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- PDB-5ock: Crystal structure of ACPA E4 in complex with CEP1 -

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Basic information

Entry
Database: PDB / ID: 5ock
TitleCrystal structure of ACPA E4 in complex with CEP1
Components
  • CEP1 peptide (from enolase)
  • Human ACPA E4 Fab fragment - Heavy chain
  • Human ACPA E4 Fab fragment - Light chain
KeywordsIMMUNE SYSTEM / anti-citrullinated protein antibody Fab fragment
Function / homology
Function and homology information


Manipulation of host energy metabolism / positive regulation of plasminogen activation / negative regulation of hypoxia-induced intrinsic apoptotic signaling pathway / phosphopyruvate hydratase / phosphopyruvate hydratase complex / phosphopyruvate hydratase activity / positive regulation of muscle contraction / Gluconeogenesis / canonical glycolysis / M band ...Manipulation of host energy metabolism / positive regulation of plasminogen activation / negative regulation of hypoxia-induced intrinsic apoptotic signaling pathway / phosphopyruvate hydratase / phosphopyruvate hydratase complex / phosphopyruvate hydratase activity / positive regulation of muscle contraction / Gluconeogenesis / canonical glycolysis / M band / Glycolysis / positive regulation of ATP biosynthetic process / nuclear outer membrane / transcription corepressor binding / glycolytic process / gluconeogenesis / RNA polymerase II transcription regulatory region sequence-specific DNA binding / negative regulation of cell growth / DNA-binding transcription repressor activity, RNA polymerase II-specific / response to virus / transcription corepressor activity / GTPase binding / cell cortex / cadherin binding / negative regulation of DNA-templated transcription / magnesium ion binding / cell surface / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / extracellular space / RNA binding / extracellular exosome / nucleus / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Enolase / Enolase, conserved site / Enolase, C-terminal TIM barrel domain / Enolase, N-terminal / Enolase, C-terminal TIM barrel domain / Enolase, N-terminal domain / Enolase signature. / Enolase, C-terminal TIM barrel domain / Enolase, N-terminal domain / Enolase-like, N-terminal ...Enolase / Enolase, conserved site / Enolase, C-terminal TIM barrel domain / Enolase, N-terminal / Enolase, C-terminal TIM barrel domain / Enolase, N-terminal domain / Enolase signature. / Enolase, C-terminal TIM barrel domain / Enolase, N-terminal domain / Enolase-like, N-terminal / Enolase-like, C-terminal domain superfamily / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsDobritzsch, D. / Ge, C. / Holmdahl, R.
Funding support Sweden, 2items
OrganizationGrant numberCountry
Knut and Alice Wallenberg FoundationKAW2010.0148 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 3, 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: Atomic model / Data collection ...Atomic model / Data collection / Database references / Polymer sequence
Category: atom_site / citation ...atom_site / citation / entity_poly / pdbx_nonpoly_scheme
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_seq_id / _atom_site.label_alt_id / _atom_site.occupancy / _citation.country / _citation.journal_id_ISSN / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_nonpoly_scheme.auth_seq_num
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
Revision 3.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: Human ACPA E4 Fab fragment - Light chain
H: Human ACPA E4 Fab fragment - Heavy chain
A: CEP1 peptide (from enolase)


Theoretical massNumber of molelcules
Total (without water)49,4823
Polymers49,4823
Non-polymers00
Water8,215456
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5610 Å2
ΔGint-13 kcal/mol
Surface area19970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.296, 101.048, 52.109
Angle α, β, γ (deg.)90.00, 101.03, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody Human ACPA E4 Fab fragment - Light chain


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


Mass: 23437.303 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: B cells of a rheumatoid arthritis patient / Source: (gene. exp.) Homo sapiens (human) / Cell (production host): Expi293F (TM) / Cell line (production host): Expi293F (TM) / Production host: Homo sapiens (human)
#3: Protein/peptide CEP1 peptide (from enolase)


Mass: 2421.771 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Biotin is attached to the aminohexanoic acid at the N-terminus Glu7 and Ile8 not modeled due to poor definition in electron density
Source: (synth.) Homo sapiens (human) / References: UniProt: P06733*PLUS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 456 / Source method: isolated from a natural source / Formula: H2O
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: 2.07 Å3/Da / Density % sol: 40.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20% PEG3350, 0.2M ammonium citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 1.6→45.63 Å / Num. obs: 51683 / % possible obs: 98.4 % / Redundancy: 3.7 % / Biso Wilson estimate: 12.5 Å2 / CC1/2: 0.961 / Rmerge(I) obs: 0.112 / Rpim(I) all: 0.089 / Net I/σ(I): 6.7
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.661 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 2575 / CC1/2: 0.498 / Rpim(I) all: 0.538 / % possible all: 98.4

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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: 1.6→45.63 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.939 / SU B: 2.382 / SU ML: 0.081 / Cross valid method: THROUGHOUT / ESU R: 0.104 / ESU R Free: 0.102 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21809 2623 5.1 %RANDOM
Rwork0.1827 ---
obs0.18456 49002 98.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 16.425 Å2
Baniso -1Baniso -2Baniso -3
1-0.31 Å20 Å20.39 Å2
2---0.63 Å2-0 Å2
3---0.15 Å2
Refinement stepCycle: 1 / Resolution: 1.6→45.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3427 0 0 456 3883
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.023687
X-RAY DIFFRACTIONr_bond_other_d0.0020.023249
X-RAY DIFFRACTIONr_angle_refined_deg1.4731.9475085
X-RAY DIFFRACTIONr_angle_other_deg22.9957630
X-RAY DIFFRACTIONr_dihedral_angle_1_deg13.8475.173519
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.31323.358134
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.5215560
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.2631517
X-RAY DIFFRACTIONr_chiral_restr0.0890.2580
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214215
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02754
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_it1.1041.5221881
X-RAY DIFFRACTIONr_mcbond_other1.1011.5211880
X-RAY DIFFRACTIONr_mcangle_it1.892.2732363
X-RAY DIFFRACTIONr_mcangle_other1.892.2742364
X-RAY DIFFRACTIONr_scbond_it1.3761.6451806
X-RAY DIFFRACTIONr_scbond_other1.3761.6441805
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.2192.3982692
X-RAY DIFFRACTIONr_long_range_B_refined4.63219.0054008
X-RAY DIFFRACTIONr_long_range_B_other4.36518.1723881
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 196 -
Rwork0.3 3641 -
obs--98.23 %

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