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- PDB-9coj: SH3-like tandem domain of human KIN protein -

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Basic information

Entry
Database: PDB / ID: 9coj
TitleSH3-like tandem domain of human KIN protein
ComponentsDNA/RNA-binding protein KIN17
KeywordsRNA BINDING PROTEIN / RNA binding / SH3-like domain / repair / KOW motif / tandem / KIN17 / C-terminal domain / nuclear protein
Function / homology
Function and homology information


Protein methylation / mRNA processing / nuclear matrix / double-stranded DNA binding / DNA recombination / DNA replication / intracellular membrane-bounded organelle / DNA repair / DNA damage response / protein-containing complex ...Protein methylation / mRNA processing / nuclear matrix / double-stranded DNA binding / DNA recombination / DNA replication / intracellular membrane-bounded organelle / DNA repair / DNA damage response / protein-containing complex / DNA binding / RNA binding / nucleoplasm / nucleus / metal ion binding / cytoplasm
Similarity search - Function
DNA/RNA-binding protein Kin17, WH-like domain / KIN17-like protein / DNA/RNA-binding protein KIN17, WH-like domain superfamily / KN17, SH3-like C-terminal domain / Kin17, KOW domain / Domain of Kin17 curved DNA-binding protein / KN17 SH3-like C-terminal domain / Domain of Kin17 curved DNA-binding protein / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / Ribosomal protein L2, domain 2
Similarity search - Domain/homology
DNA/RNA-binding protein KIN17
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / distance geometry
Authorsde Lourenco, I.O. / Fossey, M.A. / Souza, F.P. / Seixas, F.A.V. / Fernandez, M.A. / Almeida, F.C.L. / Caruso, I.P.
Funding support Brazil, 7items
OrganizationGrant numberCountry
Brazilian National Council for Scientific and Technological Development (CNPq)141886/2019-6 Brazil
Sao Paulo Research Foundation (FAPESP)2009/53989-4 Brazil
Other governmentFAPERJ: 202.279/2018 Brazil
Sao Paulo Research Foundation (FAPESP)2022/13050-5 Brazil
Brazilian National Council for Scientific and Technological Development (CNPq)317157/2023-0 Brazil
Sao Paulo Research Foundation (FAPESP)2016/17378-4 Brazil
Other governmentFINEP PROINFRA 01/2009 - 0879/10 Brazil
CitationJournal: To Be Published
Title: Solution structure of SH3-like tandem domain of human KIN protein and its interaction with RNA homo-oligonucleotides
Authors: de Lourenco, I.O. / Fossey, M.A. / Souza, F.P. / Seixas, F.A.V. / Fernandez, M.A. / Almeida, F.C.L. / Caruso, I.P.
History
DepositionJul 16, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA/RNA-binding protein KIN17


Theoretical massNumber of molelcules
Total (without water)14,3491
Polymers14,3491
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR Distance Restraints, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 200structures with favorable non-bond energy
RepresentativeModel #1lowest energy

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Components

#1: Protein DNA/RNA-binding protein KIN17 / Binding to curved DNA / KIN / antigenic determinant of recA protein homolog


Mass: 14348.669 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KIN, BTCD, KIN17 / Production host: Escherichia coli (E. coli) / References: UniProt: O60870

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic13D 1H-13C NOESY aliphatic
121isotropic13D 1H-13C NOESY aromatic
131isotropic13D 1H-15N NOESY
141isotropic12D 1H-15N HSQC
151isotropic12D 1H-13C HSQC aliphatic
161isotropic12D 1H-13C HSQC aromatic
171isotropic13D HNCO
181isotropic13D HNCA
191isotropic13D HN(CA)CB
1101isotropic13D CBCA(CO)NH
1111isotropic13D C(CO)NH
1121isotropic13D H(CCO)NH
1131isotropic13D (H)CCH-TOCSY
1141isotropic13D (H)CCH-TOCSY
1151isotropic12D (HB)CB(CGCD)HD
1161isotropic12D (HB)CB(CGCDCE)HE

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Sample preparation

DetailsType: solution
Contents: 500 uM [U-13C; U-15N] SH3-like tandem domain of human KIN protein, 0.5 mM PMSF, 3 mM EDTA, 0.02 % v/v sodium azide, 0.33 mM 98% 2H DSS, 95% H2O/5% D2O
Label: 15N_13C_sample / Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
500 uMSH3-like tandem domain of human KIN protein[U-13C; U-15N]1
0.5 mMPMSFnatural abundance1
3 mMEDTAnatural abundance1
0.02 % v/vsodium azidenatural abundance1
0.33 mMDSS98% 2H1
Sample conditionsIonic strength: 50 mM NaPi, 100 mM NaCl mM / Label: conditions_1 / pH: 6.5 / Pressure: 1 atm / Temperature: 298.4 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III HD / Manufacturer: Bruker / Model: AVANCE III HD / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CcpNmr AnalysisCCPNchemical shift assignment
ARIA2.3.2Linge, O'Donoghue and Nilgesrefinement
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure calculation
CcpNmr AnalysisCCPNpeak picking
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
ARIA2.3.2Linge, O'Donoghue and Nilgesrefinement
RefinementMethod: distance geometry / Software ordinal: 2
Details: The structures are based on a total of 5751 restraints, 4523 are NOE-derived distance constraints, and 1228 ambiguous restraints.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with favorable non-bond energy
Conformers calculated total number: 200 / Conformers submitted total number: 10

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