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- PDB-3fho: Structure of S. pombe Dbp5 -

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Basic information

Entry
Database: PDB / ID: 3fho
TitleStructure of S. pombe Dbp5
ComponentsATP-dependent RNA helicase dbp5
KeywordsHYDROLASE / RNA helicase / mRNA export / ATPase / translation termination / ATP-binding / Helicase / Membrane / mRNA transport / Nuclear pore complex / Nucleotide-binding / Nucleus / Protein transport / RNA-binding / Translocation / Transport
Function / homology
Function and homology information


cytoplasmic translational termination / poly(A)+ mRNA export from nucleus / mRNA export from nucleus / nuclear pore / cytoplasmic stress granule / nuclear envelope / nuclear membrane / RNA helicase activity / RNA helicase / RNA binding ...cytoplasmic translational termination / poly(A)+ mRNA export from nucleus / mRNA export from nucleus / nuclear pore / cytoplasmic stress granule / nuclear envelope / nuclear membrane / RNA helicase activity / RNA helicase / RNA binding / ATP binding / nucleus / cytosol
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 / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ATP-dependent RNA helicase dbp5
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsCheng, Z. / Song, H.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Solution and crystal structures of mRNA exporter Dbp5p and its interaction with nucleotides
Authors: Fan, J.S. / Cheng, Z. / Zhang, J. / Noble, C. / Zhou, Z. / Song, H. / Yang, D.
History
DepositionDec 9, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 13, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Nov 1, 2023Group: 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_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_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: ATP-dependent RNA helicase dbp5
B: ATP-dependent RNA helicase dbp5


Theoretical massNumber of molelcules
Total (without water)106,1762
Polymers106,1762
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1870 Å2
ΔGint-14 kcal/mol
Surface area33780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.736, 144.044, 79.137
Angle α, β, γ (deg.)90.00, 89.96, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B

NCS domain segments:

Component-ID: 1 / Refine code: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLNGLNLYSLYSAA141 - 317146 - 322
21GLNGLNLYSLYSBB141 - 317146 - 322
12GLUGLUTHRTHRAA320 - 483325 - 488
22GLUGLUPROPROBB320 - 481325 - 486

NCS ensembles :
ID
1
2

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Components

#1: Protein ATP-dependent RNA helicase dbp5


Mass: 53087.996 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Gene: dbp5 / Plasmid: pGEX-6P-1 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: Q09747, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
Sequence detailsTHE DEPOSITOR KNOWS THE SEQUENCE. THE DATABASE IS DBP5_SCHPO(Q09747) AND FIVE EXPRESSION TAGS, ...THE DEPOSITOR KNOWS THE SEQUENCE. THE DATABASE IS DBP5_SCHPO(Q09747) AND FIVE EXPRESSION TAGS, GPLGS, AT THE N-TERMINUS. BUT THEY COULD NOT ASSIGN THE RESIDUES (-4)-138. THE RESIUDES 12-16 IN CHAIN A AND 12-15 IN CHAIN B ARE CERTAINLY PART OF RESIDUES (-4)-138. BUT THEY DO NOT KNOW WHETHER THESE PART IS CORRECT DIRECTION. THE CORRECT SEQUENCE OF RESIDUES (-4)-138 IS, MET SER THR THR LEU GLY GLN GLU SER LYS THR ASP TRP ALA SER LEU ASP SER ASP GLU GLU VAL GLN ARG ILE SER ASP LYS VAL ASN GLN LEU ASN THR SER GLU ASN LYS ASN GLU ASP GLN LYS ALA THR ASN LEU SER ASP ARG LEU GLY PRO LYS ILE THR GLU ASN VAL ASP ALA LYS SER GLU GLN ASP LYS ALA THR ASN THR ILE ALA GLU ASP ALA ASN THR LYS GLN SER GLU ASN ASP GLU SER ASN LEU ILE PRO ASN LYS ASN GLU VAL ARG VAL LYS LEU ALA ASP LEU GLN ALA ASP PRO ASN SER PRO LEU PHE SER VAL LYS SER PHE GLU GLU LEU GLU LEU LYS PRO GLU LEU LEU LYS GLY ILE TYR SER MET LYS PHE GLN LYS PRO SER

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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: 2.92 Å3/Da / Density % sol: 57.85 %
Crystal growTemperature: 288 K / Method: evaporation / pH: 8
Details: 100mM Tris, 200mM Ca(Ac)2, 8.5-10% PEG4000, pH 8.0, EVAPORATION, temperature 288K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9725 Å
DetectorDate: May 7, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9725 Å / Relative weight: 1
ReflectionResolution: 2.8→44.81 Å / Num. obs: 29528 / % possible obs: 98.5 % / Redundancy: 3.6 % / Biso Wilson estimate: 72 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 12.6
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.343 / Mean I/σ(I) obs: 2.1 / Num. unique all: 2902

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Processing

Software
NameVersionClassification
DNAdata collection
PHASERphasing
REFMAC5.4.0077refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2j0s

2j0s


Resolution: 2.8→20 Å / Cor.coef. Fo:Fc: 0.887 / Cor.coef. Fo:Fc free: 0.85 / SU B: 37.819 / SU ML: 0.346 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.606 / ESU R Free: 0.386 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.32703 1489 5 %RANDOM
Rwork0.28964 ---
obs0.29156 28004 98.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.869 Å2
Baniso -1Baniso -2Baniso -3
1-7.82 Å2-0 Å2-0.5 Å2
2--1.15 Å20 Å2
3----8.97 Å2
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4771 0 0 0 4771
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0224818
X-RAY DIFFRACTIONr_angle_refined_deg1.3591.9686471
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2635588
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.424.378217
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.91915902
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.9651538
X-RAY DIFFRACTIONr_chiral_restr0.0950.2761
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213494
X-RAY DIFFRACTIONr_mcbond_it0.5151.53022
X-RAY DIFFRACTIONr_mcangle_it0.95424864
X-RAY DIFFRACTIONr_scbond_it1.26631796
X-RAY DIFFRACTIONr_scangle_it2.0334.51607
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A1283TIGHT POSITIONAL0.030.05
11A1283TIGHT THERMAL0.060.5
22B1020TIGHT POSITIONAL0.010.05
22B1020TIGHT THERMAL0.020.5
LS refinement shellResolution: 2.8→2.871 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.4 108 -
Rwork0.357 2025 -
obs-2025 99.21 %
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)
15.57371.3311-4.1261.1948-2.52835.7691-0.1453-1.2068-0.39220.09670.3447-0.66130.20141.3808-0.19940.18490.0916-0.07470.58580.03340.586163.19423.591725.2811
21.301-3.1134-0.14998.08072.48717.20740.4855-0.1161-0.33550.1833-0.0027-0.5750.0328-0.1911-0.48280.20560.1169-0.03430.48360.03990.430652.00153.182426.2884
31.85550.47740.55874.9117-0.68310.3440.0890.2206-0.1763-0.7708-0.0293-0.5233-0.96480.4999-0.05970.37680.13510.1090.4063-0.01790.40553.359711.394613.1843
41.83740.30040.75634.6727-0.977810.43490.0338-0.08670.19540.0808-0.0634-0.0927-2.8296-0.32540.02960.89450.22780.05230.3678-0.01620.349949.608421.015422.4449
516.76890.81166.43781.2216-1.49795.2410.16761.3687-1.4428-0.61221.2090.92531.6896-0.9398-1.37670.2205-0.1549-0.14540.34730.05650.265467.10215.237641.0055
67.5797-2.72051.54331.7340.63512.1806-0.23421.07750.45020.27040.4629-0.58520.01651.1534-0.22870.1954-0.14060.09510.63280.03850.639463.2528-3.063914.2755
70.52691.5959-0.7455.79960.958811.76020.3610.2380.4939-0.1818-0.0666-0.4159-0.03040.0173-0.29440.1308-0.21260.09280.46850.05810.531751.9879-2.577113.2784
82.223-0.1106-0.37585.21380.07079.85790.2059-0.31190.15380.9504-0.1017-0.56661.36980.5088-0.10420.5015-0.2118-0.0780.5024-0.00970.387354.1841-11.295126.2997
92.17290.0487-0.76464.7069-0.46179.95240.06760.0621-0.18360.1893-0.0542-0.0852.8891-0.4699-0.01340.9427-0.3761-0.02660.4409-0.0030.369149.2315-19.786418.4759
1013.8543-0.2437-8.85370.65670.396610.00550.3946-1.47131.42870.66461.15290.7003-0.9742-0.1829-1.54750.16890.13010.13690.32870.04390.232166.7837-15.1135-1.5554
111.8003-3.2734-0.02457.2009-2.95327.19430.25860.2063-0.164-0.389-0.3801-0.7161.35961.31990.12151.56641.1062-0.05251.7139-0.25340.934486.7017-35.8463-5.6675
123.2203-5.79255.297610.4194-9.52918.715-0.3275-0.38581.13320.0721-0.0482-0.63230.79781.11990.37581.66740.9389-0.00371.5605-0.36480.831487.4002-34.97986.4746
135.89361.52583.70475.3969-0.63128.6605-0.2552-0.46110.04250.60560.3771-0.1088-0.11360.1892-0.12191.4320.897-0.00141.2348-0.12280.59279.3688-27.66042.1086
146.5074-1.24231.99534.3573-2.12458.13060.31930.442-0.4267-0.25290.0476-0.18751.14040.7836-0.36691.39440.91930.00161.2259-0.13690.563678.825-32.6116-11.6066
157.7096-0.4484-8.0312.5601-3.347814.1091.1186-0.2063-0.6932-0.42460.3721-0.2150.65820.9777-1.49071.55420.6853-0.17171.2743-0.08390.472273.6585-30.5416-19.2601
160.56531.8673-0.3326.437-2.33525.90410.4932-0.02140.2205-0.1522-0.5416-0.874-1.38521.29870.04831.6921-1.00910.09111.8923-0.20790.856786.54836.278544.9377
176.24146.906-9.59657.6414-10.618414.75531.33070.8088-1.76510.6164-0.6283-0.6509-0.45411.6283-0.70241.798-1.2444-0.0031.8406-0.33871.005587.48435.535933.1021
185.5125-1.0778-3.14234.9577-0.58487.4319-0.21490.45320.0648-0.60990.4685-0.1489-0.14510.4336-0.25361.5674-0.98380.06491.3886-0.05770.636379.424828.23637.4664
192.99853.6048-5.798313.4923-0.37615.9604-0.04440.02240.5676-0.08350.1503-0.0164-0.22720.234-0.10591.3037-0.9638-0.03611.2311-0.05330.620273.5428.485347.5979
204.29981.0116-1.32491.9069-3.57466.78770.4475-0.34740.47990.58260.1313-0.2634-1.39910.9985-0.57881.5383-1.01830.07181.3308-0.16580.68378.287133.631455.2594
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A139 - 143
2X-RAY DIFFRACTION2A144 - 152
3X-RAY DIFFRACTION3A153 - 235
4X-RAY DIFFRACTION4A236 - 315
5X-RAY DIFFRACTION5A316 - 320
6X-RAY DIFFRACTION6B139 - 143
7X-RAY DIFFRACTION7B144 - 152
8X-RAY DIFFRACTION8B153 - 217
9X-RAY DIFFRACTION9B228 - 315
10X-RAY DIFFRACTION10B316 - 320
11X-RAY DIFFRACTION11B325 - 370
12X-RAY DIFFRACTION12B371 - 390
13X-RAY DIFFRACTION13B391 - 440
14X-RAY DIFFRACTION14B441 - 470
15X-RAY DIFFRACTION15B471 - 481
16X-RAY DIFFRACTION16A325 - 370
17X-RAY DIFFRACTION17A371 - 390
18X-RAY DIFFRACTION18A391 - 440
19X-RAY DIFFRACTION19A441 - 446
20X-RAY DIFFRACTION20A447 - 483

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