACTIONr_scbond_other1.8381.8771772
X-RAY DIFFRACTIONr_scangle_it2.8212.7312612
X-RAY DIFFRACTIONr_scangle_other2.8212.7312613
X-RAY DIFFRACTIONr_lrange_it7.16821.3673907
X-RAY DIFFRACTIONr_lrange_other7.06520.6453845
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.0520.2851510.2612866X-RAY DIFFRACTION99.8015
2.052-2.1080.3051480.262722X-RAY DIFFRACTION99.6874
2.108-2.1690.3311550.2662687X-RAY DIFFRACTION99.8595
2.169-2.2360.3421450.2982605X-RAY DIFFRACTION99.6016
2.236-2.3090.3081170.2842548X-RAY DIFFRACTION99.7754
2.309-2.390.3331260.2592464X-RAY DIFFRACTION99.6921
2.39-2.480.3071220.2342363X-RAY DIFFRACTION99.5194
2.48-2.5810.2711100.2112284X-RAY DIFFRACTION98.6403
2.581-2.6960.2851310.1922152X-RAY DIFFRACTION98.2781
2.696-2.8270.216790.1872097X-RAY DIFFRACTION97.4038
2.827-2.980.2411070.2012001X-RAY DIFFRACTION99.8579
2.98-3.160.231050.2021911X-RAY DIFFRACTION99.9504
3.16-3.3780.219950.1971793X-RAY DIFFRACTION99.8942
3.378-3.6480.2281050.1981653X-RAY DIFFRACTION99.9431
3.648-3.9950.237740.1931563X-RAY DIFFRACTION99.9389
3.995-4.4650.218760.1751428X-RAY DIFFRACTION100
4.465-5.1520.265680.1771257X-RAY DIFFRACTION100
5.152-6.3020.232410.2291096X-RAY DIFFRACTION100
6.302-8.8760.238480.204869X-RAY DIFFRACTION99.8911
8.876-52.280.23230.23517X-RAY DIFFRACTION99.2647
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.5688-0.79380.70031.4885-0.50570.8003-0.0541-0.04350.17570.0438-0.0148-0.0868-0.0944-0.04290.06890.2158-0.0299-0.0010.2182-0.01110.020114.439965.370723.87
20.8521-0.84140.72491.2336-0.97111.0330.05660.0283-0.0825-0.05380.03390.12170.0083-0.0437-0.09050.2272-0.033-0.00580.2461-0.00940.01284.166254.393313.8032
30.0358-0.46560.21338.3666-2.39011.3503-0.00210.04110.0170.0197-0.0375-0.44070.01990.31120.03970.17060.0063-0.00870.18410.01950.169430.769835.847432.792
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA2 - 401
2X-RAY DIFFRACTION2ALLB1 - 301
3X-RAY DIFFRACTION3ALLC1 - 9

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