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- PDB-3fe2: Human DEAD-BOX RNA helicase DDX5 (P68), conserved domain I in com... -

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Basic information

Entry
Database: PDB / ID: 3fe2
TitleHuman DEAD-BOX RNA helicase DDX5 (P68), conserved domain I in complex with ADP
ComponentsProbable ATP-dependent RNA helicase DDX5
KeywordsHYDROLASE / RNA HELICASE / DEAD / ADP / ATP-binding / Nucleotide-binding / RNA-binding / Helicase / Methylation / mRNA processing / mRNA splicing / Nucleus / Phosphoprotein / Spliceosome / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


MH2 domain binding / miRNA transcription / regulation of skeletal muscle cell differentiation / primary miRNA binding / primary miRNA processing / alternative mRNA splicing, via spliceosome / regulation of viral genome replication / pre-mRNA binding / myoblast differentiation / regulation of androgen receptor signaling pathway ...MH2 domain binding / miRNA transcription / regulation of skeletal muscle cell differentiation / primary miRNA binding / primary miRNA processing / alternative mRNA splicing, via spliceosome / regulation of viral genome replication / pre-mRNA binding / myoblast differentiation / regulation of androgen receptor signaling pathway / mRNA transcription / Replication of the SARS-CoV-1 genome / positive regulation of DNA damage response, signal transduction by p53 class mediator / nuclear androgen receptor binding / regulation of osteoblast differentiation / regulation of alternative mRNA splicing, via spliceosome / androgen receptor signaling pathway / SMAD binding / intrinsic apoptotic signaling pathway by p53 class mediator / R-SMAD binding / nuclear-transcribed mRNA catabolic process / epithelial to mesenchymal transition / BMP signaling pathway / ribonucleoprotein complex binding / estrogen receptor signaling pathway / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / SUMOylation of transcription cofactors / mRNA 3'-UTR binding / promoter-specific chromatin binding / mRNA splicing, via spliceosome / calcium-dependent protein binding / rhythmic process / Replication of the SARS-CoV-2 genome / Estrogen-dependent gene expression / calmodulin binding / RNA helicase activity / nuclear speck / RNA helicase / ribonucleoprotein complex / mRNA binding / regulation of transcription by RNA polymerase II / nucleolus / enzyme binding / negative regulation of transcription by RNA polymerase II / ATP hydrolysis activity / RNA binding / extracellular exosome / nucleoplasm / ATP binding / nucleus / membrane / cytoplasm / cytosol
Similarity search - Function
RNA helicase p68 repeat / P68HR (NUC004) repeat / P68HR (NUC004) repeat / 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 domain / DEAD/DEAH box helicase / Helicase conserved C-terminal domain ...RNA helicase p68 repeat / P68HR (NUC004) repeat / P68HR (NUC004) repeat / 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 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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Probable ATP-dependent RNA helicase DDX5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsKarlberg, T. / Siponen, M.I. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Dahlgren, L.G. / Edwards, A.M. / Flodin, S. / Flores, A. ...Karlberg, T. / Siponen, M.I. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Dahlgren, L.G. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Johansson, A. / Johansson, I. / Kotenyova, T. / Lehtio, L. / Moche, M. / Nilsson, M.E. / Nordlund, P. / Nyman, T. / Persson, C. / Sagemark, J. / Thorsell, A.G. / Tresaugues, L. / Van Den Berg, S. / Weigelt, J. / Welin, M. / Wikstrom, M. / Wisniewska, M. / Schuler, H. / Structural Genomics Consortium (SGC)
CitationJournal: Plos One / Year: 2010
Title: Comparative Structural Analysis of Human DEAD-Box RNA Helicases
Authors: Schutz, P. / Karlberg, T. / van den Berg, S. / Collins, R. / Lehtio, L. / Hogbom, M. / Holmberg-Schiavone, L. / Tempel, W. / Park, H.W. / Hammarstrom, M. / Moche, M. / Thorsell, A.G. / Schuler, H.
History
DepositionNov 27, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 16, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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_ncs_dom_lim / 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_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 / _struct_ref_seq_dif.details / _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
A: Probable ATP-dependent RNA helicase DDX5
B: Probable ATP-dependent RNA helicase DDX5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,7218
Polymers54,5432
Non-polymers1,1786
Water1,35175
1
A: Probable ATP-dependent RNA helicase DDX5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7953
Polymers27,2711
Non-polymers5232
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Probable ATP-dependent RNA helicase DDX5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9265
Polymers27,2711
Non-polymers6554
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)84.570, 106.870, 117.320
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: 4 / Auth seq-ID: 71 - 304 / Label seq-ID: 6 - 239

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Probable ATP-dependent RNA helicase DDX5 / DEAD-BOX RNA HELICASE / DEAD box protein 5 / RNA helicase p68


Mass: 27271.418 Da / Num. of mol.: 2 / Fragment: DOMAIN I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DDX5 / Plasmid: pNIC-BSA4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) R3 pRARE
References: UniProt: P17844, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


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


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / 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: 2.43 Å3/Da / Density % sol: 49.38 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.4
Details: 17.5% PEG3350, 0.25M Lithium Sulfate, 0.1M Bis-Tris, pH 6.4, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Oct 30, 2008 / Details: mirrors
RadiationMonochromator: Double Crystal Monochromator, Si-111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.6→35 Å / Num. all: 16601 / Num. obs: 16601 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Rmerge(I) obs: 0.142 / Rsym value: 0.188 / Net I/σ(I): 11
Reflection shellResolution: 2.6→2.67 Å / Redundancy: 4 % / Rmerge(I) obs: 0.742 / Mean I/σ(I) obs: 2.44 / Num. unique all: 1211 / Rsym value: 0.728 / % possible all: 99.8

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Processing

Software
NameVersionClassification
MxCuBEdata collection
MOLREPphasing
REFMAC5.5.0035refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2I4I

2i4i


Resolution: 2.6→31.91 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.866 / SU B: 12.161 / SU ML: 0.262 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 1.667 / ESU R Free: 0.356 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27283 831 5 %RANDOM
Rwork0.20494 ---
all0.2084 15770 --
obs0.2084 15770 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.991 Å2
Baniso -1Baniso -2Baniso -3
1-1.08 Å20 Å20 Å2
2---1.22 Å20 Å2
3---0.15 Å2
Refinement stepCycle: LAST / Resolution: 2.6→31.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3696 0 70 75 3841
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0223842
X-RAY DIFFRACTIONr_bond_other_d0.0020.022638
X-RAY DIFFRACTIONr_angle_refined_deg1.3541.9885228
X-RAY DIFFRACTIONr_angle_other_deg0.87736410
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8635466
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.68923.596178
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.50415650
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8211536
X-RAY DIFFRACTIONr_chiral_restr0.0740.2580
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214216
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02764
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5011.52336
X-RAY DIFFRACTIONr_mcbond_other0.0881.5936
X-RAY DIFFRACTIONr_mcangle_it0.97923788
X-RAY DIFFRACTIONr_scbond_it1.37631506
X-RAY DIFFRACTIONr_scangle_it2.3694.51440
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 3157 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
MEDIUM POSITIONAL0.440.5
MEDIUM THERMAL0.422
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 61 -
Rwork0.287 1141 -
obs--100 %

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