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Open data
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Basic information
Entry | Database: PDB / ID: 5ock | ||||||||||||
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Title | Crystal structure of ACPA E4 in complex with CEP1 | ||||||||||||
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![]() | IMMUNE SYSTEM / anti-citrullinated protein antibody Fab fragment | ||||||||||||
Function / homology | ![]() negative regulation of hypoxia-induced intrinsic apoptotic signaling pathway / Manipulation of host energy metabolism / positive regulation of muscle contraction / positive regulation of plasminogen activation / phosphopyruvate hydratase / phosphopyruvate hydratase complex / phosphopyruvate hydratase activity / Gluconeogenesis / nuclear outer membrane / M band ...negative regulation of hypoxia-induced intrinsic apoptotic signaling pathway / Manipulation of host energy metabolism / positive regulation of muscle contraction / positive regulation of plasminogen activation / phosphopyruvate hydratase / phosphopyruvate hydratase complex / phosphopyruvate hydratase activity / Gluconeogenesis / nuclear outer membrane / M band / canonical glycolysis / Glycolysis / positive regulation of ATP biosynthetic process / transcription corepressor binding / gluconeogenesis / glycolytic process / RNA polymerase II transcription regulatory region sequence-specific DNA binding / response to virus / negative regulation of cell growth / DNA-binding transcription repressor activity, RNA polymerase II-specific / transcription corepressor activity / GTPase binding / cell cortex / cadherin binding / negative regulation of DNA-templated transcription / cell surface / negative regulation of transcription by RNA polymerase II / magnesium ion binding / protein homodimerization activity / RNA binding / extracellular space / extracellular exosome / membrane / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Dobritzsch, D. / Ge, C. / Holmdahl, R. | ||||||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 113.6 KB | Display | ![]() |
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PDB format | ![]() | 85.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 433.9 KB | Display | ![]() |
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Full document | ![]() | 435.8 KB | Display | |
Data in XML | ![]() | 22.8 KB | Display | |
Data in CIF | ![]() | 34.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5ocxC ![]() 5ocyC ![]() 5od0C ![]() 5od8C ![]() 5odbC ![]() 3lmjS ![]() 4m1qS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Antibody | 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.) ![]() ![]() |
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#2: Antibody | 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.) ![]() ![]() |
#3: Protein/peptide | 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.) ![]() |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.07 Å3/Da / Density % sol: 40.51 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20% PEG3350, 0.2M ammonium citrate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 20, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9686 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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
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Refinement | Method to determine structure: ![]() Starting model: 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
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.425 Å2
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Refinement step | Cycle: 1 / Resolution: 1.6→45.63 Å
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Refine LS restraints |
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