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- PDB-8yfm: Crystal structure of FIP200 claw/TNIP1_FIR_pS122 -

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Basic information

Entry
Database: PDB / ID: 8yfm
TitleCrystal structure of FIP200 claw/TNIP1_FIR_pS122
Components
  • RB1-inducible coiled-coil protein 1
  • TNIP1_FIR_pS122 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 / glycophagy / phagophore assembly site membrane / piecemeal microautophagy of the nucleus / phagophore assembly site / mitogen-activated protein kinase binding ...positive regulation of protein deubiquitination / regulation of protein lipidation / ribophagy / glycoprotein biosynthetic process / Atg1/ULK1 kinase complex / glycophagy / phagophore assembly site membrane / 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 / positive regulation of cell size / autophagosome assembly / positive regulation of autophagy / extrinsic apoptotic signaling pathway / negative regulation of canonical NF-kappaB signal transduction / protein-membrane adaptor activity / 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 / nuclear membrane / cellular response to lipopolysaccharide / molecular adaptor activity / lysosome / translation / positive regulation of protein phosphorylation / inflammatory response / 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: 1.5 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

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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: TNIP1_FIR_pS122 peptide
D: RB1-inducible coiled-coil protein 1
E: TNIP1_FIR_pS122 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6846
Polymers26,4964
Non-polymers1882
Water4,288238
1
A: RB1-inducible coiled-coil protein 1
B: TNIP1_FIR_pS122 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,3443
Polymers13,2482
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1040 Å2
ΔGint-13 kcal/mol
Surface area6600 Å2
MethodPISA
2
D: RB1-inducible coiled-coil protein 1
E: TNIP1_FIR_pS122 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,3403
Polymers13,2482
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1170 Å2
ΔGint-6 kcal/mol
Surface area6390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.072, 61.072, 65.302
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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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.: 2 / 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_pS122 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.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15025
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 238 / 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: 2.65 Å3/Da / Density % sol: 53.65 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 25% v/v PEG smear medium, 0.1M sodium cacodylate, 0.2M ammonium sulfate, pH 5.5

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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: 1.5→30.54 Å / Num. obs: 43527 / % possible obs: 99.7 % / Redundancy: 9.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.041 / Net I/σ(I): 24.8
Reflection shellResolution: 1.5→1.53 Å / Rmerge(I) obs: 0.548 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 2108 / CC1/2: 0.918

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Processing

Software
NameVersionClassification
PHENIX(1.16_3549: ???)refinement
XDSdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→30.536 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 23.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2088 2108 4.84 %
Rwork0.1925 --
obs0.1932 43527 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.5→30.536 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1692 0 11 238 1941
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061767
X-RAY DIFFRACTIONf_angle_d0.8052391
X-RAY DIFFRACTIONf_dihedral_angle_d20.036654
X-RAY DIFFRACTIONf_chiral_restr0.052263
X-RAY DIFFRACTIONf_plane_restr0.006298
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5002-1.53510.36081480.30592675X-RAY DIFFRACTION96
1.5351-1.57350.28981480.27422790X-RAY DIFFRACTION100
1.5735-1.6160.26931320.2532748X-RAY DIFFRACTION100
1.616-1.66350.24471760.2292727X-RAY DIFFRACTION100
1.6635-1.71720.28481220.24982807X-RAY DIFFRACTION100
1.7172-1.77860.25781100.22422797X-RAY DIFFRACTION100
1.7786-1.84980.26761400.22972762X-RAY DIFFRACTION100
1.8498-1.9340.22531240.21662727X-RAY DIFFRACTION100
1.934-2.03590.18971420.21242844X-RAY DIFFRACTION100
2.0359-2.16340.23621540.20132718X-RAY DIFFRACTION100
2.1634-2.33040.21491570.19762749X-RAY DIFFRACTION100
2.3304-2.56480.23731360.20542795X-RAY DIFFRACTION100
2.5648-2.93570.2371120.19612770X-RAY DIFFRACTION100
2.9357-3.69770.18921620.17812744X-RAY DIFFRACTION100
3.6977-30.5360.17411450.16412766X-RAY DIFFRACTION100
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)
15.54623.4799-0.93744.8586-0.98513.6293-0.10680.36240.2219-0.12790.20790.2479-0.1498-0.3302-0.07860.16210.02990.01610.2157-0.0090.151723.902-23.410712.4048
22.03044.1546-7.24995.95062.46512.04030.41250.97640.4149-0.8746-0.0440.1254-0.5916-0.5931-0.36120.38730.02250.02510.36240.0290.28434.154-11.98294.3842
37.88861.9493-1.30592.4552-0.34663.46220.2156-0.34160.34330.1544-0.1110.079-0.36020.0557-0.0850.2267-0.00860.0030.15370.01550.15138.396-32.26930.0367
42.05074.4041-2.19536.8175-8.15342.04310.24-0.50920.20691.40110.19970.1339-0.8429-0.127-0.34910.37750.0229-0.01060.3498-0.01630.2932-6.7051-35.58137.9825
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 1491 through 1591)
2X-RAY DIFFRACTION2(chain 'B' and resid 100 through 109)
3X-RAY DIFFRACTION3(chain 'D' and resid 1491 through 1591)
4X-RAY DIFFRACTION4(chain 'E' and resid 100 through 109)

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