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- PDB-8yfk: Crystal structure of FIP200 claw/TNIP1_FIR_pS123 -

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Basic information

Entry
Database: PDB / ID: 8yfk
TitleCrystal structure of FIP200 claw/TNIP1_FIR_pS123
Components
  • RB1-inducible coiled-coil protein 1
  • TNIP1_FIR_pS123 peptide
KeywordsPROTEIN BINDING / phosphorylation / selective mitophagy
Function / homology
Function and homology information


positive regulation of protein deubiquitination / regulation of protein lipidation / ribophagy / glycoprotein biosynthetic process / Atg1/ULK1 kinase complex / autophagy of peroxisome / glycophagy / phagophore assembly site membrane / piecemeal microautophagy of the nucleus / phagophore assembly site ...positive regulation of protein deubiquitination / regulation of protein lipidation / ribophagy / glycoprotein biosynthetic process / Atg1/ULK1 kinase complex / autophagy of peroxisome / glycophagy / phagophore assembly site membrane / piecemeal microautophagy of the nucleus / phagophore assembly site / mitogen-activated protein kinase binding / autophagy of mitochondrion / MyD88-dependent toll-like receptor signaling pathway / reticulophagy / leukocyte cell-cell adhesion / negative regulation of viral genome replication / Macroautophagy / autophagosome membrane / positive regulation of cell size / autophagosome assembly / positive regulation of autophagy / negative regulation of canonical NF-kappaB signal transduction / protein-membrane adaptor activity / extrinsic apoptotic signaling pathway / liver development / negative regulation of extrinsic apoptotic signaling pathway / positive regulation of JNK cascade / negative regulation of ERK1 and ERK2 cascade / defense response / autophagy / positive regulation of inflammatory response / Ovarian tumor domain proteases / heart development / cellular response to lipopolysaccharide / nuclear membrane / molecular adaptor activity / lysosome / inflammatory response / positive regulation of protein phosphorylation / translation / negative regulation of cell population proliferation / 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: 2 Å
AuthorsLv, M.Q. / Wu, S.M.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32293210, 32293213, 32000882, 12374220, 32100958 and 32090040 China
CitationJournal: J.Biol.Chem. / Year: 2024
Title: Structural basis for TNIP1 binding to FIP200 during mitophagy.
Authors: Wu, S. / Li, M. / Wang, L. / Yang, L. / Cui, J. / Li, F. / Wang, Q. / Shi, Y. / Lv, M.
History
DepositionFeb 24, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 14, 2024Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2024Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RB1-inducible coiled-coil protein 1
B: TNIP1_FIR_pS123 peptide
G: RB1-inducible coiled-coil protein 1
H: TNIP1_FIR_pS123 peptide
C: RB1-inducible coiled-coil protein 1
D: TNIP1_FIR_pS123 peptide
E: RB1-inducible coiled-coil protein 1
F: TNIP1_FIR_pS123 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,39613
Polymers52,9928
Non-polymers4035
Water3,189177
1
A: RB1-inducible coiled-coil protein 1
B: TNIP1_FIR_pS123 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,3914
Polymers13,2482
Non-polymers1422
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1070 Å2
ΔGint-14 kcal/mol
Surface area6220 Å2
MethodPISA
2
G: RB1-inducible coiled-coil protein 1
H: TNIP1_FIR_pS123 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,3663
Polymers13,2482
Non-polymers1181
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1300 Å2
ΔGint-21 kcal/mol
Surface area6370 Å2
MethodPISA
3
C: RB1-inducible coiled-coil protein 1
D: TNIP1_FIR_pS123 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,2723
Polymers13,2482
Non-polymers241
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area990 Å2
ΔGint-14 kcal/mol
Surface area6030 Å2
MethodPISA
4
E: RB1-inducible coiled-coil protein 1
F: TNIP1_FIR_pS123 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,3663
Polymers13,2482
Non-polymers1181
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1100 Å2
ΔGint-14 kcal/mol
Surface area6260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.812, 45.936, 72.951
Angle α, β, γ (deg.)81.20, 89.67, 88.74
Int Tables number1
Space group name H-MP1

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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.: 4 / Fragment: claw domain
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
TNIP1_FIR_pS123 peptide / 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: 1208.124 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15025
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 177 / 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: 2.36 Å3/Da / Density % sol: 47.93 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.018M magnesium chloride hexahydrate, 0.018M calcium chloride dehydrate, 0.1M imidazole, 0.1M MES, 0.1M monohydrate, 10% v/v MPD, 10% PEG 1000, 10% v/v PEG 3350, pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 19, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2→37.8 Å / Num. obs: 31812 / % possible obs: 97.17 % / Redundancy: 3.4 % / CC1/2: 0.994 / Rmerge(I) obs: 0.042 / Rrim(I) all: 0.064 / Net I/σ(I): 14
Reflection shellResolution: 2→2.071 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.298 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 3108 / CC1/2: 0.908 / % possible all: 95.8

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Processing

Software
NameVersionClassification
PHENIX(1.16_3549: ???)refinement
XDSdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→37.8 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 25.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2196 1488 4.68 %
Rwork0.1828 --
obs0.1845 31812 97.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→37.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3299 0 26 177 3502
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063411
X-RAY DIFFRACTIONf_angle_d0.8434621
X-RAY DIFFRACTIONf_dihedral_angle_d23.8651247
X-RAY DIFFRACTIONf_chiral_restr0.056511
X-RAY DIFFRACTIONf_plane_restr0.005570
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.06450.30731540.2692651X-RAY DIFFRACTION96
2.0645-2.13830.32291260.25432746X-RAY DIFFRACTION96
2.1383-2.22390.27171380.22532801X-RAY DIFFRACTION97
2.2239-2.32510.25631440.2142688X-RAY DIFFRACTION97
2.3251-2.44770.28281350.20692773X-RAY DIFFRACTION98
2.4477-2.6010.27191340.20542776X-RAY DIFFRACTION98
2.601-2.80170.27441460.20822759X-RAY DIFFRACTION97
2.8017-3.08350.20821120.19482811X-RAY DIFFRACTION97
3.0835-3.52920.22471180.17552798X-RAY DIFFRACTION98
3.5292-4.44480.16131450.14362746X-RAY DIFFRACTION98
4.4448-33.45170.19511360.16572775X-RAY DIFFRACTION97
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.1686-0.2337-0.51622.453-0.27766.59750.0723-0.02560.4133-0.0868-0.0681-0.1355-0.60180.0947-0.00420.21230.0010.00030.19690.00950.3002-18.4089-0.25964.5064
27.26214.672-4.83222.0003-9.18582.0014-0.40190.26151.3925-0.89190.36880.7642-1.2174-1.01940.03520.70760.0964-0.1180.40960.06150.5717-27.2282.9902-8.8101
33.60350.87921.36032.1424-0.14376.5030.05760.02030.1218-0.01280.00870.0123-0.0015-0.0448-0.04550.15650.02240.00220.1745-0.01110.22610.8972-7.708619.0896
42.00087.4038-1.57752.0033-3.93278.91830.0521-0.0018-0.5086-0.2041-0.0105-1.54230.42650.7081-0.05530.43550.03160.04030.3749-0.0420.496512.4953-8.869532.4078
54.8987-1.0984-1.48454.1531-0.03825.887-0.1077-0.1306-0.78640.0050.02130.28320.9294-0.17320.07460.3069-0.0201-0.00420.20190.01930.32513.463512.5358-27.5876
62.00133.9221.84128.976.91986.5708-0.06240.1363-2.9594-1.0675-0.1541-2.34343.01980.71280.21241.32650.20970.13360.6029-0.08251.050913.10715.3443-38.7497
73.14820.2972-1.93984.07550.90957.0550.0090.0054-0.1591-0.0315-0.02280.05010.26180.09650.02070.16650.0391-0.03350.18270.01530.2153-15.584624.047-15.3977
82.00135.3302-5.38292.0037-1.58752.00290.34930.49190.47810.0604-0.25371.71390.6948-2.2071-0.09830.4095-0.09040.0210.6997-0.01990.5255-26.863729.2277-3.1628
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 1494 through 1594)
2X-RAY DIFFRACTION2(chain 'B' and resid 103 through 109)
3X-RAY DIFFRACTION3(chain 'G' and resid 1493 through 1591)
4X-RAY DIFFRACTION4(chain 'H' and resid 103 through 109)
5X-RAY DIFFRACTION5(chain 'C' and resid 1494 through 1591)
6X-RAY DIFFRACTION6(chain 'D' and resid 103 through 109)
7X-RAY DIFFRACTION7(chain 'E' and resid 1493 through 1590)
8X-RAY DIFFRACTION8(chain 'F' and resid 103 through 109)

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