[English] 日本語
Yorodumi
- PDB-5jpt: CRYSTAL STRUCTURE OF THE PRP43P DEAH-BOX RNA HELICASE IN COMPLEX ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5jpt
TitleCRYSTAL STRUCTURE OF THE PRP43P DEAH-BOX RNA HELICASE IN COMPLEX WITH CDP
ComponentsPre-mRNA-splicing factor ATP-dependent RNA helicase PRP43
KeywordsHYDROLASE / RNA helicase / Prp43p / DEAH/RHA
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 / ribosomal large subunit biogenesis / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / spliceosomal complex / maturation of SSU-rRNA / small-subunit processome ...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 / ribosomal large subunit biogenesis / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / spliceosomal complex / maturation of SSU-rRNA / small-subunit processome / helicase activity / 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 (HA2), winged-helix / Helicase-associated domain / 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 (HA2), winged-helix / Helicase-associated domain / 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 domain / DEAD/DEAH box helicase / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Arc Repressor Mutant, subunit A / 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 / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / CYTIDINE-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 / MOLECULAR REPLACEMENT / Resolution: 2.935 Å
AuthorsRobert-Paganin, J. / Rety, S. / Leulliot, N.
CitationJournal: Nucleic Acids Res. / Year: 2017
Title: Functional link between DEAH/RHA helicase Prp43 activation and ATP base binding.
Authors: Robert-Paganin, J. / Halladjian, M. / Blaud, M. / Lebaron, S. / Delbos, L. / Chardon, F. / Capeyrou, R. / Humbert, O. / Henry, Y. / Henras, A.K. / Rety, S. / Leulliot, N.
History
DepositionMay 4, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Feb 22, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: 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 / pdbx_struct_conn_angle / struct_conn
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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)176,4309
Polymers175,3662
Non-polymers1,0657
Water46826
1
A: Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP43
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,3206
Polymers87,6831
Non-polymers6375
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP43
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,1103
Polymers87,6831
Non-polymers4272
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)118.070, 118.070, 252.150
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

-
Components

-
Protein , 1 types, 2 molecules AB

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


Mass: 87682.750 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: PRP43, YGL120C / Production host: Escherichia coli (E. coli) / References: UniProt: P53131, RNA helicase

-
Non-polymers , 6 types, 33 molecules

#2: Chemical ChemComp-CDP / CYTIDINE-5'-DIPHOSPHATE


Mass: 403.176 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H15N3O11P2
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.89 Å3/Da / Density % sol: 57.49 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop
Details: 7.25% PEG 4000, 100 mM ammonium acetate and 50 mM sodium cacodylate pH 6.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1.0882 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 30, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0882 Å / Relative weight: 1
ReflectionResolution: 2.935→48.31 Å / Num. obs: 44183 / % possible obs: 99.57 % / Redundancy: 6.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.1172 / Net I/σ(I): 14.81
Reflection shellResolution: 2.935→3.04 Å / Rmerge(I) obs: 0.7213

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2XAU

2xau


Resolution: 2.935→48.309 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 26.64
RfactorNum. reflection% reflection
Rfree0.2574 2210 5 %
Rwork0.2034 --
obs0.2061 44177 99.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.935→48.309 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11951 0 63 26 12040
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00512265
X-RAY DIFFRACTIONf_angle_d0.97416610
X-RAY DIFFRACTIONf_dihedral_angle_d13.6394674
X-RAY DIFFRACTIONf_chiral_restr0.0391833
X-RAY DIFFRACTIONf_plane_restr0.0052169
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9347-2.99850.38711300.30482466X-RAY DIFFRACTION95
2.9985-3.06820.37481350.28742568X-RAY DIFFRACTION100
3.0682-3.14490.31481370.2782599X-RAY DIFFRACTION100
3.1449-3.22990.31991360.27322582X-RAY DIFFRACTION100
3.2299-3.3250.33611370.26882609X-RAY DIFFRACTION100
3.325-3.43230.35281380.2592614X-RAY DIFFRACTION100
3.4323-3.55490.29041370.23182602X-RAY DIFFRACTION100
3.5549-3.69720.22461370.21882609X-RAY DIFFRACTION100
3.6972-3.86540.2641380.20782610X-RAY DIFFRACTION100
3.8654-4.06910.24971370.19312617X-RAY DIFFRACTION100
4.0691-4.32390.25141390.18272625X-RAY DIFFRACTION100
4.3239-4.65750.19031380.16622630X-RAY DIFFRACTION100
4.6575-5.12570.24281400.16252658X-RAY DIFFRACTION100
5.1257-5.86630.23111400.18622667X-RAY DIFFRACTION100
5.8663-7.38660.24071420.19162701X-RAY DIFFRACTION100
7.3866-48.31580.20881490.16492810X-RAY DIFFRACTION99

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more