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- PDB-2khu: Solution Structure of the Ubiquitin-Binding Motif of Human Polyme... -

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Basic information

Entry
Database: PDB / ID: 2khu
TitleSolution Structure of the Ubiquitin-Binding Motif of Human Polymerase Iota
ComponentsImmunoglobulin G-binding protein G, DNA polymerase iota
KeywordsTransferase/protein binding / UBM / ubiquitin-binding domain / polymerase iota / translesion synthesis / TLS / Immunoglobulin G-binding protein / ubiquitin-BINDING PROTEIN / Transferase-protein binding complex
Function / homology
Function and homology information


IgG binding / error-prone translesion synthesis / translesion synthesis / Translesion synthesis by POLI / Termination of translesion DNA synthesis / cytoplasmic ribonucleoprotein granule / DNA replication / damaged DNA binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity ...IgG binding / error-prone translesion synthesis / translesion synthesis / Translesion synthesis by POLI / Termination of translesion DNA synthesis / cytoplasmic ribonucleoprotein granule / DNA replication / damaged DNA binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nuclear speck / DNA repair / extracellular region / nucleoplasm / metal ion binding
Similarity search - Function
IgG-binding B / B domain / M protein-type anchor domain / GA-like domain / GA-like domain / Immunoglobulin/albumin-binding domain superfamily / YSIRK Gram-positive signal peptide / DNA polymerase, Y-family, little finger domain / impB/mucB/samB family C-terminal domain / UmuC domain ...IgG-binding B / B domain / M protein-type anchor domain / GA-like domain / GA-like domain / Immunoglobulin/albumin-binding domain superfamily / YSIRK Gram-positive signal peptide / DNA polymerase, Y-family, little finger domain / impB/mucB/samB family C-terminal domain / UmuC domain / DNA polymerase, Y-family, little finger domain superfamily / impB/mucB/samB family / UmuC domain profile. / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
Immunoglobulin G-binding protein G / DNA polymerase iota
Similarity search - Component
Biological speciesStreptococcus sp. (bacteria)
Homo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsBomar, M.G. / D'Souza, S. / Bienko, M. / Dikic, I. / Walker, G.
CitationJournal: Mol.Cell / Year: 2010
Title: Unconventional Ubiquitin Recognition by the Ubiquitin-Binding Motif within the Y Family DNA Polymerases iota and Rev1.
Authors: Bomar, M.G. / D'Souza, S. / Bienko, M. / Dikic, I. / Walker, G.C. / Zhou, P.
History
DepositionApr 11, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Feb 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.3May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Immunoglobulin G-binding protein G, DNA polymerase iota


Theoretical massNumber of molelcules
Total (without water)12,3491
Polymers12,3491
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)25 / 40structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Antibody Immunoglobulin G-binding protein G, DNA polymerase iota / IgG-binding protein G / RAD30 homolog B / Eta2


Mass: 12348.556 Da / Num. of mol.: 1 / Fragment: UNP residues 304-357, 676-715
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus sp., Homo sapiens / Gene: spg, POLI, RAD30B / Production host: Escherichia coli (E. coli)
References: UniProt: P19909, UniProt: Q9UNA4, DNA-directed DNA polymerase
Sequence detailsACCORDING TO THE AUTHORS THE N-TERMINAL PART IS A GB1 TAG USED FOR ENHANCEMENT OF PROTEIN ...ACCORDING TO THE AUTHORS THE N-TERMINAL PART IS A GB1 TAG USED FOR ENHANCEMENT OF PROTEIN SOLUBILITY. THEY CHOOSE TO DEPOSIT ONLY THE C-TERMINAL PART OF THE SEQUENCE CORRESPONDING TO DNA POLYMERASE IOTA. THESE 2 SEGMENTS ARE LINKED BY THE RESIDUES GSDE

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: Solution Structure of the Ubiquitin-Binding Motif of Human Polymerase Iota
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D (H)CCH-TOCSY
1213D HNCA
1313D HN(CA)CB
1413D HN(CO)CA
1513D HNCO
1613D HN(COCA)CB
1713D 1H-15N NOESY
1813D 1H-13C NOESY

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Sample preparation

DetailsContents: 1-4 mM [U-100% 13C; U-100% 15N] D2O-1, 1-4 mM [U-100% 13C; U-100% 15N] H2O-2, 100% D2O
Solvent system: 100% D2O
Sample
UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMD2O-1[U-100% 13C; U-100% 15N]1-41
mMH2O-2[U-100% 13C; U-100% 15N]1-41
Sample conditionsIonic strength: 0.1 / pH: 7 / Pressure: ambient / Temperature: 25 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA8001
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR NIH2.19Schwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIH2.19Schwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 40 / Conformers submitted total number: 25

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