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- PDB-3l11: Crystal Structure of the Ring Domain of RNF168 -

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Basic information

Entry
Database: PDB / ID: 3l11
TitleCrystal Structure of the Ring Domain of RNF168
ComponentsE3 ubiquitin-protein ligase RNF168
KeywordsLIGASE / E3 Ligase / RING domain / DNA damage / Chromatin regulator / Chromosomal protein / DNA repair / Metal-binding / Nucleus / Phosphoprotein / Ubl conjugation pathway / Zinc-finger / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


histone H2AK15 ubiquitin ligase activity / histone ubiquitin ligase activity / isotype switching / double-strand break repair via classical nonhomologous end joining / DNA repair-dependent chromatin remodeling / K63-linked polyubiquitin modification-dependent protein binding / response to ionizing radiation / negative regulation of transcription elongation by RNA polymerase II / protein K63-linked ubiquitination / nucleosome binding ...histone H2AK15 ubiquitin ligase activity / histone ubiquitin ligase activity / isotype switching / double-strand break repair via classical nonhomologous end joining / DNA repair-dependent chromatin remodeling / K63-linked polyubiquitin modification-dependent protein binding / response to ionizing radiation / negative regulation of transcription elongation by RNA polymerase II / protein K63-linked ubiquitination / nucleosome binding / SUMOylation of DNA damage response and repair proteins / interstrand cross-link repair / ubiquitin ligase complex / positive regulation of DNA repair / epigenetic regulation of gene expression / ubiquitin binding / Nonhomologous End-Joining (NHEJ) / RING-type E3 ubiquitin transferase / G2/M DNA damage checkpoint / double-strand break repair via nonhomologous end joining / ubiquitin-protein transferase 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 / histone binding / ubiquitin-dependent protein catabolic process / protein ubiquitination / DNA damage response / chromatin binding / protein-containing complex / nucleoplasm / nucleus / metal ion binding / cytosol
Similarity search - Function
Prokaryotic RING finger family 4 / E3 ubiquitin-protein ligase RNF168 / : / Zinc finger, C3HC4 RING-type / Zinc finger, C3HC4 type (RING finger) / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type ...Prokaryotic RING finger family 4 / E3 ubiquitin-protein ligase RNF168 / : / Zinc finger, C3HC4 RING-type / Zinc finger, C3HC4 type (RING finger) / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
MALONATE ION / E3 ubiquitin-protein ligase RNF168
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / S-SAD coupled with molecular replacement / Resolution: 2.12 Å
AuthorsNeculai, D. / Yermekbayeva, L. / Crombet, L. / Weigelt, J. / Bountra, C. / Edwards, A.M. / Arrowsmith, C.H. / Bochkarev, A. / Dhe-Paganon, S. / Structural Genomics Consortium (SGC)
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Molecular insights into the function of RING finger (RNF)-containing proteins hRNF8 and hRNF168 in Ubc13/Mms2-dependent ubiquitylation.
Authors: Campbell, S.J. / Edwards, R.A. / Leung, C.C. / Neculai, D. / Hodge, C.D. / Dhe-Paganon, S. / Glover, J.N.
History
DepositionDec 10, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 19, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 26, 2012Group: Database references
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase RNF168
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,4665
Polymers13,1311
Non-polymers3354
Water61334
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.706, 49.706, 110.149
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein E3 ubiquitin-protein ligase RNF168 / RING finger protein 168


Mass: 13131.254 Da / Num. of mol.: 1 / Fragment: ring domain (UNP residues 1-113)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BC033791, RNF168 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q8IYW5, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H2O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / Source method: isolated from a natural source / Formula: H2O

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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: 2.59 Å3/Da / Density % sol: 52.52 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.3
Details: 1.5 M NaMalonate, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN A200 / Detector: CCD / Date: Nov 11, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.12→45.31 Å / Num. all: 8436 / Num. obs: 8384 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 53.39 % / Rmerge(I) obs: 0.1238 / Net I/σ(I): 40.1
Reflection shellResolution: 2.12→2.22 Å / Redundancy: 54.28 % / Rmerge(I) obs: 0.6495 / Mean I/σ(I) obs: 5.17 / Num. unique all: 1047 / % possible all: 99.7

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Processing

Software
NameVersionClassification
CrystalCleardata collection
SHELXDphasing
MOLREPphasing
REFMAC5.6.0041refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: S-SAD coupled with molecular replacement
Starting model: 3FL2

3fl2


Resolution: 2.12→45.49 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.94 / SU B: 7.525 / SU ML: 0.104 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.182 / ESU R Free: 0.155 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS.
RfactorNum. reflection% reflectionSelection details
Rfree0.21477 420 5 %RANDOM
Rwork0.18734 ---
all0.1887 8384 --
obs0.1887 7964 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.912 Å2
Baniso -1Baniso -2Baniso -3
1-1.38 Å20 Å20 Å2
2--1.38 Å20 Å2
3----2.76 Å2
Refinement stepCycle: LAST / Resolution: 2.12→45.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms830 0 16 34 880
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.022872
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.4231.9871178
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9525104
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.78121.17634
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.94815159
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0341510
X-RAY DIFFRACTIONr_chiral_restr0.2150.2132
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021646
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.0550.25045
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.12→2.175 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.368 31 -
Rwork0.228 574 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 10.1396 Å / Origin y: 21.323 Å / Origin z: 14.7529 Å
111213212223313233
T0.0891 Å20.0029 Å2-0.0106 Å2-0.147 Å20.0058 Å2--0.0503 Å2
L0.278 °20.3217 °2-0.5527 °2-1.0211 °2-0.2658 °2--1.7554 °2
S0.0075 Å °-0.0764 Å °0.0385 Å °0.0023 Å °0.0553 Å °0.0223 Å °-0.2066 Å °0.1468 Å °-0.0628 Å °

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