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- PDB-3kx2: Crystal structure of Prp43p in complex with ADP -

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Basic information

Entry
Database: PDB / ID: 3kx2
TitleCrystal structure of Prp43p in complex with ADP
ComponentsPre-mRNA-splicing factor ATP-dependent RNA helicase PRP43
KeywordsHYDROLASE / Rec-A domains / OB fold / winged-helix domain / ATP-binding / mRNA processing / mRNA splicing / Nucleotide-binding
Function / homology
Function and homology information


spliceosomal complex disassembly / post-mRNA release spliceosomal complex / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 90S preribosome / maturation of SSU-rRNA / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / small-subunit processome / helicase activity ...spliceosomal complex disassembly / post-mRNA release spliceosomal complex / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 90S preribosome / maturation of SSU-rRNA / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / small-subunit processome / helicase activity / spliceosomal complex / rRNA processing / RNA helicase activity / RNA helicase / mRNA binding / nucleolus / ATP hydrolysis activity / mitochondrion / RNA binding / ATP binding
Similarity search - Function
DEAH helicase family, winged-helix domain / DHX15, 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 helicase family, winged-helix domain / DHX15, 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. / 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 / Arc Repressor Mutant, subunit A / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP43
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsNielsen, K.H. / Andersen, G.R. / He, Y.
CitationJournal: Embo Rep. / Year: 2010
Title: Structural basis for the function of DEAH helicases
Authors: He, Y. / Andersen, G.R. / Nielsen, K.H.
History
DepositionDec 2, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 26, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Data collection / Refinement description / Category: diffrn_source / software / Item: _diffrn_source.pdbx_synchrotron_site
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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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
B: Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP43
A: Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP43
hetero molecules


Theoretical massNumber of molelcules
Total (without water)176,2696
Polymers175,3662
Non-polymers9034
Water17,691982
1
B: Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP43
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,1343
Polymers87,6831
Non-polymers4522
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP43
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,1343
Polymers87,6831
Non-polymers4522
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)118.152, 118.152, 253.601
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11B-1363-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11b
21a

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain bb0
211chain aa0

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Components

#1: Protein Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP43 / PRP43P / Helicase JA1


Mass: 87682.750 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: S288C / Gene: YGL120C / Plasmid: pET-52b(+) 3C/LIC / Production host: Escherichia coli (E. coli) / Strain (production host): ROSETTA(DE3)
References: UniProt: P53131, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 982 / 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: 2.91 Å3/Da / Density % sol: 57.79 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.75
Details: 100mM Mes-NaOH, pH 6.75, 14% PEG 8000, 300mM NaOAc, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSLS X06SA10.98
SYNCHROTRONMAX II I911-320.9795
Detector
TypeIDDetectorDate
PSI PILATUS 6M1PIXELAug 7, 2009
MARMOSAIC 225 mm CCD2CCDSep 9, 2009
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Fixed-exit LN2 cooled Double Crystal MonochromatorSINGLE WAVELENGTHMx-ray1
2Double crystal monochromator, Si(111). The first crystal is water cooled.SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.981
20.97951
ReflectionResolution: 2.2→50 Å / Num. all: 104963 / Num. obs: 104418 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.2 % / Rmerge(I) obs: 0.012
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.75 / Num. unique all: 12891 / % possible all: 99.6

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Processing

Software
NameClassification
SHELXSphasing
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.2→48.423 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.11 / σ(F): 1.17 / Phase error: 25.77 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2497 9826 4.99 %RANDOM
Rwork0.2063 ---
all0.2085 104963 --
obs0.2085 104407 98.01 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 53.347 Å2 / ksol: 0.317 e/Å3
Displacement parametersBiso max: 258.09 Å2 / Biso mean: 53.766 Å2 / Biso min: 11.89 Å2
Baniso -1Baniso -2Baniso -3
1--3.601 Å2-0 Å20 Å2
2---3.601 Å20 Å2
3---5.868 Å2
Refinement stepCycle: LAST / Resolution: 2.2→48.423 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12134 0 56 982 13172
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00612458
X-RAY DIFFRACTIONf_angle_d1.01316884
X-RAY DIFFRACTIONf_chiral_restr0.0721850
X-RAY DIFFRACTIONf_plane_restr0.0052202
X-RAY DIFFRACTIONf_dihedral_angle_d17.9664742
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11B6094X-RAY DIFFRACTIONPOSITIONAL0.043
12A6094X-RAY DIFFRACTIONPOSITIONAL0.043
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.2250.32583210.28736236X-RAY DIFFRACTION97
2.225-2.25120.33253230.2936139X-RAY DIFFRACTION97
2.2512-2.27860.32993240.2916127X-RAY DIFFRACTION96
2.2786-2.30750.31133310.2756216X-RAY DIFFRACTION98
2.3075-2.33780.3073350.26886195X-RAY DIFFRACTION98
2.3378-2.36990.2893360.2566341X-RAY DIFFRACTION98
2.3699-2.40370.3063230.25416222X-RAY DIFFRACTION98
2.4037-2.43960.2933290.25256253X-RAY DIFFRACTION98
2.4396-2.47770.30633280.24086264X-RAY DIFFRACTION98
2.4777-2.51830.29793270.22796329X-RAY DIFFRACTION98
2.5183-2.56180.3073160.24166180X-RAY DIFFRACTION98
2.5618-2.60830.30623270.24036207X-RAY DIFFRACTION98
2.6083-2.65850.30243270.23036191X-RAY DIFFRACTION97
2.6585-2.71280.27053170.2316215X-RAY DIFFRACTION97
2.7128-2.77170.27413230.21356178X-RAY DIFFRACTION97
2.7717-2.83620.2843320.21786231X-RAY DIFFRACTION98
2.8362-2.90710.25633280.22346190X-RAY DIFFRACTION98
2.9071-2.98570.27153320.22136314X-RAY DIFFRACTION99
2.9857-3.07360.28293230.21016246X-RAY DIFFRACTION99
3.0736-3.17280.26983300.19986284X-RAY DIFFRACTION99
3.1728-3.28610.25323260.21156333X-RAY DIFFRACTION99
3.2861-3.41770.25813270.21146233X-RAY DIFFRACTION98
3.4177-3.57320.24613240.19086236X-RAY DIFFRACTION98
3.5732-3.76150.24463270.19186223X-RAY DIFFRACTION98
3.7615-3.9970.21573370.17016303X-RAY DIFFRACTION99
3.997-4.30550.2053300.16546281X-RAY DIFFRACTION99
4.3055-4.73840.19223320.15966315X-RAY DIFFRACTION98
4.7384-5.42330.19253300.15856195X-RAY DIFFRACTION98
5.4233-6.82970.18993250.17376269X-RAY DIFFRACTION98
6.8297-48.43490.20263360.17346237X-RAY DIFFRACTION98
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)
11.2294-0.5821-0.30190.6536-0.24441.83590.10880.1632-0.1514-0.2060.23960.1631-0.3888-0.6896-0.3340.15360.19750.12030.38310.31190.25833.6768-0.8852-6.7852
21.6856-0.1143-1.43731.3996-0.92243.28570.27110.29110.24090.09910.1212-0.0693-0.5253-0.4994-0.37980.28430.11120.1160.23920.11530.209336.10743.44083.9539
31.35680.1219-0.1331.798-0.6205-0.4474-0.0704-0.2353-0.20820.4961-0.00650.0361-0.11440.08370.080.34390.01370.07470.26980.06490.215228.8907-19.429428.2922
40.18660.3275-0.92961.5166-0.4841.07530.0863-0.04970.06470.2456-0.1024-0.1854-0.02790.03630.0220.2281-0.00010.020.24740.01870.180336.8284-12.274822.4983
50.0729-0.482-0.75591.11520.59681.4311-0.105-0.1137-0.1394-0.0908-0.0104-0.05140.14010.07450.1030.21260.02040.06590.20010.0570.400650.5517-17.3639-6.0704
62.96152.1383-1.81190.2001-0.36532.6382-0.5861-0.2293-0.879-0.301-0.33680.00370.83330.02530.83510.35640.05720.30630.12390.13750.531546.0501-35.6091-2.3092
71.426-0.4933-0.28911.14240.03270.42830.0766-0.52250.05810.12630.14590.1039-0.19690.011-0.21720.1281-0.02170.16650.1036-0.05780.0442-13.484-30.451951.3781
80.6692-0.3863-0.16781.292-0.13021.23790.0904-0.153-0.10430.00920.06260.2209-0.0398-0.1325-0.1350.12530.0180.07430.25440.03770.2508-18.4045-29.667840.6479
91.18220.5933-0.14990.76690.28940.0703-0.06120.2371-0.0944-0.08430.0973-0.0713-0.03330.0208-0.04240.1816-0.00450.01320.30690.00110.20075.0383-32.982316.0253
101.5631-0.5207-0.12540.1677-0.49030.65250.10050.2174-0.0798-0.00240.03960.19740.0062-0.1109-0.10480.1663-0.0290.0040.26240.00370.2118-5.1082-36.737821.5627
111.0007-0.11720.18941.0565-0.77991.1209-0.0473-0.4575-0.36-0.06050.05340.17670.09370.009-0.02080.16320.01290.04970.34220.15530.3238-7.5357-53.162249.0507
121.89970.4633-0.68760.5804-0.65981.1599-0.2271-0.4017-0.5812-0.0673-0.0324-0.31080.16370.28920.29710.15630.06380.13430.27040.19060.375210.5551-58.010644.9715
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1resid 1:93 and chain aa1 - 93
2X-RAY DIFFRACTION2resid 94:270 and chain aa94 - 270
3X-RAY DIFFRACTION3resid 271:349 and chain aa271 - 349
4X-RAY DIFFRACTION4resid 350:457 and chain aa350 - 457
5X-RAY DIFFRACTION5resid 458:556 and chain aa458 - 556
6X-RAY DIFFRACTION6resid 557:752 and chain aa557 - 752
7X-RAY DIFFRACTION7resid 1:93 and chain bb1 - 93
8X-RAY DIFFRACTION8resid 94:270 and chain bb94 - 270
9X-RAY DIFFRACTION9resid 271:349 and chain bb271 - 349
10X-RAY DIFFRACTION10resid 350:457 and chain bb350 - 457
11X-RAY DIFFRACTION11resid 458:556 and chain bb458 - 556
12X-RAY DIFFRACTION12resid 557:752 and chain bb557 - 752

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