[English] 日本語
Yorodumi
- PDB-5ltk: Crystal structure of the Prp43-ADP-BeF3 complex (in hexagonal spa... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ltk
TitleCrystal structure of the Prp43-ADP-BeF3 complex (in hexagonal space group)
ComponentsPre-mRNA-splicing factor ATP-dependent RNA helicase PRP43
KeywordsHYDROLASE / Spliceosome / RNA HELICASE / DEAH-BOX PROTEIN / DHX15
Function / homology
Function and homology information


RNA splicing / spliceosomal complex / mRNA processing / hydrolase activity / RNA helicase activity / RNA helicase / RNA binding / ATP binding / metal ion binding
Similarity search - Function
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. ...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 / 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 / BERYLLIUM TRIFLUORIDE ION / RNA helicase
Similarity search - Component
Biological speciesChaetomium thermophilum var. thermophilum DSM 1495 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.241 Å
AuthorsTauchert, M.J. / Ficner, R.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationSFB860 Germany
CitationJournal: Elife / Year: 2017
Title: Structural insights into the mechanism of the DEAH-box RNA helicase Prp43.
Authors: Tauchert, M.J. / Fourmann, J.B. / Luhrmann, R. / Ficner, R.
History
DepositionSep 6, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 25, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Author supporting evidence / Data collection / Category: diffrn_source / pdbx_audit_support
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_audit_support.funding_organization
Revision 1.2Jan 17, 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,3516
Polymers81,6411
Non-polymers7105
Water724
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1570 Å2
ΔGint-47 kcal/mol
Surface area31760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)184.342, 184.342, 82.317
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

-
Components

-
Protein , 1 types, 1 molecules A

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


Mass: 81641.336 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
Gene: CTHT_0005780 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta 2 / References: UniProt: G0RY84

-
Non-polymers , 5 types, 9 molecules

#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: BeF3
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 4.95 Å3/Da / Density % sol: 75.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 40 % (v/v) pentaerythritol propoxylate (5/4 PO/OH), 6 % (v/v) ethanol, 16 % (v/v) glycerine and 100 mM Tris/HCl pH 8.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 26, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 3.24→92.171 Å / Num. obs: 25305 / % possible obs: 98.8 % / Redundancy: 4 % / Biso Wilson estimate: 91.9 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.098 / Net I/σ(I): 14.65
Reflection shellResolution: 3.24→3.39 Å / Redundancy: 3.59 % / Rmerge(I) obs: 0.762 / Mean I/σ(I) obs: 2.26 / CC1/2: 0.638 / % possible all: 94.9

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LTA

5lta


Resolution: 3.241→92.171 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.96
RfactorNum. reflection% reflection
Rfree0.2166 1919 7.58 %
Rwork0.1821 --
obs0.1846 25304 98.87 %
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å
Refinement stepCycle: LAST / Resolution: 3.241→92.171 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5622 0 42 4 5668
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035787
X-RAY DIFFRACTIONf_angle_d0.6727834
X-RAY DIFFRACTIONf_dihedral_angle_d11.7362205
X-RAY DIFFRACTIONf_chiral_restr0.026873
X-RAY DIFFRACTIONf_plane_restr0.0031009
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2405-3.32160.32611280.29841553X-RAY DIFFRACTION92
3.3216-3.41140.30341270.26491670X-RAY DIFFRACTION99
3.4114-3.51180.23641300.23391642X-RAY DIFFRACTION99
3.5118-3.62510.27761360.22581679X-RAY DIFFRACTION100
3.6251-3.75470.24341320.20811669X-RAY DIFFRACTION99
3.7547-3.9050.23151380.19441671X-RAY DIFFRACTION99
3.905-4.08280.22921390.17641665X-RAY DIFFRACTION100
4.0828-4.2980.19321360.15741689X-RAY DIFFRACTION100
4.298-4.56730.1961420.16021673X-RAY DIFFRACTION100
4.5673-4.91990.19241440.16031680X-RAY DIFFRACTION100
4.9199-5.4150.20341460.16751674X-RAY DIFFRACTION100
5.415-6.19840.26191380.19761697X-RAY DIFFRACTION100
6.1984-7.80870.21191450.18611693X-RAY DIFFRACTION100
7.8087-92.20830.17751380.15281730X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: -77.1246 Å / Origin y: -21.7338 Å / Origin z: -3.0492 Å
111213212223313233
T0.5885 Å2-0.021 Å2-0.0352 Å2-0.4851 Å20.0656 Å2--0.5004 Å2
L0.8522 °2-0.4821 °2-0.0794 °2-3.2185 °20.7677 °2--0.677 °2
S0.077 Å °-0.0507 Å °-0.0026 Å °0.1104 Å °-0.0908 Å °-0.0841 Å °-0.0333 Å °0.1169 Å °0.0207 Å °
Refinement TLS groupSelection details: Chain A

+
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