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- PDB-6dce: X-ray structure of FIP200 claw domain -

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Basic information

Entry
Database: PDB / ID: 6dce
TitleX-ray structure of FIP200 claw domain
ComponentsRB1-inducible coiled-coil protein 1
KeywordsSTRUCTURAL PROTEIN / autophagy / FIP200
Function / homology
Function and homology information


regulation of protein lipidation / ribophagy / glycophagy / Atg1/ULK1 kinase complex / phagophore assembly site membrane / piecemeal microautophagy of the nucleus / phagophore assembly site / reticulophagy / Macroautophagy / autophagosome membrane ...regulation of protein lipidation / ribophagy / glycophagy / Atg1/ULK1 kinase complex / phagophore assembly site membrane / piecemeal microautophagy of the nucleus / phagophore assembly site / reticulophagy / Macroautophagy / autophagosome membrane / autophagosome assembly / positive regulation of cell size / positive regulation of autophagy / extrinsic apoptotic signaling pathway / protein-membrane adaptor activity / liver development / negative regulation of extrinsic apoptotic signaling pathway / positive regulation of JNK cascade / autophagy / heart development / nuclear membrane / lysosome / molecular adaptor activity / positive regulation of protein phosphorylation / cell cycle / negative regulation of cell population proliferation / endoplasmic reticulum membrane / protein kinase binding / cytosol
Similarity search - Function
Autophagy-related protein 11, C-terminal / Autophagy-related protein 11 / Autophagy-related protein 11
Similarity search - Domain/homology
RB1-inducible coiled-coil protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.56 Å
AuthorsSu, M.-Y. / Hurley, J.H.
CitationJournal: Mol. Cell / Year: 2019
Title: FIP200 Claw Domain Binding to p62 Promotes Autophagosome Formation at Ubiquitin Condensates.
Authors: Turco, E. / Witt, M. / Abert, C. / Bock-Bierbaum, T. / Su, M.Y. / Trapannone, R. / Sztacho, M. / Danieli, A. / Shi, X. / Zaffagnini, G. / Gamper, A. / Schuschnig, M. / Fracchiolla, D. / ...Authors: Turco, E. / Witt, M. / Abert, C. / Bock-Bierbaum, T. / Su, M.Y. / Trapannone, R. / Sztacho, M. / Danieli, A. / Shi, X. / Zaffagnini, G. / Gamper, A. / Schuschnig, M. / Fracchiolla, D. / Bernklau, D. / Romanov, J. / Hartl, M. / Hurley, J.H. / Daumke, O. / Martens, S.
History
DepositionMay 5, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2May 1, 2019Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RB1-inducible coiled-coil protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,9064
Polymers11,6171
Non-polymers2883
Water1,26170
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)30.779, 89.220, 80.098
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein RB1-inducible coiled-coil protein 1 / FAK family kinase-interacting protein of 200 kDa / FIP200


Mass: 11617.370 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RB1CC1, KIAA0203, RBICC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8TDY2
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 70 / 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: 2.38 Å3/Da / Density % sol: 48.24 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / Details: 0.1 M HEPES pH 7.4, 2 M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 29, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.56→44.63 Å / Num. obs: 16114 / % possible obs: 99.1 % / Redundancy: 2 % / Net I/σ(I): 22.1
Reflection shellResolution: 1.56→1.62 Å

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
Cootmodel building
XDSdata scaling
SHELXphasing
XDSdata reduction
RefinementMethod to determine structure: SAD / Resolution: 1.56→19.672 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 0.05 / Phase error: 22.94
RfactorNum. reflection% reflection
Rfree0.241 1508 9.52 %
Rwork0.2079 --
obs0.211 15835 98.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.56→19.672 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms758 0 15 70 843
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006789
X-RAY DIFFRACTIONf_angle_d0.8191065
X-RAY DIFFRACTIONf_dihedral_angle_d18.09468
X-RAY DIFFRACTIONf_chiral_restr0.053115
X-RAY DIFFRACTIONf_plane_restr0.006130
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.56-1.61030.26581290.25541222X-RAY DIFFRACTION93
1.6103-1.66790.26681300.23061235X-RAY DIFFRACTION95
1.6679-1.73460.23931330.21571264X-RAY DIFFRACTION96
1.7346-1.81350.1961350.19521285X-RAY DIFFRACTION98
1.8135-1.9090.23281330.19751267X-RAY DIFFRACTION97
1.909-2.02850.22511370.19521304X-RAY DIFFRACTION99
2.0285-2.1850.21751390.2021316X-RAY DIFFRACTION99
2.185-2.40450.24871380.20971320X-RAY DIFFRACTION100
2.4045-2.75160.27821420.23881338X-RAY DIFFRACTION100
2.7516-3.46370.24591420.2211352X-RAY DIFFRACTION100
3.4637-19.67370.23431500.19041424X-RAY DIFFRACTION100

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