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- PDB-9if9: Crystal structure of the Pellino 1 FHA domain in complex with a M... -

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Basic information

Entry
Database: PDB / ID: 9if9
TitleCrystal structure of the Pellino 1 FHA domain in complex with a MDC1-TQxF phosphopeptide.
Components
  • E3 ubiquitin-protein ligase pellino homolog 1
  • Mediator of DNA damage checkpoint protein 1
KeywordsPEPTIDE BINDING PROTEIN / FHA / phosphopeptide binding domain / RING / E3 ligase / DNA damage / DNA repair
Function / homology
Function and homology information


regulation of Toll signaling pathway / response to dsRNA / positive regulation of toll-like receptor 3 signaling pathway / positive regulation of toll-like receptor 4 signaling pathway / regulation of necroptotic process / DNA replication checkpoint signaling / chromatin-protein adaptor activity / negative regulation of necroptotic process / protein localization to site of double-strand break / mitotic intra-S DNA damage checkpoint signaling ...regulation of Toll signaling pathway / response to dsRNA / positive regulation of toll-like receptor 3 signaling pathway / positive regulation of toll-like receptor 4 signaling pathway / regulation of necroptotic process / DNA replication checkpoint signaling / chromatin-protein adaptor activity / negative regulation of necroptotic process / protein localization to site of double-strand break / mitotic intra-S DNA damage checkpoint signaling / ubiquitin-ubiquitin ligase activity / protein K63-linked ubiquitination / positive regulation of double-strand break repair via homologous recombination / SUMOylation of DNA damage response and repair proteins / protein K48-linked ubiquitination / T cell proliferation / negative regulation of TORC1 signaling / negative regulation of T cell proliferation / positive regulation of B cell proliferation / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / positive regulation of protein ubiquitination / histone reader activity / positive regulation of cytokine production / Nonhomologous End-Joining (NHEJ) / TP53 Regulates Transcription of DNA Repair Genes / G2/M DNA damage checkpoint / RING-type E3 ubiquitin transferase / Regulation of necroptotic cell death / Interleukin-1 signaling / ubiquitin protein ligase activity / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / site of double-strand break / chromosome / Processing of DNA double-strand break ends / response to lipopolysaccharide / proteasome-mediated ubiquitin-dependent protein catabolic process / positive regulation of canonical NF-kappaB signal transduction / nuclear body / focal adhesion / DNA repair / DNA damage response / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Pellino family / : / : / Pellino, FHA domain / Pellino, RING domain / : / Regulator of Ty1 transposition protein 107 BRCT domain / BRCT domain / Forkhead associated domain / Forkhead-associated (FHA) domain profile. ...Pellino family / : / : / Pellino, FHA domain / Pellino, RING domain / : / Regulator of Ty1 transposition protein 107 BRCT domain / BRCT domain / Forkhead associated domain / Forkhead-associated (FHA) domain profile. / FHA domain / Forkhead-associated (FHA) domain / SMAD/FHA domain superfamily / BRCT domain profile. / BRCT domain / BRCT domain superfamily
Similarity search - Domain/homology
Mediator of DNA damage checkpoint protein 1 / E3 ubiquitin-protein ligase pellino homolog 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsStewart, M.J. / Torres Esteban, M. / Smerdon, S.J. / Stucki, M.
Funding support Switzerland, United Kingdom, 6items
OrganizationGrant numberCountry
Swiss National Science Foundation31003A_163141 Switzerland
Swiss National Science Foundation310030_189141 Switzerland
Biotechnology and Biological Sciences Research Council (BBSRC)BB/T00746X/1 United Kingdom
Cancer Research UKFC001003 United Kingdom
Medical Research Council (MRC, United Kingdom)FC001003 United Kingdom
Wellcome TrustFC001003 United Kingdom
CitationJournal: Life Sci Alliance / Year: 2025
Title: MDC1 mediates Pellino recruitment to sites of DNA double-strand breaks.
Authors: Torres Esteban, M. / Stewart, M.J. / Bragginton, E. / Meroni, A. / Pellizzari, A. / Jeanrenaud, A. / Smerdon, S.J. / Stucki, M.
History
DepositionFeb 17, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 5, 2025Provider: repository / Type: Initial release
Revision 1.1Mar 26, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: E3 ubiquitin-protein ligase pellino homolog 1
A: E3 ubiquitin-protein ligase pellino homolog 1
C: Mediator of DNA damage checkpoint protein 1
D: Mediator of DNA damage checkpoint protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,3759
Polymers57,8954
Non-polymers4805
Water1,26170
1
A: E3 ubiquitin-protein ligase pellino homolog 1
C: Mediator of DNA damage checkpoint protein 1
hetero molecules

B: E3 ubiquitin-protein ligase pellino homolog 1
D: Mediator of DNA damage checkpoint protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,3759
Polymers57,8954
Non-polymers4805
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x+1/2,-y,z+1/21
Buried area4740 Å2
ΔGint-78 kcal/mol
Surface area23590 Å2
2


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5960 Å2
ΔGint-79 kcal/mol
Surface area22360 Å2
Unit cell
Length a, b, c (Å)52.853, 75.087, 165.134
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein E3 ubiquitin-protein ligase pellino homolog 1 / Pellino-1 / Pellino-related intracellular-signaling molecule / RING-type E3 ubiquitin transferase ...Pellino-1 / Pellino-related intracellular-signaling molecule / RING-type E3 ubiquitin transferase pellino homolog 1


Mass: 27566.004 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PELI1, PRISM / Plasmid: pGEX-6P-1
Details (production host): N-terminal GST tag, N-terminal precission protease cleavage, ColE1
Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q96FA3, RING-type E3 ubiquitin transferase
#2: Protein/peptide Mediator of DNA damage checkpoint protein 1 / Nuclear factor with BRCT domains 1


Mass: 1381.249 Da / Num. of mol.: 2 / Mutation: A1 Y2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q14676
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / 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: 2.97 Å3/Da / Density % sol: 58.56 %
Description: Orthorhombic crystals, colorless and transparent, with well-formed morphology.
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.1M Tris pH 8.0, 1.5M Ammonium sulphate, 20% (w/v) PEG400
PH range: 8 / Temp details: NA

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: NA / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Aug 3, 2023 / Details: NA
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.55→68.35 Å / Num. obs: 15881 / % possible obs: 91.9 % / Redundancy: 12.9 % / CC1/2: 0.997 / Rmerge(I) obs: 0.215 / Rpim(I) all: 0.062 / Rrim(I) all: 0.224 / Net I/σ(I): 8.9
Reflection shell

Num. unique obs: 794 / Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsCC1/2Rpim(I) allRrim(I) all% possible all
8.08-68.3511.50.0621.10.9990.0190.06399.9
2.55-2.778.31.6821.30.4640.6261.80363.1

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Processing

Software
NameVersionClassification
PHENIX1.21.2-5419refinement
autoPROC1.0.5data reduction
Aimless0.7.9data scaling
PHENIX1.21.2-5419phasing
XDSJan 10, 2022data reduction
STARANISO2.3.94data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.55→50.34 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.27 / Stereochemistry target values: LS_WUNIT_K1
RfactorNum. reflection% reflection
Rfree0.2108 15869 5 %
Rwork0.2108 --
obs0.2108 15869 71.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.55→50.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3722 0 25 70 3817
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093801
X-RAY DIFFRACTIONf_angle_d1.0175145
X-RAY DIFFRACTIONf_dihedral_angle_d8.849517
X-RAY DIFFRACTIONf_chiral_restr0.056574
X-RAY DIFFRACTIONf_plane_restr0.011661
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.55-2.570.261120.26112X-RAY DIFFRACTION2
2.58-2.60.3123450.312345X-RAY DIFFRACTION7
2.61-2.640.331820.33182X-RAY DIFFRACTION11
2.64-2.670.33391290.3339129X-RAY DIFFRACTION18
2.67-2.70.28551680.2855168X-RAY DIFFRACTION23
2.7-2.740.3122100.312210X-RAY DIFFRACTION29
2.74-2.780.28592460.2859246X-RAY DIFFRACTION33
2.78-2.820.30372810.3037281X-RAY DIFFRACTION40
2.82-2.870.27393230.2739323X-RAY DIFFRACTION44
2.87-2.910.25823580.2582358X-RAY DIFFRACTION49
2.91-2.960.25053930.2505393X-RAY DIFFRACTION54
2.96-3.020.26724870.2672487X-RAY DIFFRACTION67
3.02-3.080.26235740.2623574X-RAY DIFFRACTION78
3.08-3.140.24596400.2459640X-RAY DIFFRACTION86
3.14-3.210.25016550.2501655X-RAY DIFFRACTION91
3.21-3.280.24227130.2422713X-RAY DIFFRACTION94
3.28-3.360.2336990.233699X-RAY DIFFRACTION98
3.36-3.450.21087380.2108738X-RAY DIFFRACTION100
3.45-3.560.21217540.2121754X-RAY DIFFRACTION100
3.56-3.670.20457200.2045720X-RAY DIFFRACTION99
3.67-3.80.19327550.1932755X-RAY DIFFRACTION99
3.8-3.950.18577350.1857735X-RAY DIFFRACTION100
3.96-4.130.1677430.167743X-RAY DIFFRACTION100
4.13-4.350.16017570.1601757X-RAY DIFFRACTION100
4.35-4.620.15747370.1574737X-RAY DIFFRACTION100
4.63-4.980.16427720.1642772X-RAY DIFFRACTION100
4.98-5.480.19517560.1951756X-RAY DIFFRACTION100
5.48-6.270.22947610.2294761X-RAY DIFFRACTION100
6.27-7.90.21987890.2198789X-RAY DIFFRACTION100
7.92-50.340.24458370.2445837X-RAY DIFFRACTION99

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