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- PDB-6i3p: Crystal structure of DEAH-box ATPase Prp22 with bound ssRNA -

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Basic information

Entry
Database: PDB / ID: 6i3p
TitleCrystal structure of DEAH-box ATPase Prp22 with bound ssRNA
Components
  • Putative pre-mRNA splicing factor
  • RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
KeywordsHYDROLASE / Splicing / DEAH / ATPase / helicase
Function / homology
Function and homology information


spliceosomal complex disassembly / catalytic step 2 spliceosome / RNA helicase activity / hydrolase activity / RNA helicase / RNA binding / ATP binding
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)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.75 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

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Assembly

Deposited unit
A: Putative pre-mRNA splicing factor
E: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
B: Putative pre-mRNA splicing factor
F: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
C: Putative pre-mRNA splicing factor
G: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
D: Putative pre-mRNA splicing factor
H: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')


Theoretical massNumber of molelcules
Total (without water)317,6548
Polymers317,6548
Non-polymers00
Water00
1
A: Putative pre-mRNA splicing factor
E: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')


Theoretical massNumber of molelcules
Total (without water)79,4132
Polymers79,4132
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2740 Å2
ΔGint-27 kcal/mol
Surface area28110 Å2
MethodPISA
2
B: Putative pre-mRNA splicing factor
F: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')


Theoretical massNumber of molelcules
Total (without water)79,4132
Polymers79,4132
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2740 Å2
ΔGint-29 kcal/mol
Surface area27890 Å2
MethodPISA
3
C: Putative pre-mRNA splicing factor
G: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')


Theoretical massNumber of molelcules
Total (without water)79,4132
Polymers79,4132
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2640 Å2
ΔGint-30 kcal/mol
Surface area28750 Å2
MethodPISA
4
D: Putative pre-mRNA splicing factor
H: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')


Theoretical massNumber of molelcules
Total (without water)79,4132
Polymers79,4132
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2710 Å2
ΔGint-29 kcal/mol
Surface area28530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.790, 140.500, 159.550
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
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERLEULEUAA549 - 11754 - 630
21SERSERLEULEUBC549 - 11754 - 630
12SERSERALAALAAA549 - 11764 - 631
22SERSERALAALACE549 - 11764 - 631
13SERSERTHRTHRAA549 - 11784 - 633
23SERSERTHRTHRDG549 - 11784 - 633
14SERSERLYSLYSBC549 - 11744 - 629
24SERSERLYSLYSCE549 - 11744 - 629
15SERSERLYSLYSBC549 - 11744 - 629
25SERSERLYSLYSDG549 - 11744 - 629
16ASNASNALAALACE547 - 11762 - 631
26ASNASNALAALADG547 - 11762 - 631

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Putative pre-mRNA splicing factor


Mass: 76396.719 Da / Num. of mol.: 4
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) / References: UniProt: G0S700
#2: RNA chain
RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')


Mass: 3016.700 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others)

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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: 2.47 Å3/Da / Density % sol: 50.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 100mM Bis-Tris propane pH8.5, 250mM NaF, 22% 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: 2.75→49.24 Å / Num. obs: 82130 / % possible obs: 99.9 % / Redundancy: 7.791 % / Biso Wilson estimate: 72.839 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.11 / Rrim(I) all: 0.118 / Χ2: 1.062 / Net I/σ(I): 14.28 / Num. measured all: 639883 / Scaling rejects: 43
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.75-2.878.1541.4691.5197530.751.567100
2.87-37.9370.9912.2888770.831.05999.9
3-3.27.7480.6573.41110390.9180.704100
3.2-3.48.2060.386.2385920.9750.406100
3.4-3.77.8530.19910.6497050.9910.214100
3.7-4.27.7760.10317.67106390.9970.111100
4.2-57.5960.05826.9994500.9990.062100
5-67.7670.05627.9158210.9990.06100
6-87.1980.04332.747040.9990.04699.9
8-107.4670.02350.26170910.025100
10-206.4360.0254.64161310.02299.8
20-504.0610.02443.032280.9980.02894.6
49.24-50

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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: 2.75→49.24 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.937 / SU B: 42.838 / SU ML: 0.355 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.363
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2531 4107 5 %RANDOM
Rwork0.2218 ---
obs0.2233 78023 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 158.68 Å2 / Biso mean: 72.077 Å2 / Biso min: 47.8 Å2
Baniso -1Baniso -2Baniso -3
1--2.08 Å2-0 Å2-0 Å2
2---0.43 Å20 Å2
3---2.51 Å2
Refinement stepCycle: final / Resolution: 2.75→49.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19804 736 0 0 20540
Num. residues----2549
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.01321018
X-RAY DIFFRACTIONr_bond_other_d0.0340.01719429
X-RAY DIFFRACTIONr_angle_refined_deg1.7721.64128638
X-RAY DIFFRACTIONr_angle_other_deg2.2831.59745177
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.84552500
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.53622.0161027
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.345153552
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.93615142
X-RAY DIFFRACTIONr_chiral_restr0.1120.22862
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0222664
X-RAY DIFFRACTIONr_gen_planes_other0.0170.024234
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.14 Å / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumber
11A18690
12B18690
21A18759
22C18759
31A18853
32D18853
41B18748
42C18748
51B18666
52D18666
61C19071
62D19071
LS refinement shellResolution: 2.75→2.821 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.388 298 -
Rwork0.373 5668 -
all-5966 -
obs--99.95 %
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)
11.55650.0616-0.51711.4352-0.12860.8180.0137-0.11510.06720.18770.0192-0.1893-0.06720.0751-0.03290.05540.0551-0.05380.1394-0.02470.2594-2.25439.9114-41.2406
22.15790.3521-2.06451.3206-1.40162.89310.1126-0.1728-0.4794-0.2043-0.06550.56760.04140.1338-0.04710.11830.1197-0.16940.2287-0.03050.6381-5.7058-0.2221-42.6145
31.4740.17670.37481.15760.12880.9502-0.0525-0.09890.01780.11450.00170.04340.0778-0.09020.05080.05180.03930.04860.0974-0.01910.239-75.7356-10.3797-40.8225
40.0947-0.15440.0336.1414-2.41413.6690.05850.02550.142-0.1001-0.412-0.47190.06460.13530.35360.06110.07290.04310.1966-0.00330.3282-72.2771-0.2018-41.6866
50.64860.09120.00511.7159-0.29250.8742-0.01870.0219-0.0027-0.0656-0.0345-0.1380.1173-0.01920.05320.06480.03480.00560.037-0.04020.2949-40.9897-37.0891-0.1109
60.94470.8464-0.71882.5808-1.48223.58430.0651-0.19840.28040.2313-0.0729-0.43640.2213-0.06130.00780.23740.04950.02590.0907-0.05460.4352-30.8403-33.43351.3453
70.84280.245-0.0491.81380.13370.6992-0.02890.04740.027-0.03720.00440.0019-0.11660.01310.02450.14610.0372-0.06850.03810.02720.2453-21.843436.98570.8393
80.53640.94541.00132.35542.98054.158-0.1766-0.26110.0036-0.2055-0.00670.2608-0.11470.36140.18340.22460.1293-0.04040.44840.11830.5647-31.98633.37082.6516
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A549 - 1178
2X-RAY DIFFRACTION2E1 - 10
3X-RAY DIFFRACTION3B549 - 1175
4X-RAY DIFFRACTION4F1 - 10
5X-RAY DIFFRACTION5C546 - 1177
6X-RAY DIFFRACTION6G1 - 10
7X-RAY DIFFRACTION7D547 - 1178
8X-RAY DIFFRACTION8H1 - 10

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