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- PDB-7czm: Crystal structure of FIP200 Claw/p-OPtineurin LIR complex -

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Basic information

Entry
Database: PDB / ID: 7czm
TitleCrystal structure of FIP200 Claw/p-OPtineurin LIR complex
Components
  • Optineurin LIR
  • RB1-inducible coiled-coil protein 1
KeywordsSIGNALING PROTEIN/PROTEIN BINDING / autophagy / FIP200 / Optineurin / SIGNALING PROTEIN / SIGNALING PROTEIN-PROTEIN BINDING complex
Function / homology
Function and homology information


type 2 mitophagy / Atg1/ULK1 kinase complex / ribophagy / cell death / glycophagy / negative regulation of receptor recycling / Golgi ribbon formation / positive regulation of xenophagy / protein localization to Golgi apparatus / phagophore assembly site membrane ...type 2 mitophagy / Atg1/ULK1 kinase complex / ribophagy / cell death / glycophagy / negative regulation of receptor recycling / Golgi ribbon formation / positive regulation of xenophagy / protein localization to Golgi apparatus / phagophore assembly site membrane / pexophagy / autophagy of mitochondrion / piecemeal microautophagy of the nucleus / Golgi to plasma membrane protein transport / phagophore assembly site / TBC/RABGAPs / regulation of canonical NF-kappaB signal transduction / reticulophagy / TNFR1-induced proapoptotic signaling / K63-linked polyubiquitin modification-dependent protein binding / Macroautophagy / Golgi organization / autophagosome membrane / polyubiquitin modification-dependent protein binding / autophagosome assembly / positive regulation of cell size / cellular response to unfolded protein / extrinsic apoptotic signaling pathway / protein-membrane adaptor activity / negative regulation of canonical NF-kappaB signal transduction / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / positive regulation of autophagy / TICAM1-dependent activation of IRF3/IRF7 / autophagosome / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / PINK1-PRKN Mediated Mitophagy / TNFR1-induced NF-kappa-B signaling pathway / negative regulation of extrinsic apoptotic signaling pathway / positive regulation of JNK cascade / Regulation of TNFR1 signaling / trans-Golgi network / liver development / autophagy / recycling endosome membrane / Regulation of PLK1 Activity at G2/M Transition / heart development / nuclear membrane / protein-macromolecule adaptor activity / defense response to Gram-negative bacterium / defense response to virus / molecular adaptor activity / lysosome / Golgi membrane / negative regulation of cell population proliferation / innate immune response / protein kinase binding / endoplasmic reticulum membrane / perinuclear region of cytoplasm / Golgi apparatus / signal transduction / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Autophagy-related protein 11, C-terminal / Autophagy-related protein 11 / Autophagy-related protein 11 / NF-kappa-B essential modulator NEMO, N-terminal / : / NF-kappa-B essential modulator NEMO / C2H2 type zinc-finger / NEMO, Zinc finger / Zinc finger CCHC NOA-type profile. / NF-kappa-B essential modulator NEMO, CC2-LZ domain / Leucine zipper of domain CC2 of NEMO, NF-kappa-B essential modulator
Similarity search - Domain/homology
RB1-inducible coiled-coil protein 1 / Optineurin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsZhou, Z.X. / Pan, L.F.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31470749 China
National Natural Science Foundation of China (NSFC)21621002 China
CitationJournal: Nat Commun / Year: 2021
Title: Phosphorylation regulates the binding of autophagy receptors to FIP200 Claw domain for selective autophagy initiation.
Authors: Zhou, Z. / Liu, J. / Fu, T. / Wu, P. / Peng, C. / Gong, X. / Wang, Y. / Zhang, M. / Li, Y. / Wang, Y. / Xu, X. / Li, M. / Pan, L.
History
DepositionSep 9, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 31, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 6, 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

Downloads & links

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Assembly

Deposited unit
A: RB1-inducible coiled-coil protein 1
B: RB1-inducible coiled-coil protein 1
C: Optineurin LIR
D: Optineurin LIR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,29410
Polymers27,9684
Non-polymers3266
Water1,53185
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4450 Å2
ΔGint-62 kcal/mol
Surface area12210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.978, 70.624, 56.337
Angle α, β, γ (deg.)90.000, 109.270, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-1603-

CL

21B-1842-

HOH

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Components

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


Mass: 12403.336 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RB1CC1, KIAA0203, RBICC / Production host: Escherichia coli (E. coli) / References: UniProt: Q8TDY2
#2: Protein/peptide Optineurin LIR


Mass: 1580.587 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: OPTN, FIP2, GLC1E, HIP7, HYPL, NRP / Production host: Escherichia coli (E. coli) / References: UniProt: Q96CV9
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / 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: 2.56 Å3/Da / Density % sol: 51.88 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: Potassium iodide, MES pH 6.5, PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 3, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2→35.32 Å / Num. obs: 18560 / % possible obs: 99.6 % / Redundancy: 6.6 % / Biso Wilson estimate: 41.48 Å2 / Rmerge(I) obs: 0.034 / Net I/σ(I): 31.6
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.254 / Num. unique obs: 1836

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6DCE

6dce


Resolution: 2→34.96 Å / Cross valid method: FREE R-VALUE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2234 844 4.76 %
Rwork0.2028 --
obs-18543 99.87 %
Displacement parametersBiso mean: 56.42 Å2
Refinement stepCycle: LAST / Resolution: 2→34.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1718 0 16 85 1819
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00691789
X-RAY DIFFRACTIONf_angle_d0.86492410
X-RAY DIFFRACTIONf_chiral_restr0.0545261
X-RAY DIFFRACTIONf_plane_restr0.0048298
X-RAY DIFFRACTIONf_dihedral_angle_d26.4447683

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