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- PDB-6qic: Crystal structure of DEAH-box ATPase Prp22-S837A with bound ssRNA -

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Basic information

Entry
Database: PDB / ID: 6qic
TitleCrystal structure of DEAH-box ATPase Prp22-S837A with bound ssRNA
Components
  • Putative pre-mRNA splicing factor
  • RNA (5'-R(P*UP*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 (HA2), winged-helix / Helicase-associated domain / 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 (HA2), winged-helix / Helicase-associated domain / 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 domain / DEAD/DEAH box helicase / 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 / P-loop containing nucleotide triphosphate hydrolases / Nucleic acid-binding, OB-fold / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
RNA / RNA (> 10) / RNA helicase
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsHamann, F. / Ficner, R. / Enders, M.
CitationJournal: Nucleic Acids Res. / Year: 2019
Title: Structural basis for RNA translocation by DEAH-box ATPases.
Authors: Hamann, F. / Enders, M. / Ficner, R.
History
DepositionJan 18, 2019Deposition 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
E: RNA (5'-R(P*UP*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*UP*U)-3')
C: Putative pre-mRNA splicing factor
G: RNA (5'-R(P*UP*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*UP*U)-3')


Theoretical massNumber of molelcules
Total (without water)318,8148
Polymers318,8148
Non-polymers00
Water181
1
A: Putative pre-mRNA splicing factor
E: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')


Theoretical massNumber of molelcules
Total (without water)79,7042
Polymers79,7042
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3220 Å2
ΔGint-30 kcal/mol
Surface area28410 Å2
MethodPISA
2
B: Putative pre-mRNA splicing factor
F: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')


Theoretical massNumber of molelcules
Total (without water)79,7042
Polymers79,7042
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2930 Å2
ΔGint-29 kcal/mol
Surface area27830 Å2
MethodPISA
3
C: Putative pre-mRNA splicing factor
G: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')


Theoretical massNumber of molelcules
Total (without water)79,7042
Polymers79,7042
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3060 Å2
ΔGint-30 kcal/mol
Surface area28590 Å2
MethodPISA
4
D: Putative pre-mRNA splicing factor
H: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')


Theoretical massNumber of molelcules
Total (without water)79,7042
Polymers79,7042
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3040 Å2
ΔGint-31 kcal/mol
Surface area28010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.610, 139.960, 164.660
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
14E
24F
15E
25G
16E
26H
17B
27C
18B
28D
19F
29G
110F
210H
111C
211D
112G
212H

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
11ASNASNPROPROAA547 - 11772 - 632
21ASNASNPROPROBC547 - 11772 - 632
12SERSERALAALAAA549 - 11764 - 631
22SERSERALAALACE549 - 11764 - 631
13METMETALAALAAA548 - 11763 - 631
23METMETALAALADG548 - 11763 - 631
14UUUUEB1 - 111 - 11
24UUUUFD1 - 111 - 11
15UUUUEB1 - 111 - 11
25UUUUGF1 - 111 - 11
16UUUUEB1 - 111 - 11
26UUUUHH1 - 111 - 11
17SERSERPROPROBC549 - 11774 - 632
27SERSERPROPROCE549 - 11774 - 632
18METMETPROPROBC548 - 11773 - 632
28METMETPROPRODG548 - 11773 - 632
19UUUUFD1 - 111 - 11
29UUUUGF1 - 111 - 11
110UUUUFD1 - 111 - 11
210UUUUHH1 - 111 - 11
111SERSERALAALACE549 - 11764 - 631
211SERSERALAALADG549 - 11764 - 631
112UUUUGF1 - 111 - 11
212UUUUHH1 - 111 - 11

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12

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Components

#1: Protein
Putative pre-mRNA splicing factor


Mass: 76380.719 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) / Strain (production host): Rosetta II (DE3) / References: UniProt: G0S700
#2: RNA chain
RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')


Mass: 3322.866 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.52 Å3/Da / Density % sol: 51.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 100 mM Bis-Tris propane pH 8.5, 250 mM NaF, 22% (w/v) 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: P14 (MX2) / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 7, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.7→106.49 Å / Num. obs: 88822 / % possible obs: 99.7 % / Redundancy: 9.251 % / Biso Wilson estimate: 81.23 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.077 / Rrim(I) all: 0.081 / Χ2: 1.058 / Net I/σ(I): 19.56
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.7-2.829.4421.4741.69107190.7051.56199.8
2.82-39.4150.8732.8130910.8680.92499.8
3-3.39.3220.4525.09159610.960.47999.8
3.3-3.59.4440.21310.3578420.990.22599.8
3.5-3.79.4110.1315.9462090.9960.13799.7
3.7-4.29.2180.08123.67109380.9980.08699.9
4.2-58.9560.04737.2396590.9990.0599.6
5-69.1870.04241.3959810.9990.04599.8
6-89.0340.03253.09478710.03499.4
8-108.4890.0274.65173410.02199.7
10-208.4590.01891.09165210.01999.3
20-507.0760.01687.0923810.01796.4
50-106.492.8180.01848.141110.02255

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XSCALEdata scaling
PDB_EXTRACT3.24data extraction
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6I3P

6i3p


Resolution: 2.7→106.49 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.93 / SU B: 43.937 / SU ML: 0.364 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.87 / ESU R Free: 0.355
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2614 4441 5 %RANDOM
Rwork0.2122 ---
obs0.2146 84380 99.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 206.02 Å2 / Biso mean: 85.903 Å2 / Biso min: 52.02 Å2
Baniso -1Baniso -2Baniso -3
1--3.37 Å2-0 Å2-0 Å2
2---1.94 Å20 Å2
3---5.31 Å2
Refinement stepCycle: final / Resolution: 2.7→106.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19755 832 0 1 20588
Biso mean---71.53 -
Num. residues----2554
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01321083
X-RAY DIFFRACTIONr_bond_other_d0.0340.01719408
X-RAY DIFFRACTIONr_angle_refined_deg1.5111.63928766
X-RAY DIFFRACTIONr_angle_other_deg2.2951.645142
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.80452503
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.13522.1921013
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.958153520
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.33215135
X-RAY DIFFRACTIONr_chiral_restr0.0790.22889
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0222683
X-RAY DIFFRACTIONr_gen_planes_other0.0110.024211
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A186460.15
12B186460.15
21A186110.15
22C186110.15
31A187690.14
32D187690.14
41E6380.12
42F6380.12
51E6280.15
52G6280.15
61E6340.14
62H6340.14
71B186840.14
72C186840.14
81B187830.15
82D187830.15
91F6380.15
92G6380.15
101F6350.16
102H6350.16
111C188130.14
112D188130.14
121G6430.13
122H6430.13
LS refinement shellResolution: 2.7→2.77 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.386 323 -
Rwork0.376 6152 -
all-6475 -
obs--99.72 %
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)
13.83340.2103-0.41551.0081-0.12771.55930.04370.34950.07690.0007-0.03940.11450.0762-0.0164-0.00430.01350.04650.0050.2833-0.00690.0278-70.1149-6.607341.4984
22.46133.5541.23496.8833-0.85217.1671-0.2708-0.18970.3325-1.3019-0.2513-0.23971.30760.22970.52210.49550.08250.31060.394-00.6015-65.1891-0.681242.6571
32.4520.3126-0.37611.47380.01061.5898-0.09470.02160.15830.01270.0949-0.344-0.0610.121-0.00020.02070.07-0.01010.45860.0060.10513.590812.931339.6744
41.2477-0.3684-2.31197.08931.8815.4449-0.0712-0.2152-0.0175-0.9055-0.12750.7473-0.3207-0.0240.19880.21750.0999-0.1050.57520.01540.2965-0.40714.980440.0075
51.4702-0.09150.58242.34630.57461.385-0.23660.15980.3639-0.02170.0807-0.0405-0.36870.23540.15590.21510.0773-0.03840.45080.10850.1015-25.531333.124784.4096
67.49550.003-1.42021.74822.32733.4183-0.4528-0.8906-0.6499-0.26140.22130.0527-0.13360.51690.23150.4470.1510.01120.28290.22030.3902-32.813428.706682.9756
71.49990.37110.2671.7609-0.43641.42730.15910.0298-0.1859-0.0869-0.09650.0030.2435-0.1652-0.06260.12420.1176-0.06520.3441-0.07070.0476-45.6522-40.815385.2089
87.64720.35262.98941.4488-1.41973.53050.0857-0.58861.3922-0.3915-0.22530.16850.3094-0.38820.13960.36080.2042-0.03190.3804-0.02180.4319-37.9147-37.034384.5444
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A546 - 1177
2X-RAY DIFFRACTION2E1 - 11
3X-RAY DIFFRACTION3B547 - 1177
4X-RAY DIFFRACTION4F1 - 11
5X-RAY DIFFRACTION5C549 - 1177
6X-RAY DIFFRACTION6G1 - 11
7X-RAY DIFFRACTION7D548 - 1178
8X-RAY DIFFRACTION8H1 - 11

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