[English] 日本語
Yorodumi
- PDB-5m5p: S. cerevisiae spliceosomal helicase Brr2 (271-end) in complex wit... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5m5p
TitleS. cerevisiae spliceosomal helicase Brr2 (271-end) in complex with the Jab/MPN domain of S. cerevisiae Prp8
Components
  • Pre-mRNA-splicing factor 8
  • Pre-mRNA-splicing helicase BRR2
KeywordsHYDROLASE / splicing / helicase / complex
Function / homology
Function and homology information


spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / generation of catalytic spliceosome for second transesterification step / mRNA 3'-splice site recognition / mRNA 5'-splice site recognition / spliceosomal tri-snRNP complex assembly / U5 snRNA binding / U5 snRNP / spliceosomal snRNP assembly / U2 snRNA binding / U6 snRNA binding ...spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / generation of catalytic spliceosome for second transesterification step / mRNA 3'-splice site recognition / mRNA 5'-splice site recognition / spliceosomal tri-snRNP complex assembly / U5 snRNA binding / U5 snRNP / spliceosomal snRNP assembly / U2 snRNA binding / U6 snRNA binding / pre-mRNA intronic binding / U1 snRNA binding / U4/U6 x U5 tri-snRNP complex / catalytic step 2 spliceosome / spliceosomal complex / mRNA splicing, via spliceosome / metallopeptidase activity / RNA helicase activity / nucleic acid binding / RNA helicase / mRNA binding / ATP hydrolysis activity / ATP binding / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Brr2, N-terminal helicase PWI domain / : / N-terminal helicase PWI domain / Pre-mRNA-splicing helicase BRR2 plug domain / Sec63 Brl domain / Sec63 domain / Sec63 Brl domain / PROCT domain / Prp8 RNase domain IV, fingers region / PROCT (NUC072) domain ...Brr2, N-terminal helicase PWI domain / : / N-terminal helicase PWI domain / Pre-mRNA-splicing helicase BRR2 plug domain / Sec63 Brl domain / Sec63 domain / Sec63 Brl domain / PROCT domain / Prp8 RNase domain IV, fingers region / PROCT (NUC072) domain / PRO8NT domain / PROCN domain / Pre-mRNA-processing-splicing factor 8, U6-snRNA-binding / Pre-mRNA-processing-splicing factor 8, U5-snRNA-binding / RNA recognition motif, spliceosomal PrP8 / PRP8 domain IV core / Pre-mRNA-processing-splicing factor 8, U5-snRNA-binding domain superfamily / Prp8 RNase domain IV, palm region / PRO8NT (NUC069), PrP8 N-terminal domain / PROCN (NUC071) domain / U6-snRNA interacting domain of PrP8 / U5-snRNA binding site 2 of PrP8 / RNA recognition motif of the spliceosomal PrP8 / PRP8 domain IV core / Pre-mRNA-processing-splicing factor 8 / JAB/MPN domain / JAB1/MPN/MOV34 metalloenzyme domain / MPN domain / MPN domain profile. / DEAD/DEAH box helicase / DEAD/DEAH box helicase domain / C2 domain superfamily / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Immunoglobulin E-set / 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 / Winged helix DNA-binding domain superfamily / Ribonuclease H-like superfamily / Winged helix-like DNA-binding domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Pre-mRNA-splicing helicase BRR2 / Pre-mRNA-splicing factor 8
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 4.2 Å
AuthorsBecke, C. / Absmeier, E. / Wollenhaupt, J. / Santos, K.F. / Wahl, M.C.
Funding support Germany, 4items
OrganizationGrant numberCountry
German Research FoundationSFB 740 Germany
Bundesministerium fuer Bildung und Forschung05K10KEC Germany
Einstein Foundation BerlinA-2012-140 Germany
Freie Universitaet BerlinDahlem International Network PostDoc Fellowship Germany
CitationJournal: Cell Cycle / Year: 2017
Title: Interplay of cis- and trans-regulatory mechanisms in the spliceosomal RNA helicase Brr2.
Authors: Absmeier, E. / Becke, C. / Wollenhaupt, J. / Santos, K.F. / Wahl, M.C.
History
DepositionOct 22, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 7, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2017Group: Database references
Revision 1.2Jan 25, 2017Group: Database references
Revision 1.3Sep 6, 2017Group: Author supporting evidence / Data collection / Refinement description
Category: diffrn / diffrn_detector ...diffrn / diffrn_detector / diffrn_radiation / diffrn_radiation_wavelength / pdbx_audit_support / software
Item: _diffrn.ambient_temp / _pdbx_audit_support.funding_organization
Revision 1.4Oct 18, 2017Group: Data collection / Category: diffrn / diffrn_radiation / Item: _diffrn.ambient_temp
Revision 1.5Nov 21, 2018Group: Advisory / Data collection / Derived calculations / Category: pdbx_validate_close_contact / struct_conn
Revision 1.6Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.7Jan 17, 2024Group: 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_asym_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_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Pre-mRNA-splicing helicase BRR2
B: Pre-mRNA-splicing factor 8
C: Pre-mRNA-splicing helicase BRR2
D: Pre-mRNA-splicing factor 8


Theoretical massNumber of molelcules
Total (without water)492,6154
Polymers492,6154
Non-polymers00
Water0
1
A: Pre-mRNA-splicing helicase BRR2
B: Pre-mRNA-splicing factor 8


Theoretical massNumber of molelcules
Total (without water)246,3072
Polymers246,3072
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3190 Å2
ΔGint-15 kcal/mol
Surface area94760 Å2
MethodPISA
2
C: Pre-mRNA-splicing helicase BRR2
D: Pre-mRNA-splicing factor 8


Theoretical massNumber of molelcules
Total (without water)246,3072
Polymers246,3072
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3120 Å2
ΔGint-19 kcal/mol
Surface area96290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)185.970, 196.870, 191.030
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain C
12chain B
22chain D

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYSLYSLYSchain AAA271 - 21635 - 1897
21SERSERLYSLYSchain CCC275 - 21639 - 1897
12SERSERPHEPHEchain BBB2148 - 23955 - 252
22SERSERPHEPHEchain DDD2148 - 23955 - 252

NCS ensembles :
ID
1
2

-
Components

#1: Protein Pre-mRNA-splicing helicase BRR2 / Protein Snu246


Mass: 215817.031 Da / Num. of mol.: 2 / Fragment: UNP residues 271-2163
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Gene: BRR2, RSS1, SNU246, YER172C, SYGP-ORF66 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P32639, RNA helicase
#2: Protein Pre-mRNA-splicing factor 8


Mass: 30490.338 Da / Num. of mol.: 2 / Fragment: UNP residues 2147-2413
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Gene: PRP8, DBF3, DNA39, RNA8, SLT21, USA2, YHR165C / Plasmid: pETM-11 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P33334

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.55 Å3/Da / Density % sol: 65.35 % / Description: needles
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1 M MES pH 6.5 9.2% (w/v) PEG 4000 0.4 M MgCl2

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONBESSY 14.210.9184
SYNCHROTRONBESSY 14.120.9184
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Apr 16, 2013
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 4.2→95.5 Å / Num. obs: 51802 / % possible obs: 99.9 % / Redundancy: 10.8 % / CC1/2: 0.995 / Rsym value: 0.315 / Net I/σ(I): 8.6

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
XSCALEdata scaling
PHASERphasing
PHENIX1.9_1692refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4bgd

4bgd


Resolution: 4.2→95.5 Å / SU ML: 0.74 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 38.06
RfactorNum. reflection% reflection
Rfree0.3349 2666 5.15 %
Rwork0.307 --
obs0.3085 51754 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 184.21 Å2 / Biso mean: 157.9082 Å2 / Biso min: 136.88 Å2
Refinement stepCycle: final / Resolution: 4.2→95.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms33653 0 0 0 33653
Num. residues----4196
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00334379
X-RAY DIFFRACTIONf_angle_d0.75746599
X-RAY DIFFRACTIONf_chiral_restr0.035277
X-RAY DIFFRACTIONf_plane_restr0.0045951
X-RAY DIFFRACTIONf_dihedral_angle_d10.1212777
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A21660X-RAY DIFFRACTION6.572TORSIONAL
12C21660X-RAY DIFFRACTION6.572TORSIONAL
21B2896X-RAY DIFFRACTION6.572TORSIONAL
22D2896X-RAY DIFFRACTION6.572TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
4.2-4.27640.43351400.380625352675100
4.2764-4.35860.38181330.386525812714100
4.3586-4.44760.40031460.376725372683100
4.4476-4.54430.39031350.358125372672100
4.5443-4.650.38961170.360825652682100
4.65-4.76630.39411540.354125632717100
4.7663-4.89510.40071510.35725412692100
4.8951-5.03920.36271450.349725662711100
5.0392-5.20180.3811250.349225672692100
5.2018-5.38770.37441440.357125532697100
5.3877-5.60340.35391280.347525972725100
5.6034-5.85840.34861390.343725712710100
5.8584-6.16720.40731300.344926132743100
6.1672-6.55350.37861480.337625562704100
6.5535-7.05940.35671460.312126042750100
7.0594-7.76950.28671270.296526222749100
7.7695-8.8930.2881440.254226312775100
8.893-11.20150.22571640.215526192783100
11.2015-95.53970.31821500.25732730288098

+
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