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- PDB-7d0e: Crystal structure of FIP200 Claw/p-CCPG1 FIR2 -

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Basic information

Entry
Database: PDB / ID: 7d0e
TitleCrystal structure of FIP200 Claw/p-CCPG1 FIR2
Components
  • Cell cycle progression protein 1 FIR2
  • RB1-inducible coiled-coil protein 1
KeywordsSIGNALING PROTEIN/PROTEIN BINDING / autophagy / FIP200 / CCPG1 / SIGNALING PROTEIN / SIGNALING PROTEIN-PROTEIN BINDING complex
Function / homology
Function and homology information


regulation of Rho guanyl-nucleotide exchange factor activity / regulation of protein lipidation / ribophagy / glycophagy / Atg1/ULK1 kinase complex / phagophore assembly site membrane / piecemeal microautophagy of the nucleus / phagophore assembly site / reticulophagy / Macroautophagy ...regulation of Rho guanyl-nucleotide exchange factor activity / 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 / positive regulation of cell size / autophagosome assembly / positive regulation of autophagy / positive regulation of cell cycle / 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 / membrane => GO:0016020 / molecular adaptor activity / lysosome / positive regulation of protein phosphorylation / cell cycle / negative regulation of cell population proliferation / positive regulation of cell population proliferation / endoplasmic reticulum membrane / protein kinase binding / positive regulation of transcription by RNA polymerase II / membrane / cytosol
Similarity search - Function
Cell cycle progression protein 1 / Autophagy-related protein 11, C-terminal / Autophagy-related protein 11 / Autophagy-related protein 11
Similarity search - Domain/homology
Chem-GO9 / DI(HYDROXYETHYL)ETHER / RB1-inducible coiled-coil protein 1 / Cell cycle progression protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 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

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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: Cell cycle progression protein 1 FIR2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9554
Polymers13,5362
Non-polymers4182
Water1,71195
1
A: RB1-inducible coiled-coil protein 1
B: Cell cycle progression protein 1 FIR2
hetero molecules

A: RB1-inducible coiled-coil protein 1
B: Cell cycle progression protein 1 FIR2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9108
Polymers27,0734
Non-polymers8374
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area4840 Å2
ΔGint-10 kcal/mol
Surface area12360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.438, 51.438, 86.151
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-1770-

HOH

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Components

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


Mass: 12039.970 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) / References: UniProt: Q8TDY2
#2: Protein/peptide Cell cycle progression protein 1 FIR2


Mass: 1496.487 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CCPG1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9ULG6
#3: Chemical ChemComp-GO9 / 3-(2-hydroxyethyloxy)-2-[2-(2-hydroxyethyloxy)ethoxymethyl]-2-(2-hydroxyethyloxymethyl)propan-1-ol


Mass: 312.357 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C13H28O8
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.1 Å3/Da / Density % sol: 41.57 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: KCl, Pentaerythritol ethoxylate (15/4 EO/OH), MES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97876 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 12, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97876 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. obs: 23548 / % possible obs: 99.8 % / Redundancy: 25.1 % / Biso Wilson estimate: 12.28 Å2 / Rmerge(I) obs: 0.037 / Net I/σ(I): 98.9
Reflection shellResolution: 1.4→1.42 Å / Num. unique obs: 1143 / Rpim(I) all: 0.174

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6DCE

6dce


Resolution: 1.4→25.07 Å / Cross valid method: FREE R-VALUE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2068 1151 4.91 %
Rwork0.1869 --
obs-23439 99.65 %
Displacement parametersBiso mean: 24.49 Å2
Refinement stepCycle: LAST / Resolution: 1.4→25.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms880 0 28 95 1003
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01581026
X-RAY DIFFRACTIONf_angle_d1.48121401
X-RAY DIFFRACTIONf_chiral_restr0.1087156
X-RAY DIFFRACTIONf_plane_restr0.0098172
X-RAY DIFFRACTIONf_dihedral_angle_d24.2422429

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