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- PDB-9d34: FIP200 C-terminal CLAW domain (resid. 1490-1594) in complex with ... -

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Basic information

Entry
Database: PDB / ID: 9d34
TitleFIP200 C-terminal CLAW domain (resid. 1490-1594) in complex with phosphorylated TNIP1 FIP200 interacting peptide
Components
  • RB1-inducible coiled-coil protein 1
  • TNFAIP3-interacting protein 1
KeywordsPROTEIN BINDING / Autophagy
Function / homology
Function and homology information


positive regulation of protein deubiquitination / glycoprotein biosynthetic process / Atg1/ULK1 kinase complex / ribophagy / glycophagy / phagophore assembly site membrane / autophagy of mitochondrion / pexophagy / piecemeal microautophagy of the nucleus / phagophore assembly site ...positive regulation of protein deubiquitination / glycoprotein biosynthetic process / Atg1/ULK1 kinase complex / ribophagy / glycophagy / phagophore assembly site membrane / autophagy of mitochondrion / pexophagy / piecemeal microautophagy of the nucleus / phagophore assembly site / mitogen-activated protein kinase binding / reticulophagy / MyD88-dependent toll-like receptor signaling pathway / leukocyte cell-cell adhesion / negative regulation of viral genome replication / Macroautophagy / autophagosome membrane / autophagosome assembly / positive regulation of cell size / protein-membrane adaptor activity / extrinsic apoptotic signaling pathway / negative regulation of canonical NF-kappaB signal transduction / positive regulation of autophagy / liver development / negative regulation of extrinsic apoptotic signaling pathway / positive regulation of JNK cascade / defense response / negative regulation of ERK1 and ERK2 cascade / autophagy / positive regulation of inflammatory response / Ovarian tumor domain proteases / heart development / cellular response to lipopolysaccharide / molecular adaptor activity / nuclear membrane / defense response to virus / lysosome / inflammatory response / translation / negative regulation of cell population proliferation / innate immune response / endoplasmic reticulum membrane / regulation of transcription by RNA polymerase II / protein kinase binding / positive regulation of transcription by RNA polymerase II / nucleoplasm / identical protein binding / cytosol
Similarity search - Function
Autophagy-related protein 11, C-terminal / Autophagy-related protein 11 / Autophagy-related protein 11
Similarity search - Domain/homology
TNFAIP3-interacting protein 1 / RB1-inducible coiled-coil protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.42 Å
AuthorsRadford, K.M. / Rosencrans, W. / Chou, T.F.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS) United States
CitationJournal: To Be Published
Title: FIP200 C-terminal CLAW domain (resid. 1490-1594) in complex with phosphorylated TNIP1 FIP200 interacting peptide
Authors: Radford, K.M. / Rosencrans, W. / Chou, T.F.
History
DepositionAug 9, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2024Provider: repository / Type: Initial release

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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
C: TNFAIP3-interacting protein 1


Theoretical massNumber of molelcules
Total (without water)13,5302
Polymers13,5302
Non-polymers00
Water84747
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area690 Å2
ΔGint-5 kcal/mol
Surface area5690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.339, 51.339, 88.280
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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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 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q8TDY2
#2: Protein/peptide TNFAIP3-interacting protein 1 / A20-binding inhibitor of NF-kappa-B activation 1 / ABIN-1 / HIV-1 Nef-interacting protein / Nef- ...A20-binding inhibitor of NF-kappa-B activation 1 / ABIN-1 / HIV-1 Nef-interacting protein / Nef-associated factor 1 / Naf1 / Nip40-1 / Virion-associated nuclear shuttling protein / VAN / hVAN


Mass: 1490.415 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNIP1, KIAA0113, NAF1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15025
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 2.15 Å3/Da / Density % sol: 42.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Morpheus E4 (12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD, 0.03 M of each ethylene glycol, 0.1 M MES/imidazole pH 6.5)

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-1 / Wavelength: 0.97946 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 29, 2024
RadiationMonochromator: Liquid nitrogen-cooled double-crystal Si(111) monochromator with a 0.01% energy bandpass
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.42→33.57 Å / Num. obs: 22984 / % possible obs: 96.3 % / Redundancy: 20 % / CC1/2: 0.996 / CC star: 0.999 / Net I/σ(I): 21.41
Reflection shellResolution: 1.42→1.471 Å / Rmerge(I) obs: 1.496 / Num. unique obs: 1889 / CC1/2: 0.814 / CC star: 0.947 / Rpim(I) all: 0.3252 / % possible all: 83.99

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.42→33.57 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 0.05 / Phase error: 24.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.234 1085 4.9 %
Rwork0.2023 --
obs0.2037 22153 96.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.42→33.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms735 0 0 47 782
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011775
X-RAY DIFFRACTIONf_angle_d1.2541061
X-RAY DIFFRACTIONf_dihedral_angle_d7.381106
X-RAY DIFFRACTIONf_chiral_restr0.102122
X-RAY DIFFRACTIONf_plane_restr0.011132
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.42-1.480.34541140.25312272X-RAY DIFFRACTION85
1.48-1.560.22781320.17542441X-RAY DIFFRACTION92
1.56-1.660.21331380.17112586X-RAY DIFFRACTION96
1.66-1.790.28411470.21572637X-RAY DIFFRACTION98
1.79-1.970.23751350.17162693X-RAY DIFFRACTION99
1.97-2.250.21221580.18112707X-RAY DIFFRACTION100
2.25-2.840.2251220.21022791X-RAY DIFFRACTION100
2.84-100.23671390.20812941X-RAY DIFFRACTION100

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