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- PDB-6i3o: Crystal structure of DEAH-box ATPase Prp22 -

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Basic information

Entry
Database: PDB / ID: 6i3o
TitleCrystal structure of DEAH-box ATPase Prp22
ComponentsPutative pre-mRNA splicing factor
KeywordsHYDROLASE / Splicing / DEAH / ATPase / helicase
Function / homology
Function and homology information


RNA splicing / mRNA processing / nucleic acid binding / RNA helicase / hydrolase activity / ribonucleoprotein complex / ATP binding / nucleus
Similarity search - Function
: / : / : / 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 ...: / : / : / 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 / 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 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Biological speciesChaetomium thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.25 Å
AuthorsHamann, F. / Ficner, R.
CitationJournal: Nucleic Acids Res. / Year: 2019
Title: Structural basis for RNA translocation by DEAH-box ATPases.
Authors: Hamann, F. / Enders, M. / Ficner, R.
History
DepositionNov 7, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 6, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jul 3, 2019Group: Data collection / Database references
Category: citation / database_PDB_rev ...citation / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative pre-mRNA splicing factor
B: Putative pre-mRNA splicing factor


Theoretical massNumber of molelcules
Total (without water)152,7932
Polymers152,7932
Non-polymers00
Water0
1
A: Putative pre-mRNA splicing factor


Theoretical massNumber of molelcules
Total (without water)76,3971
Polymers76,3971
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Putative pre-mRNA splicing factor


Theoretical massNumber of molelcules
Total (without water)76,3971
Polymers76,3971
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.530, 93.640, 218.430
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: PRO / End label comp-ID: PRO / Refine code: 0 / Auth seq-ID: 549 - 1177 / Label seq-ID: 4 - 632

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Putative pre-mRNA splicing factor


Mass: 76396.719 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0035640 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: G0S700

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 45.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 100mM Bis-Tris propane pH6.5, 400mM K-Thiocyanate, 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9919 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 16, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9919 Å / Relative weight: 1
ReflectionResolution: 3.25→86.06 Å / Num. obs: 22460 / % possible obs: 99.5 % / Redundancy: 5.205 % / Biso Wilson estimate: 76.354 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.113 / Rrim(I) all: 0.126 / Χ2: 1.042 / Net I/σ(I): 12.04 / Num. measured all: 116904 / Scaling rejects: 5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
3.25-3.354.9761.061.5218590.6571.18196.3
3.35-3.455.0540.752.1216820.8130.83799.9
3.45-3.65.4390.5023.2322440.9440.55599.8
3.6-3.95.4720.325.2334830.9590.35399.9
3.9-4.45.1440.1659.2639140.9860.18399.8
4.4-4.95.4360.09515.324990.9950.10599.9
4.9-5.55.180.08815.7319490.9940.09899.9
5.5-6.55.2510.0817.2218510.9950.08999.8
6.5-85.1380.04824.813470.9980.05499.9
8-104.7910.02839.647790.9990.03199.6
10-204.5860.02245.237370.9990.02598.3
20-502.8270.02433.521100.9980.02893.2
50-86.061.3330.01623.8460.02366.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XSCALEdata scaling
PHASERphasing
PDB_EXTRACT3.24data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6fa5

6fa5


Resolution: 3.25→86.06 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.903 / SU B: 78.219 / SU ML: 0.548 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.574
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2637 1123 5 %RANDOM
Rwork0.2475 ---
obs0.2483 21337 99.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 233.92 Å2 / Biso mean: 103.034 Å2 / Biso min: 41.94 Å2
Baniso -1Baniso -2Baniso -3
1-2.07 Å20 Å20 Å2
2---0.76 Å20 Å2
3----1.31 Å2
Refinement stepCycle: final / Resolution: 3.25→86.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9208 0 0 0 9208
Num. residues----1166
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0139391
X-RAY DIFFRACTIONr_bond_other_d0.0340.0178936
X-RAY DIFFRACTIONr_angle_refined_deg1.7231.65312720
X-RAY DIFFRACTIONr_angle_other_deg2.2941.57220720
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0551154
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.82821.966473
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.975151655
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.871565
X-RAY DIFFRACTIONr_chiral_restr0.090.21267
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0210318
X-RAY DIFFRACTIONr_gen_planes_other0.0090.021921
Refine LS restraints NCS

Ens-ID: 1 / Number: 16030 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.2 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 3.251→3.336 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.404 79 -
Rwork0.368 1510 -
all-1589 -
obs--98.03 %
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)
15.19480.9172-2.30665.4361.16313.4979-0.0421-0.41070.31710.13150.0345-0.4553-0.13090.06660.00750.09780.0360.0030.07560.03920.424419.184-22.359.902
23.28041.9045-0.57932.49570.69511.6916-0.108-1.30770.44940.1482-0.34730.77730.0084-1.16990.45530.52510.0798-0.09931.4424-0.02770.9529.969-35.68438.462
32.2621-1.3258-1.66543.31830.45323.50030.0606-0.27020.05010.24840.10770.0944-0.03540.0458-0.16840.1374-0.0221-0.08470.0520.04360.3616-4.926-38.23725.378
42.4325-1.213-1.09394.5265-0.05796.504-0.0191-0.4084-0.2360.5420.14580.04440.19220.0004-0.12670.5624-0.1355-0.0450.29760.14350.5774-7.5133.72134.648
55.83420.69081.9986.1788-0.30416.48810.30491.03850.3519-0.17440.1781-0.24330.12880.5322-0.48290.9280.0652-0.0611.6850.25790.805220.97712.67146.784
63.4296-1.3392-1.33284.09861.3621.7264-0.10970.1047-0.2785-0.23080.0773-0.3431-0.05580.06430.03240.4268-0.0094-0.03640.04560.07990.416610.24119.76511.397
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A546 - 733
2X-RAY DIFFRACTION2A734 - 909
3X-RAY DIFFRACTION3A910 - 1186
4X-RAY DIFFRACTION4B546 - 733
5X-RAY DIFFRACTION5B734 - 909
6X-RAY DIFFRACTION6B910 - 1186

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