[English] 日本語
Yorodumi
- PDB-8yfk: Crystal structure of FIP200 claw/TNIP1_FIR_pS123 -

+
Open data


ID or keywords:

Loading...

-
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 / glycoprotein biosynthetic process / Atg1/ULK1 kinase complex / ribophagy / glycophagy / autophagy of peroxisome / phagophore assembly site membrane / piecemeal microautophagy of the nucleus / phagophore assembly site ...positive regulation of protein deubiquitination / regulation of protein lipidation / glycoprotein biosynthetic process / Atg1/ULK1 kinase complex / ribophagy / glycophagy / autophagy of peroxisome / 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 / autophagy of mitochondrion / negative regulation of viral genome replication / leukocyte cell-cell adhesion / 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 / translation / positive regulation of protein phosphorylation / 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
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more