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- PDB-2xau: Crystal structure of the Prp43p DEAH-box RNA helicase in complex ... -

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Basic information

Entry
Database: PDB / ID: 2xau
TitleCrystal structure of the Prp43p DEAH-box RNA helicase in complex with ADP
ComponentsPRE-MRNA-SPLICING FACTOR ATP-DEPENDENT RNA HELICASE PRP43
KeywordsHYDROLASE / RIBOSOME BIOGENESIS / ATPASE / ATP-BINDING / OB-FOLD
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
ACETATE ION / ADENOSINE-5'-DIPHOSPHATE / NICKEL (II) ION / Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP43
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsWalbott, H. / Mouffok, S. / Capeyrou, R. / Lebaron, S. / van Tilbeurgh, H. / Henry, Y. / Leulliot, N.
CitationJournal: Embo J. / Year: 2010
Title: Prp43P Contains a Processive Helicase Structural Architecture with a Specific Regulatory Domain.
Authors: Walbott, H. / Mouffok, S. / Capeyrou, R. / Lebaron, S. / Humbert, O. / Van Tilbeurgh, H. / Henry, Y. / Leulliot, N.
History
DepositionMar 31, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 9, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 30, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.4Feb 6, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.5May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.status_code_sf / _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.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_symmetry / _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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AD" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AD" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 5-STRANDED BARREL THIS IS REPRESENTED BY A 6-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BD" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 5-STRANDED BARREL THIS IS REPRESENTED BY A 6-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PRE-MRNA-SPLICING FACTOR ATP-DEPENDENT RNA HELICASE PRP43
B: PRE-MRNA-SPLICING FACTOR ATP-DEPENDENT RNA HELICASE PRP43
hetero molecules


Theoretical massNumber of molelcules
Total (without water)178,34612
Polymers177,0232
Non-polymers1,32310
Water25,5631419
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A: PRE-MRNA-SPLICING FACTOR ATP-DEPENDENT RNA HELICASE PRP43
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,1736
Polymers88,5121
Non-polymers6615
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: PRE-MRNA-SPLICING FACTOR ATP-DEPENDENT RNA HELICASE PRP43
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,1736
Polymers88,5121
Non-polymers6615
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)117.551, 117.551, 254.605
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.50288, 0.86436, -0.00118), (0.86235, 0.50181, 0.06734), (0.0588, 0.03285, -0.99773)
Vector: 2.89092, -5.80149, 124.52824)

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein PRE-MRNA-SPLICING FACTOR ATP-DEPENDENT RNA HELICASE PRP43 / HELICASE JA1 / DEAH-BOX RNA HELICASE PRP43P


Mass: 88511.641 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Plasmid: PSL18 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): SE1
References: UniProt: P53131, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides

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Non-polymers , 6 types, 1429 molecules

#2: 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
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#5: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1419 / 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: 2.87 Å3/Da / Density % sol: 57.21 % / Description: NONE
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 8% PEG 4000, 0.1 M AMMONIUM ACETATE, 0.05 M SODIUM CACODYLATE PH 6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9793
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 28, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.9→102 Å / Num. obs: 160290 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 5.3 % / Biso Wilson estimate: 27.07 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 13.4
Reflection shellResolution: 1.9→2 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 2.2 / % possible all: 98.6

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
autoSHARPphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.9→34.252 Å / SU ML: 0.26 / σ(F): 1.34 / Phase error: 21.62 / Stereochemistry target values: ML
Details: ELECTRON DENSITY WAS NOT VISIBLE FOR RESIDUES 1-2 AND 750-767 AND 6-HISTIDINE TAG, PROBABLY DUE TO STRUCTURAL DISORDER, AND ARE THEREFORE ABSENT FROM THE MODEL
RfactorNum. reflection% reflection
Rfree0.224 8044 5 %
Rwork0.1837 --
obs0.1857 160181 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.242 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 32.1 Å2
Baniso -1Baniso -2Baniso -3
1--2.5314 Å2-0 Å20 Å2
2---2.5314 Å2-0 Å2
3---5.0627 Å2
Refinement stepCycle: LAST / Resolution: 1.9→34.252 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11951 0 78 1419 13448
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01712279
X-RAY DIFFRACTIONf_angle_d1.55716628
X-RAY DIFFRACTIONf_dihedral_angle_d18.2984634
X-RAY DIFFRACTIONf_chiral_restr0.1041833
X-RAY DIFFRACTIONf_plane_restr0.0082170
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.92160.31642500.27084778X-RAY DIFFRACTION95
1.9216-1.94420.27132690.26044935X-RAY DIFFRACTION99
1.9442-1.96790.26432340.24285034X-RAY DIFFRACTION100
1.9679-1.99280.29092660.23435081X-RAY DIFFRACTION100
1.9928-2.0190.27442970.21054975X-RAY DIFFRACTION100
2.019-2.04670.26112800.21714982X-RAY DIFFRACTION100
2.0467-2.07590.25682430.21615081X-RAY DIFFRACTION100
2.0759-2.10690.26432840.20315010X-RAY DIFFRACTION100
2.1069-2.13980.23332960.20025032X-RAY DIFFRACTION100
2.1398-2.17490.23182720.18915084X-RAY DIFFRACTION100
2.1749-2.21240.27152470.18794984X-RAY DIFFRACTION100
2.2124-2.25260.2262710.17985068X-RAY DIFFRACTION100
2.2526-2.29590.23432480.18135073X-RAY DIFFRACTION100
2.2959-2.34280.21692630.17475070X-RAY DIFFRACTION100
2.3428-2.39370.2432620.17745065X-RAY DIFFRACTION100
2.3937-2.44940.25192560.17845076X-RAY DIFFRACTION100
2.4494-2.51060.2222500.1675066X-RAY DIFFRACTION100
2.5106-2.57850.22462990.17315009X-RAY DIFFRACTION100
2.5785-2.65430.22832560.17815087X-RAY DIFFRACTION100
2.6543-2.740.26572580.18015094X-RAY DIFFRACTION100
2.74-2.83790.24242550.17395087X-RAY DIFFRACTION100
2.8379-2.95140.24082650.18115114X-RAY DIFFRACTION100
2.9514-3.08570.23292700.17675094X-RAY DIFFRACTION100
3.0857-3.24820.2152850.17795078X-RAY DIFFRACTION100
3.2482-3.45160.20992750.1755122X-RAY DIFFRACTION100
3.4516-3.71780.18142870.165099X-RAY DIFFRACTION100
3.7178-4.09140.1862680.15235145X-RAY DIFFRACTION100
4.0914-4.68210.16832740.14265194X-RAY DIFFRACTION100
4.6821-5.89410.20862840.16435209X-RAY DIFFRACTION100
5.8941-34.25720.21262800.20595411X-RAY DIFFRACTION99

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