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- PDB-2lrr: Solution structure of the R3H domain from human Smubp-2 in comple... -

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Basic information

Entry
Database: PDB / ID: 2lrr
TitleSolution structure of the R3H domain from human Smubp-2 in complex with 2'-deoxyguanosine-5'-monophosphate
ComponentsDNA-binding protein SMUBP-2
KeywordsHYDROLASE / DNA Binding Protein
Function / homology
Function and homology information


double-stranded DNA helicase activity / RNA secondary structure unwinding / ATP-dependent activity, acting on RNA / DNA duplex unwinding / transcription factor binding / ATP-dependent activity, acting on DNA / DNA helicase activity / 5'-3' RNA helicase activity / ribosome binding / single-stranded DNA binding ...double-stranded DNA helicase activity / RNA secondary structure unwinding / ATP-dependent activity, acting on RNA / DNA duplex unwinding / transcription factor binding / ATP-dependent activity, acting on DNA / DNA helicase activity / 5'-3' RNA helicase activity / ribosome binding / single-stranded DNA binding / 5'-3' DNA helicase activity / growth cone / DNA helicase / tRNA binding / single-stranded RNA binding / nuclear body / RNA helicase / ribonucleoprotein complex / axon / ATP hydrolysis activity / DNA binding / RNA binding / zinc ion binding / nucleoplasm / ATP binding / identical protein binding / membrane / nucleus / cytoplasm
Similarity search - Function
Helicase SMUBP-2/Hcs1-like / DNA-binding protein SMUBP-2, R3H domain / : / Helicase SMUBP-2/HCS1, 1B domain / R3H-like domain / Putative single-stranded nucleic acids-binding domain / R3H domain / R3H domain / R3H domain superfamily / R3H domain profile. ...Helicase SMUBP-2/Hcs1-like / DNA-binding protein SMUBP-2, R3H domain / : / Helicase SMUBP-2/HCS1, 1B domain / R3H-like domain / Putative single-stranded nucleic acids-binding domain / R3H domain / R3H domain / R3H domain superfamily / R3H domain profile. / Zinc finger, AN1-type / AN1-like Zinc finger / AN1-like Zinc finger / Zinc finger AN1-type profile. / AN1-like Zinc finger / : / DNA2/NAM7 helicase, helicase domain / AAA domain / Ribosomal Protein S8; Chain: A, domain 1 / DNA2/NAM7 helicase-like, C-terminal / AAA domain / DEAD-like helicases superfamily / Helicase superfamily 1/2, ATP-binding domain / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE / DNA-binding protein SMUBP-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics, simulated annealing
Model detailsclosest to the average, model 1
AuthorsJaudzems, K. / Zhulenkovs, D. / Otting, G. / Liepinsh, E.
CitationJournal: J.Mol.Biol. / Year: 2012
Title: Structural Basis for 5'-End-Specific Recognition of Single-Stranded DNA by the R3H Domain from Human Smubp-2
Authors: Jaudzems, K. / Jia, X. / Yagi, H. / Zhulenkovs, D. / Graham, B. / Otting, G. / Liepinsh, E.
History
DepositionApr 12, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Oct 24, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp / database_2 ...chem_comp / database_2 / pdbx_database_status / pdbx_nmr_software / struct_ref_seq_dif / struct_site
Item: _chem_comp.type / _database_2.pdbx_DOI ..._chem_comp.type / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA-binding protein SMUBP-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,0542
Polymers9,7071
Non-polymers3471
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 / 100target function
RepresentativeModel #1closest to the average

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Components

#1: Protein DNA-binding protein SMUBP-2 / ATP-dependent helicase IGHMBP2 / Glial factor 1 / GF-1 / Immunoglobulin mu-binding protein 2


Mass: 9706.846 Da / Num. of mol.: 1 / Fragment: R3H domain residues 711-786
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGHMBP2, SMBP2, smubp-2, SMUBP2 / Production host: Escherichia coli (E. coli) / Strain (production host): M15 / References: UniProt: P38935, DNA helicase, RNA helicase
#2: Chemical ChemComp-DGP / 2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-1H TOCSY
1312D 1H-1H NOESY
1413D 1H-15N NOESY
1513D HNHA

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Sample preparation

DetailsContents: 0.9 mM [U-99% 15N] Smubp2_R3H, 5.5 mM 2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE, 5 % [U-100% 2H] D2O, 10 mM sodium phosphate, 100 mM sodium chloride, 0.03 % sodium azide, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.9 mMSmubp2_R3H-1[U-99% 15N]1
5.5 mM2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE-21
5 %D2O-3[U-100% 2H]1
10 mMsodium phosphate-41
100 mMsodium chloride-51
0.03 %sodium azide-61
Sample conditionsIonic strength: 0.12 / pH: 6.3 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
VnmrJ2.1bVariancollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
XEASYBartels et al.chemical shift assignment
XEASYBartels et al.peak picking
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
CYANA2.1Guntert, Mumenthaler and Wuthrichdata analysis
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
CYANA2.1Guntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: torsion angle dynamics, simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 1359 / NOE intraresidue total count: 347 / NOE long range total count: 431 / NOE medium range total count: 273 / NOE sequential total count: 308
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20 / Maximum upper distance constraint violation: 0.34 Å
NMR ensemble rmsDistance rms dev: 0.0089 Å / Distance rms dev error: 0.0011 Å

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