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- PDB-3i4u: Crystal Structure Analysis of a helicase associated domain -

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Basic information

Entry
Database: PDB / ID: 3i4u
TitleCrystal Structure Analysis of a helicase associated domain
ComponentsATP-dependent RNA helicase DHX8
KeywordsHYDROLASE / helicase / splicing / ATP-binding / mRNA processing / mRNA splicing / Nucleotide-binding / Nucleus / Phosphoprotein / Spliceosome
Function / homology
Function and homology information


spliceosomal complex disassembly / ATP-dependent activity, acting on RNA / U2-type catalytic step 2 spliceosome / RNA processing / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / RNA splicing / spliceosomal complex / mRNA splicing, via spliceosome / RNA helicase activity ...spliceosomal complex disassembly / ATP-dependent activity, acting on RNA / U2-type catalytic step 2 spliceosome / RNA processing / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / RNA splicing / spliceosomal complex / mRNA splicing, via spliceosome / RNA helicase activity / nuclear body / RNA helicase / ATP hydrolysis activity / RNA binding / nucleoplasm / ATP binding / identical protein binding / nucleus / cytosol
Similarity search - Function
Four Helix Bundle (Hemerythrin (Met), subunit A) - #1080 / DHX8/ Prp22, DEXH-box helicase domain / : / : / : / Helicase associated domain (HA2), ratchet-like / DEAD-box helicase, OB fold / Oligonucleotide/oligosaccharide-binding (OB)-fold / Helicase-associated domain / Helicase associated domain (HA2), winged-helix ...Four Helix Bundle (Hemerythrin (Met), subunit A) - #1080 / DHX8/ Prp22, DEXH-box helicase domain / : / : / : / Helicase associated domain (HA2), ratchet-like / DEAD-box helicase, OB fold / Oligonucleotide/oligosaccharide-binding (OB)-fold / Helicase-associated domain / Helicase associated domain (HA2), winged-helix / Helicase associated domain (HA2) Add an annotation / DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site / DEAH-box subfamily ATP-dependent helicases signature. / S1 domain profile. / Ribosomal protein S1-like RNA-binding domain / S1 RNA binding domain / S1 domain / DEAD/DEAH box helicase / DEAD/DEAH box helicase domain / Four Helix Bundle (Hemerythrin (Met), subunit A) / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / Nucleic acid-binding, OB-fold / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Mainly Alpha
Similarity search - Domain/homology
BROMIDE ION / ATP-dependent RNA helicase DHX8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsKudlinzki, D. / Ficner, R.
CitationJournal: Biol.Chem. / Year: 2012
Title: Structural analysis of the C-terminal domain of the spliceosomal helicase Prp22
Authors: Kudlinzki, D. / Schmitt, A. / Christian, H. / Ficner, R.
History
DepositionJul 2, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 7, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 21, 2012Group: Database references
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ATP-dependent RNA helicase DHX8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,09211
Polymers31,2081
Non-polymers88410
Water3,423190
1
A: ATP-dependent RNA helicase DHX8
hetero molecules

A: ATP-dependent RNA helicase DHX8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,18522
Polymers62,4162
Non-polymers1,76920
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area1720 Å2
ΔGint-23 kcal/mol
Surface area24080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.854, 78.854, 88.793
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
DetailsAUTHOR DETERMINED BIOLOGICAL ASSEMBLY: UNKNOWN.

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Components

#1: Protein ATP-dependent RNA helicase DHX8 / DEAH box protein 8 / RNA helicase HRH1


Mass: 31208.006 Da / Num. of mol.: 1 / Fragment: UNP residues 950-1183
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DHX8, DDX8 / Plasmid: pPR-IBA1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q14562, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
#2: Chemical ChemComp-BR / BROMIDE ION / Bromide


Mass: 79.904 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Br
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 190 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.21 Å3/Da / Density % sol: 44.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 2uL drop (1:1); 1.7M (NH4)2SO4, 0.1M Tris/HCl, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONEMBL/DESY, HAMBURG BW7A10.91164
SYNCHROTRONBESSY 14.220.97976, 0.9799, 0.95, 1.0
Detector
TypeIDDetectorDate
MAR CCD 165 mm1CCDDec 8, 2006
MAR CCD 165 mm2CCDAug 12, 2007
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.911641
20.979761
30.97991
40.951
511
ReflectionResolution: 2.1→50 Å / Num. obs: 31239 / % possible obs: 99.7 % / Biso Wilson estimate: 36.8 Å2 / Rsym value: 0.069 / Net I/σ(I): 29.2 / Num. measured all: 557688

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHARPphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.1→29.48 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.92 / SU B: 11.853 / SU ML: 0.141 / Cross valid method: THROUGHOUT / ESU R Free: 0.197 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24486 843 5.1 %RANDOM
Rwork0.19278 ---
obs0.19532 15845 98.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.097 Å2
Baniso -1Baniso -2Baniso -3
1-0.34 Å20 Å20 Å2
2--0.34 Å20 Å2
3----0.68 Å2
Refinement stepCycle: LAST / Resolution: 2.1→29.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1952 0 45 190 2187
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0222070
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.8811.9722783
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6985248
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.74323.26395
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.35415385
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.5981517
X-RAY DIFFRACTIONr_chiral_restr0.0610.2301
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.021520
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1780.21015
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2930.21421
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1010.2163
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1480.255
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1110.211
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6071.51265
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.73121977
X-RAY DIFFRACTIONr_scbond_it2.1663915
X-RAY DIFFRACTIONr_scangle_it3.8654.5802
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 72 -
Rwork0.208 1153 -
obs--99.76 %
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)
10.18710.00070.06340.0109-0.0330.12310.0084-0.0102-0.0269-0.00240.00420.00620.00150.0018-0.0126-0.00310.0003-0.00220.00140.0033-0.006350.359622.305943.6884
2000000000000000000000000
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A948 - 965
2X-RAY DIFFRACTION1A966 - 974
3X-RAY DIFFRACTION1A975 - 982
4X-RAY DIFFRACTION1A983 - 986
5X-RAY DIFFRACTION1A987 - 1000
6X-RAY DIFFRACTION1A1001 - 1014
7X-RAY DIFFRACTION1A1015 - 1024
8X-RAY DIFFRACTION1A1025 - 1039
9X-RAY DIFFRACTION1A1040 - 1057
10X-RAY DIFFRACTION1A1058 - 1066
11X-RAY DIFFRACTION1A1067 - 1090
12X-RAY DIFFRACTION1A1091 - 1099
13X-RAY DIFFRACTION1A1100 - 1111
14X-RAY DIFFRACTION1A1112 - 1114
15X-RAY DIFFRACTION1A1115 - 1118
16X-RAY DIFFRACTION1A1119 - 1123
17X-RAY DIFFRACTION1A1124 - 1127
18X-RAY DIFFRACTION1A1128 - 1130
19X-RAY DIFFRACTION1A1131 - 1135
20X-RAY DIFFRACTION1A1136 - 1147
21X-RAY DIFFRACTION1A1148 - 1157
22X-RAY DIFFRACTION1A1158 - 1168
23X-RAY DIFFRACTION1A1169 - 1178
24X-RAY DIFFRACTION1A1179 - 1184
25X-RAY DIFFRACTION2A1191 - 1194

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