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- PDB-2mrf: NMR structure of the ubiquitin-binding zinc finger (UBZ) domain f... -

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Basic information

Entry
Database: PDB / ID: 2mrf
TitleNMR structure of the ubiquitin-binding zinc finger (UBZ) domain from human Rad18
ComponentsE3 ubiquitin-protein ligase RAD18
KeywordsLIGASE / translesion synthesis / DNA repair
Function / homology
Function and homology information


Rad6-Rad18 complex / positive regulation of chromosome segregation / Y-form DNA binding / nuclear inclusion body / postreplication repair / protein monoubiquitination / polyubiquitin modification-dependent protein binding / protein autoubiquitination / replication fork / Recognition of DNA damage by PCNA-containing replication complex ...Rad6-Rad18 complex / positive regulation of chromosome segregation / Y-form DNA binding / nuclear inclusion body / postreplication repair / protein monoubiquitination / polyubiquitin modification-dependent protein binding / protein autoubiquitination / replication fork / Recognition of DNA damage by PCNA-containing replication complex / RING-type E3 ubiquitin transferase / ubiquitin protein ligase activity / E3 ubiquitin ligases ubiquitinate target proteins / site of double-strand break / single-stranded DNA binding / damaged DNA binding / nuclear body / DNA repair / centrosome / ubiquitin protein ligase binding / DNA damage response / protein-containing complex binding / nucleoplasm / identical protein binding / nucleus / metal ion binding / cytoplasm
Similarity search - Function
E3 ubiquitin-protein ligase Rad18 / Rad18-like CCHC zinc finger / Zinc finger, C3HC4 type (RING finger) / SAP domain superfamily / SAP domain / SAP motif profile. / Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation / SAP domain / Rad18, zinc finger UBZ4-type / Zinc finger UBZ4-type profile. ...E3 ubiquitin-protein ligase Rad18 / Rad18-like CCHC zinc finger / Zinc finger, C3HC4 type (RING finger) / SAP domain superfamily / SAP domain / SAP motif profile. / Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation / SAP domain / Rad18, zinc finger UBZ4-type / Zinc finger UBZ4-type profile. / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
E3 ubiquitin-protein ligase RAD18
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing, torsian angle dynamics, molecular dynamics
Model detailslowest energy, model10
AuthorsRizzo, A.A. / Salerno, P.E. / Bezsonova, I. / Korzhnev, D.M.
CitationJournal: Biochemistry / Year: 2014
Title: NMR Structure of the Human Rad18 Zinc Finger in Complex with Ubiquitin Defines a Class of UBZ Domains in Proteins Linked to the DNA Damage Response.
Authors: Rizzo, A.A. / Salerno, P.E. / Bezsonova, I. / Korzhnev, D.M.
History
DepositionJul 3, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Oct 1, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 8, 2014Group: Database references
Revision 1.2May 1, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / 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_nmr_software.name / _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.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_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

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase RAD18
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,6942
Polymers3,6281
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 400structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide E3 ubiquitin-protein ligase RAD18 / Postreplication repair protein RAD18 / hHR18 / hRAD18 / RING finger protein 73


Mass: 3628.125 Da / Num. of mol.: 1 / Fragment: unp residues 198-227
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAD18, RNF73 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9NS91, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HNCO
1313D HN(CA)CB
1413D (H)CCH-TOCSY
1513D HBHA(CO)NH
1613D 1H-15N NOESY
1713D 1H-13C NOESY
1813D CBCA(CO)NH
1913D CCH-TOCSY

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Sample preparation

DetailsContents: 0.05-1.5 mM [U-13C; U-15N] Rad18_UBZ, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
SampleUnits: mM / Component: Rad18_UBZ-1 / Isotopic labeling: [U-13C; U-15N] / Conc. range: 0.05-1.5
Sample conditionsIonic strength: 150 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian VNMRSVarianVNMRS8001
Varian VNMRSVarianVNMRS6002
Varian VNMRSVarianVNMRS5003

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
CcpNmr AnalysisCCPNchemical shift assignment
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
CYANArefinement
RefinementMethod: simulated annealing, torsian angle dynamics, molecular dynamics
Software ordinal: 1 / Details: CNS refinement in explicit water
NMR constraintsNOE constraints total: 706 / NOE intraresidue total count: 129 / NOE long range total count: 207 / NOE medium range total count: 158 / NOE sequential total count: 212 / Hydrogen bond constraints total count: 24 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 400 / Conformers submitted total number: 20 / Maximum lower distance constraint violation: 0.5 Å / Maximum torsion angle constraint violation: 5 ° / Maximum upper distance constraint violation: 0.5 Å / Torsion angle constraint violation method: CNS
NMR ensemble rmsDistance rms dev: 0.025 Å / Distance rms dev error: 0.0023 Å

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