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- PDB-4b3g: crystal structure of Ighmbp2 helicase in complex with RNA -

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Basic information

Entry
Database: PDB / ID: 4b3g
Titlecrystal structure of Ighmbp2 helicase in complex with RNA
Components
  • DNA-BINDING PROTEIN SMUBP-2
  • RNA (5'-(AP*AP*AP*AP*AP*AP*AP*AP*AP)-3')
KeywordsHYDROLASE/RNA / HYDROLASE-RNA COMPLEX / HYDROLASE / HELICASE / RNA
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
Elongation Factor Tu (Ef-tu); domain 3 - #270 / Helicase SMUBP-2/Hcs1-like / DNA-binding protein SMUBP-2, R3H domain / : / Helicase SMUBP-2/HCS1, 1B domain / Putative single-stranded nucleic acids-binding domain / R3H domain / R3H domain / R3H domain superfamily / R3H domain profile. ...Elongation Factor Tu (Ef-tu); domain 3 - #270 / Helicase SMUBP-2/Hcs1-like / DNA-binding protein SMUBP-2, R3H domain / : / Helicase SMUBP-2/HCS1, 1B 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 / Elongation Factor Tu (Ef-tu); domain 3 / DNA2/NAM7 helicase-like, C-terminal / AAA domain / DEAD-like helicases superfamily / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Beta Barrel / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
RNA / DNA-binding protein SMUBP-2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsLim, S.C. / Song, H.
CitationJournal: Nucleic Acids Res. / Year: 2012
Title: The Ighmbp2 Helicase Structure Reveals the Molecular Basis for Disease-Causing Mutations in Dmsa1.
Authors: Lim, S.C. / Bowler, M.W. / Lai, T.F. / Song, H.
History
DepositionJul 24, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 26, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 19, 2012Group: Database references
Revision 1.2May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_sheet
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_sheet.number_strands
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA-BINDING PROTEIN SMUBP-2
B: DNA-BINDING PROTEIN SMUBP-2
G: RNA (5'-(AP*AP*AP*AP*AP*AP*AP*AP*AP)-3')
H: RNA (5'-(AP*AP*AP*AP*AP*AP*AP*AP*AP)-3')


Theoretical massNumber of molelcules
Total (without water)149,1224
Polymers149,1224
Non-polymers00
Water2,612145
1
A: DNA-BINDING PROTEIN SMUBP-2
G: RNA (5'-(AP*AP*AP*AP*AP*AP*AP*AP*AP)-3')


Theoretical massNumber of molelcules
Total (without water)74,5612
Polymers74,5612
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2480 Å2
ΔGint-8.5 kcal/mol
Surface area28160 Å2
MethodPISA
2
B: DNA-BINDING PROTEIN SMUBP-2
H: RNA (5'-(AP*AP*AP*AP*AP*AP*AP*AP*AP)-3')


Theoretical massNumber of molelcules
Total (without water)74,5612
Polymers74,5612
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2300 Å2
ΔGint-7.6 kcal/mol
Surface area28270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.288, 87.288, 372.692
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein DNA-BINDING PROTEIN SMUBP-2 / IGHMBP2 / ATP-DEPENDENT HELICASE IGHMBP2 / GLIAL FACTOR 1 / GF-1 / IMMUNOGLOBULIN MU-BINDING PROTEIN 2


Mass: 71642.938 Da / Num. of mol.: 2 / Fragment: RESIDUES 3-648
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGEX6P-1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): ROSETTA / References: UniProt: P38935, DNA helicase, RNA helicase
#2: RNA chain RNA (5'-(AP*AP*AP*AP*AP*AP*AP*AP*AP)-3')


Mass: 2917.895 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.75 Å3/Da / Density % sol: 55.25 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Type: ESRF / Wavelength: 0.976
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.85→19.97 Å / Num. obs: 39419 / % possible obs: 90.2 % / Observed criterion σ(I): 2 / Redundancy: 2 % / Biso Wilson estimate: 62.98 Å2 / Rmerge(I) obs: 0.03 / Net I/σ(I): 12.5
Reflection shellResolution: 2.85→2.85 Å / Redundancy: 2 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 1.9 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.85→19.97 Å / SU ML: 0.42 / σ(F): 0.03 / Phase error: 27.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2922 1942 5 %
Rwork0.2064 --
obs0.2108 38694 97.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.024 Å2 / ksol: 0.286 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-4.1302 Å20 Å20 Å2
2--4.1302 Å20 Å2
3----8.2604 Å2
Refinement stepCycle: LAST / Resolution: 2.85→19.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9460 374 0 145 9979
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00910018
X-RAY DIFFRACTIONf_angle_d1.33813641
X-RAY DIFFRACTIONf_dihedral_angle_d19.0523783
X-RAY DIFFRACTIONf_chiral_restr0.0861638
X-RAY DIFFRACTIONf_plane_restr0.0051682
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8501-2.95170.37161530.27413388X-RAY DIFFRACTION92
2.9517-3.06950.35631910.23973504X-RAY DIFFRACTION95
3.0695-3.20860.32861960.21863622X-RAY DIFFRACTION97
3.2086-3.3770.31571840.21333627X-RAY DIFFRACTION98
3.377-3.58750.30961830.2043708X-RAY DIFFRACTION99
3.5875-3.86260.2821930.2093690X-RAY DIFFRACTION99
3.8626-4.2480.2752370.18543664X-RAY DIFFRACTION99
4.248-4.85490.2562050.1683774X-RAY DIFFRACTION99
4.8549-6.08780.29742080.1943760X-RAY DIFFRACTION99
6.0878-19.97010.25231920.1944015X-RAY DIFFRACTION99

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