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- PDB-4nho: Structure of the spliceosomal DEAD-box protein Prp28 -

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Basic information

Entry
Database: PDB / ID: 4nho
TitleStructure of the spliceosomal DEAD-box protein Prp28
ComponentsProbable ATP-dependent RNA helicase DDX23
KeywordsHYDROLASE / DEAD-BOX / HELICASE
Function / homology
Function and homology information


R-loop processing / cis assembly of pre-catalytic spliceosome / RNA splicing, via transesterification reactions / mRNA Splicing - Minor Pathway / U5 snRNP / U4/U6 x U5 tri-snRNP complex / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / RNA splicing / mRNA splicing, via spliceosome ...R-loop processing / cis assembly of pre-catalytic spliceosome / RNA splicing, via transesterification reactions / mRNA Splicing - Minor Pathway / U5 snRNP / U4/U6 x U5 tri-snRNP complex / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / RNA splicing / mRNA splicing, via spliceosome / RNA helicase activity / RNA helicase / mRNA binding / chromatin / nucleolus / ATP hydrolysis activity / RNA binding / extracellular exosome / nucleoplasm / ATP binding / nucleus
Similarity search - Function
DEAD-box subfamily ATP-dependent helicases signature. / ATP-dependent RNA helicase DEAD-box, conserved site / RNA helicase, DEAD-box type, Q motif / DEAD-box RNA helicase Q motif profile. / 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-box subfamily ATP-dependent helicases signature. / ATP-dependent RNA helicase DEAD-box, conserved site / RNA helicase, DEAD-box type, Q motif / DEAD-box RNA helicase Q motif profile. / 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 / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Probable ATP-dependent RNA helicase DDX23
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsMoehlmann, S. / Neumann, P. / Ficner, R.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Structural and functional analysis of the human spliceosomal DEAD-box helicase Prp28.
Authors: Mohlmann, S. / Mathew, R. / Neumann, P. / Schmitt, A. / Luhrmann, R. / Ficner, R.
History
DepositionNov 5, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 18, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 24, 2014Group: Database references
Revision 1.2Sep 4, 2019Group: Data collection / Derived calculations / Category: reflns / struct_conn
Item: _reflns.pdbx_Rsym_value / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable ATP-dependent RNA helicase DDX23
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,09910
Polymers55,0121
Non-polymers1,0869
Water3,963220
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)125.430, 136.770, 73.220
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-1199-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Probable ATP-dependent RNA helicase DDX23 / 100 kDa U5 snRNP-specific protein / DEAD box protein 23 / PRP28 homolog / U5-100kD


Mass: 55012.285 Da / Num. of mol.: 1 / Fragment: RecA domains (UNP residues 338-820)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DDX23 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 STAR (DE3) / References: UniProt: Q9BUQ8, RNA helicase

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Non-polymers , 5 types, 229 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CXS / 3-CYCLOHEXYL-1-PROPYLSULFONIC ACID


Mass: 221.317 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H19NO3S / Comment: pH buffer*YM
#5: Chemical ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Hg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 220 / 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: 2.85 Å3/Da / Density % sol: 56.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 2.2 M ammonium sulfate, 20 % (v/v) glycerol, 0.1 M CAPS, mixing 1 ul of protein with 1 ul of reservoir solution, pH 9.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONBESSY 14.111.001212
SYNCHROTRONBESSY 14.121.00858
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 6, 2005 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.0012121
21.008581
ReflectionRedundancy: 4.9 % / Av σ(I) over netI: 6.7 / Number: 209358 / Rmerge(I) obs: 0.038 / Rsym value: 0.064 / D res high: 2 Å / Num. obs: 81386 / % possible obs: 99.2
Diffraction reflection shell

ID: 1

Highest resolution (Å)Lowest resolution (Å)Num. obs% possible obs (%)Rmerge(I) obsRsym valueRedundancy
5039.080.0290.0264.6
175011686.60.0130.054.9
141710096.20.010.0534.9
4.5514662398.70.0150.0425
4.124.55239197.90.0190.0665
3.694.12359298.50.0190.1065
3.263.695861990.0240.1525
2.43.262837599.50.0620.245
2.22.41407299.50.2050.3685
2.12.2915299.30.3310.5844.9
22.11110499.20.498
ReflectionResolution: 2→39.97 Å / Num. all: 42906 / Num. obs: 42906 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Biso Wilson estimate: 32.7 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 12.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allRsym value% possible all
2-2.114.90.5842.362190.652100
6.32-39.974.60.02630.214590.02999.1

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Processing

Software
NameVersionClassificationNB
SCALA3.3.12data scaling
SOLOMONphasing
PHENIX1.5_2refinement
PDB_EXTRACT3.11data extraction
MAR345dtbdata collection
MOSFLMdata reduction
SHARPphasing
RefinementMethod to determine structure: SAD
Starting model: PDB entry 2DB3

2db3


Resolution: 2→28.825 Å / Occupancy max: 1 / Occupancy min: 0.23 / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / σ(I): 0 / Phase error: 26.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2176 2159 5.04 %RANDOM
Rwork0.1931 ---
obs0.1943 42839 99.87 %-
all-42906 --
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 74.104 Å2 / ksol: 0.361 e/Å3
Displacement parametersBiso max: 187.48 Å2 / Biso mean: 59.0384 Å2 / Biso min: 26.43 Å2
Baniso -1Baniso -2Baniso -3
1-24.5474 Å2-0 Å2-0 Å2
2---11.2129 Å2-0 Å2
3----13.3345 Å2
Refinement stepCycle: LAST / Resolution: 2→28.825 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3505 0 52 220 3777
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0123679
X-RAY DIFFRACTIONf_angle_d1.2764983
X-RAY DIFFRACTIONf_chiral_restr0.086551
X-RAY DIFFRACTIONf_plane_restr0.006643
X-RAY DIFFRACTIONf_dihedral_angle_d18.9181418
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2-2.04650.3971230.33826992822
2.0465-2.09770.3151520.296626902842
2.0977-2.15440.27581430.25726892832
2.1544-2.21780.30251590.229426592818
2.2178-2.28930.21711440.208426452789
2.2893-2.37110.24871400.185527042844
2.3711-2.4660.21151440.179327032847
2.466-2.57820.23071460.179126722818
2.5782-2.7140.23881310.191927152846
2.714-2.88390.22821490.194526992848
2.8839-3.10630.25831480.20227172865
3.1063-3.41850.21651250.184127262851
3.4185-3.91210.171650.167827262891
3.9121-4.92480.17491570.155427582915
4.9248-28.82830.19831330.194128783011
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)
10.2456-0.1138-0.17240.782-0.20960.2354-0.22150.3160.1438-0.10980.06070.59020.3638-0.1980.19380.618-0.0724-0.08850.4173-0.13130.568716.174439.528919.0778
21.43750.32880.44461.56590.55681.1309-0.02480.16260.0327-0.6904-0.0928-0.0914-0.0858-0.04210.08670.53440.08420.08280.2530.01670.249440.191261.42418.6217
31.538-0.29460.0043.04010.40221.1499-0.0203-0.12050.01430.4607-0.2502-0.14620.157-0.13570.19460.508-0.08240.02560.35050.00430.337235.981646.33748.5969
40.20990.0008-0.14531.61671.52081.7613-0.1372-0.03230.09860.3536-0.74820.66690.851-1.03220.72170.8378-0.290.35930.8489-0.33190.778318.251540.84251.1186
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1CHAIN A AND (RESID 352:366)A345 - 366
2X-RAY DIFFRACTION2CHAIN A AND (RESID 367:632)A367 - 632
3X-RAY DIFFRACTION3CHAIN A AND (RESID 633:672 OR RESID 733:806)A633 - 672
4X-RAY DIFFRACTION4CHAIN A AND (RESID 673:732)A673 - 732

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