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- PDB-4b3f: crystal structure of Ighmbp2 helicase -

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Basic information

Entry
Database: PDB / ID: 4b3f
Titlecrystal structure of Ighmbp2 helicase
ComponentsDNA-BINDING PROTEIN SMUBP-2
KeywordsHYDROLASE / HELICASE
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 / Zinc finger, AN1-type / R3H domain / AN1-like Zinc finger ...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 / Zinc finger, AN1-type / R3H domain / AN1-like Zinc finger / R3H domain superfamily / AN1-like Zinc finger / Zinc finger AN1-type profile. / R3H domain 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
PHOSPHATE ION / DNA-binding protein SMUBP-2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.5 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 2, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_beamline
Revision 1.3May 16, 2018Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site / _diffrn_source.type
Revision 1.4May 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_site
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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "XA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "XA" 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

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Assembly

Deposited unit
X: DNA-BINDING PROTEIN SMUBP-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,7232
Polymers71,6281
Non-polymers951
Water1,78399
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)116.566, 76.717, 88.536
Angle α, β, γ (deg.)90.00, 107.33, 90.00
Int Tables number5
Space group name H-MC121

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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: 71627.969 Da / Num. of mol.: 1 / Fragment: RESIDUES 3-648
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P38935, DNA helicase, RNA helicase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / 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: 2.64 Å3/Da / Density % sol: 53.37 % / Description: NONE

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
31001
Diffraction source
SourceSiteBeamlineTypeIDWavelength
SYNCHROTRONESRF ID14-4ESRF 10.9795
SYNCHROTRONNSRRC BL13B120.99315
SYNCHROTRONNSRRC BL13B131.54
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
3SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
20.993151
31.541
ReflectionResolution: 2.5→20 Å / Num. obs: 25840 / % possible obs: 91.8 % / Observed criterion σ(I): 20 / Redundancy: 2 % / Biso Wilson estimate: 49.95 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 16
Reflection shellHighest resolution: 2.5 Å / Redundancy: 2 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 2.3 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MIRAS
Starting model: NONE

Resolution: 2.5→55.639 Å / SU ML: 0.33 / σ(F): 0.02 / Phase error: 30.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2523 1218 5.1 %
Rwork0.1902 --
obs0.1934 23987 92.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 66.34 Å2 / ksol: 0.341 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--8.0504 Å20 Å24.1327 Å2
2---12.1905 Å20 Å2
3---20.2409 Å2
Refinement stepCycle: LAST / Resolution: 2.5→55.639 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4853 0 5 99 4957
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084927
X-RAY DIFFRACTIONf_angle_d1.1816666
X-RAY DIFFRACTIONf_dihedral_angle_d17.7161846
X-RAY DIFFRACTIONf_chiral_restr0.078793
X-RAY DIFFRACTIONf_plane_restr0.004855
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.60010.34261060.25722241X-RAY DIFFRACTION82
2.6001-2.71840.33871070.24492301X-RAY DIFFRACTION84
2.7184-2.86170.34741280.22552376X-RAY DIFFRACTION87
2.8617-3.0410.30141300.22282474X-RAY DIFFRACTION91
3.041-3.27580.31421340.2192590X-RAY DIFFRACTION95
3.2758-3.60540.24271370.19492661X-RAY DIFFRACTION98
3.6054-4.12690.25731560.16982690X-RAY DIFFRACTION99
4.1269-5.19890.221620.14952713X-RAY DIFFRACTION99
5.1989-55.65250.20441580.16572723X-RAY DIFFRACTION97
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.01210.2604-1.07490.5345-0.13091.29530.46930.55120.63990.46410.25290.0996-0.0549-0.4596-0.44980.43570.212-0.05650.51470.21140.295829.047360.696914.6171
21.57580.5656-0.47181.94330.19870.4696-0.1010.39070.25230.08760.4087-0.0339-0.0394-0.2896-0.26170.70370.07740.01210.5954-0.05450.429936.347356.519415.619
32.5740.6147-0.32430.198-0.11991.607-0.1661-0.0553-1.20570.05560.1405-0.30210.127-0.01110.01690.2230.0150.06320.27-0.17760.587742.977633.460726.5054
40.70180.7813-0.24782.9317-1.53461.231-0.1582-0.2108-0.06790.1353-0.0597-1.1283-0.33410.20880.10980.4021-0.0630.03730.3676-0.13660.592152.722760.368721.4822
50.8497-0.1664-0.04841.2554-0.12290.30050.06450.5228-0.1689-0.52180.0348-0.0635-0.0515-0.242-0.00280.5275-0.03210.07620.5919-0.20570.40640.432744.97913.9245
60.9252-0.09450.04742.25820.63031.6029-0.14170.1060.028-0.08420.13150.7063-0.0832-0.1514-0.00260.03360.002-0.06320.07210.05780.492515.544443.867640.0985
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN X AND RESID 3:67)
2X-RAY DIFFRACTION2(CHAIN X AND RESID 68:184)
3X-RAY DIFFRACTION3(CHAIN X AND RESID 185:254)
4X-RAY DIFFRACTION4(CHAIN X AND RESID 255:309)
5X-RAY DIFFRACTION5(CHAIN X AND RESID 316:441)
6X-RAY DIFFRACTION6(CHAIN X AND RESID 442:648)

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