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- PDB-4ayc: RNF8 RING domain structure -

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Basic information

Entry
Database: PDB / ID: 4ayc
TitleRNF8 RING domain structure
Components(E3 UBIQUITIN-PROTEIN LIGASE ...) x 2
KeywordsLIGASE / DNA DAMAGE / K63 CHAINS
Function / homology
Function and homology information


sperm DNA condensation / protein K6-linked ubiquitination / isotype switching / response to ionizing radiation / DNA repair-dependent chromatin remodeling / negative regulation of transcription elongation by RNA polymerase II / protein K63-linked ubiquitination / signal transduction in response to DNA damage / ubiquitin ligase complex / positive regulation of double-strand break repair via homologous recombination ...sperm DNA condensation / protein K6-linked ubiquitination / isotype switching / response to ionizing radiation / DNA repair-dependent chromatin remodeling / negative regulation of transcription elongation by RNA polymerase II / protein K63-linked ubiquitination / signal transduction in response to DNA damage / ubiquitin ligase complex / positive regulation of double-strand break repair via homologous recombination / interstrand cross-link repair / protein K48-linked ubiquitination / protein autoubiquitination / positive regulation of DNA repair / epigenetic regulation of gene expression / ubiquitin binding / Nonhomologous End-Joining (NHEJ) / G2/M DNA damage checkpoint / RING-type E3 ubiquitin transferase / double-strand break repair via nonhomologous end joining / ubiquitin protein ligase activity / double-strand break repair / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / site of double-strand break / Processing of DNA double-strand break ends / midbody / ubiquitin-dependent protein catabolic process / histone binding / chromosome, telomeric region / cell division / ubiquitin protein ligase binding / DNA damage response / chromatin binding / protein homodimerization activity / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytosol
Similarity search - Function
E3 ubiquitin-protein ligase RNF8 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #170 / Forkhead associated domain / Forkhead-associated (FHA) domain profile. / FHA domain / Forkhead-associated (FHA) domain / Zinc finger, C3HC4 type (RING finger) / SMAD/FHA domain superfamily / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 ...E3 ubiquitin-protein ligase RNF8 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #170 / Forkhead associated domain / Forkhead-associated (FHA) domain profile. / FHA domain / Forkhead-associated (FHA) domain / Zinc finger, C3HC4 type (RING finger) / SMAD/FHA domain superfamily / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
E3 ubiquitin-protein ligase RNF8
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsMattiroli, F. / Vissers, J.H.A. / Van Dijk, W.J. / Ikpa, P. / Citterio, E. / Vermeulen, W. / Marteijn, J.A. / Sixma, T.K.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2012
Title: Rnf168 Ubiquitinates K13-15 on H2A/H2Ax to Drive DNA Damage Signaling
Authors: Mattiroli, F. / Vissers, J.H.A. / Van Dijk, W.J. / Ikpa, P. / Citterio, E. / Vermeulen, W. / Marteijn, J.A. / Sixma, T.K.
History
DepositionJun 20, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 26, 2012Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Sep 11, 2024Group: Derived calculations / Category: struct_conn
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: E3 UBIQUITIN-PROTEIN LIGASE RNF8
B: E3 UBIQUITIN-PROTEIN LIGASE RNF8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,26212
Polymers32,7222
Non-polymers1,53910
Water1,04558
1
A: E3 UBIQUITIN-PROTEIN LIGASE RNF8
B: E3 UBIQUITIN-PROTEIN LIGASE RNF8
hetero molecules

A: E3 UBIQUITIN-PROTEIN LIGASE RNF8
B: E3 UBIQUITIN-PROTEIN LIGASE RNF8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,52324
Polymers65,4444
Non-polymers3,07920
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area12650 Å2
ΔGint-163.2 kcal/mol
Surface area31500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.374, 213.717, 34.102
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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E3 UBIQUITIN-PROTEIN LIGASE ... , 2 types, 2 molecules AB

#1: Protein E3 UBIQUITIN-PROTEIN LIGASE RNF8 / RING FINGER PROTEIN 8


Mass: 16353.082 Da / Num. of mol.: 1 / Fragment: RING DOMAIN, RESIDUES 351-485
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS
References: UniProt: O76064, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Protein E3 UBIQUITIN-PROTEIN LIGASE RNF8 / RING FINGER PROTEIN 8


Mass: 16369.082 Da / Num. of mol.: 1 / Fragment: RING DOMAIN, RESIDUES 351-485
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS
References: UniProt: O76064, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)

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Non-polymers , 6 types, 68 molecules

#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CPQ / N,N-BIS(3-D-GLUCONAMIDOPROPYL)DEOXYCHOLAMIDE / DEOXY-BIGCHAP


Mass: 862.056 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C42H75N3O15 / Comment: detergent*YM
#5: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.8 Å3/Da / Density % sol: 56.1 % / Description: NONE
Crystal growpH: 6.9
Details: 0.1 M NA CACODYLATE, PH 6.9, 2.5 M AMMONIUM SULPHATE, 0.8 MM N,N-BIS(3-D-GLUCONAMIDOPROPYL)DEOXYCHOLAMIDE

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Data collection

DiffractionMean temperature: 193 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.282
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 5, 2010
RadiationMonochromator: FIXED-EXIT LN2 COOLED DOUBLE CRYSTAL MONOCHROMATOR
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.282 Å / Relative weight: 1
ReflectionResolution: 1.9→47.37 Å / Num. obs: 28115 / % possible obs: 99.1 % / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 25.8
Reflection shellResolution: 1.9→2 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 2.7 / % possible all: 95.2

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
XDSdata reduction
SCALAdata scaling
SHELXDphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.9→46.29 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.953 / SU B: 7.513 / SU ML: 0.108 / Cross valid method: THROUGHOUT / ESU R: 0.143 / ESU R Free: 0.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: RELATIVE TO THE PUBLICATION TWO SIDECHAIN WERE ADDED TO THE MODEL (RESIDUES A482 AND B485) RESULTING IN SLIGHTLY DIFFERENT STATISTICS.
RfactorNum. reflection% reflectionSelection details
Rfree0.22948 1414 5 %RANDOM
Rwork0.19973 ---
obs0.20136 26652 98.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 50.632 Å2
Baniso -1Baniso -2Baniso -3
1-0.23 Å20 Å2-0 Å2
2---0.46 Å2-0 Å2
3---0.23 Å2
Refinement stepCycle: LAST / Resolution: 1.9→46.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2164 0 86 58 2308
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0192327
X-RAY DIFFRACTIONr_bond_other_d0.0010.022310
X-RAY DIFFRACTIONr_angle_refined_deg1.2312.013127
X-RAY DIFFRACTIONr_angle_other_deg0.74235374
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5675279
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.67225.575113
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.00715500
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.7631515
X-RAY DIFFRACTIONr_chiral_restr0.0760.2360
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022515
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02484
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.348 79 -
Rwork0.296 1762 -
obs--91.14 %
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)
13.2277-3.5257-2.179930.08625.51075.03470.1568-0.05770.10880.71780.09140.2477-0.2793-0.0517-0.24810.49720.110.12780.08310.03730.3551-11.16380.93725.861
24.0254-12.33351.978437.852-6.07320.9862-0.3942-0.15590.00211.35750.44390.0672-0.2721-0.1081-0.04970.7860.12540.06340.14780.0360.6592-3.23145.46329.748
32.21830.5543-0.10615.446-0.55271.4446-0.0326-0.0248-0.03020.3469-0.0232-0.3027-0.19490.07160.05580.1923-0.0472-0.04670.01930.01930.29328.114.19627.551
47.0547-2.3377-3.627811.54860.3648.19650.2016-0.01160.30640.1786-0.045-0.6669-0.15060.2889-0.15650.3281-0.0778-0.07630.06530.04260.33915.12525.15218.356
50.74083.8556-0.517547.2799-5.06360.5826-0.12320.05820.172-0.52010.242-0.08490.075-0.0539-0.11880.55580.08590.00290.14210.04670.6209-4.35851.37820.838
67.0732-0.5894-1.18324.24950.29651.60410.00620.51390.0193-0.054-0.03810.8475-0.1684-0.35110.03180.1308-0.0023-0.00370.10030.02830.5098-13.1419.59723.889
73.1303-0.5307-0.78344.2478-0.48763.23470.07670.07480.35570.4082-0.04380.5427-0.2611-0.2887-0.03290.19120.0080.03660.05870.01460.428-7.12415.70329.048
87.27621.7241-0.90088.9392-0.29565.57580.3059-0.77980.11462.06280.29840.9096-0.1936-0.3817-0.60430.66450.11240.26150.34620.03170.6863-15.30615.95238.52
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A348 - 370
2X-RAY DIFFRACTION2A371 - 398
3X-RAY DIFFRACTION3A399 - 465
4X-RAY DIFFRACTION3A900 - 901
5X-RAY DIFFRACTION4A466 - 483
6X-RAY DIFFRACTION5B358 - 402
7X-RAY DIFFRACTION6B403 - 440
8X-RAY DIFFRACTION6B900 - 901
9X-RAY DIFFRACTION7B441 - 467
10X-RAY DIFFRACTION8B468 - 485

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