[English] 日本語
Yorodumi
- PDB-3im2: Structure of the C-terminal Sec63 unit of yeast Brr2, P41212 Form -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3im2
TitleStructure of the C-terminal Sec63 unit of yeast Brr2, P41212 Form
ComponentsPre-mRNA-splicing helicase BRR2
KeywordsHYDROLASE / ATPase / RNA helicase / RNPase / RNA unwindase / molecular modeling / pre-mRNA splicing / spliceosome catalytic activation / U5-200K protein/Brr2 / ATP-binding / Helicase / mRNA processing / mRNA splicing / Nucleotide-binding / Nucleus / Phosphoprotein / Spliceosome
Function / homology
Function and homology information


spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / U5 snRNP / U4/U6 x U5 tri-snRNP complex / spliceosomal complex / mRNA splicing, via spliceosome / nucleic acid binding / RNA helicase activity / RNA helicase / ATP hydrolysis activity / ATP binding ...spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / U5 snRNP / U4/U6 x U5 tri-snRNP complex / spliceosomal complex / mRNA splicing, via spliceosome / nucleic acid binding / RNA helicase activity / RNA helicase / ATP hydrolysis activity / ATP binding / identical protein binding / nucleus
Similarity search - Function
Sec63 N-terminal domain-like domain / Sec63 N-terminal domain-like fold / 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 ...Sec63 N-terminal domain-like domain / Sec63 N-terminal domain-like fold / 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 / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / 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 / Winged helix-like DNA-binding domain superfamily / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Pre-mRNA-splicing helicase BRR2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsPena, V. / Hrmann, R.L. / Wahl, M.C.
CitationJournal: To be Published
Title: Common Design Principles in the Spliceosomal RNA Helicase Brr2 and in the Hel308 DNA Helicase
Authors: Pena, V. / Jovin, S.M. / Fabrizio, P. / Orlowski, J. / Bujnicki, J.M. / Hrmann, R.L. / Wahl, M.C.
History
DepositionAug 9, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 25, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / 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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Pre-mRNA-splicing helicase BRR2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3492
Polymers37,1551
Non-polymers1941
Water6,341352
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)104.090, 104.090, 77.373
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-73-

HOH

21A-255-

HOH

-
Components

#1: Protein Pre-mRNA-splicing helicase BRR2


Mass: 37155.250 Da / Num. of mol.: 1 / Fragment: Sec63 unit (UNP residues 1839-2163)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: BRR2, RSS1, SNU246, SYGP-ORF66, YER172C / Plasmid: pETM-11 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 (DE3)
References: UniProt: P32639, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
#2: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 352 / 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: 2.82 Å3/Da / Density % sol: 56.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 100mM sodium cacodylate, pH 6.0, 100mM Li2SO4, 15 % PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.05 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 4, 2006 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.05 Å / Relative weight: 1
ReflectionResolution: 1.99→30 Å / Num. all: 29754 / Num. obs: 29516 / % possible obs: 99.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.1 % / Biso Wilson estimate: 35.3 Å2 / Rsym value: 0.1 / Net I/σ(I): 13.7
Reflection shellResolution: 2→2.12 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 1.7 / Num. unique all: 4644 / Rsym value: 0.56 / % possible all: 99.3

-
Processing

Software
NameVersionClassification
MAR345dtbdata collection
MOLREPphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID 3IM1

3im1


Resolution: 1.99→20 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.934 / SU B: 6.968 / SU ML: 0.106 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.168 / ESU R Free: 0.159 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23655 1503 5.1 %RANDOM
Rwork0.18765 ---
all0.19009 28257 --
obs0.19009 27975 99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.145 Å2
Baniso -1Baniso -2Baniso -3
1-0.2 Å20 Å20 Å2
2--0.2 Å20 Å2
3----0.4 Å2
Refinement stepCycle: LAST / Resolution: 1.99→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2560 0 13 352 2925
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222773
X-RAY DIFFRACTIONr_angle_refined_deg1.1921.9753786
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5715351
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.08625.556126
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.49915504
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4821511
X-RAY DIFFRACTIONr_chiral_restr0.080.2441
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022089
X-RAY DIFFRACTIONr_nbd_refined0.180.21177
X-RAY DIFFRACTIONr_nbtor_refined0.2890.21908
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1670.2248
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1690.258
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1810.246
X-RAY DIFFRACTIONr_mcbond_it0.3811.51758
X-RAY DIFFRACTIONr_mcangle_it0.61522795
X-RAY DIFFRACTIONr_scbond_it0.97231158
X-RAY DIFFRACTIONr_scangle_it1.5394.5991
LS refinement shellResolution: 1.988→2.039 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 98 -
Rwork0.259 1924 -
obs-2022 93.87 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.66912.06252.08281.62942.162810.2211-0.2606-0.03761.15790.326-0.0016-0.6278-0.8989-0.5750.26220.0716-0.0935-0.0023-0.06730.03640.101818.0166-18.2943-10.5366
25.29151.4165-0.53592.0631-0.56972.5188-0.09420.13180.2225-0.07680.11420.1094-0.39380.0916-0.0199-0.0223-0.05740.0107-0.1-0.0079-0.067210.5393-25.85-19.2096
319.2318-3.9499-8.58925.0437-0.92465.54410.11820.24610.5547-0.105-0.0039-0.1922-0.20920.1388-0.1144-0.0423-0.07140.0227-0.0918-0.0342-0.088813.9764-32.4964-23.5646
48.21543.2690.13394.73332.48585.3224-0.09020.32840.6578-0.41010.2180.0313-0.25810.2632-0.1278-0.0204-0.00030.0316-0.0729-0.0024-0.043515.5869-43.4557-32.6175
52.09140.0421-1.15860.64341.59995.25620.02370.1295-0.14980.028-0.04260.04850.1261-0.14430.0189-0.0977-0.0075-0.0214-0.0678-0.0193-0.03863.4559-46.1247-24.2484
617.2861-17.8656-9.901819.387212.446711.72020.28640.633-1.4213-0.3327-0.50061.7655-0.7723-1.37810.21420.07050.07920.04780.16050.07150.14012.7552-35.5262-31.0453
71.74450.8227-1.10071.7592-1.87095.8097-0.03020.0344-0.0921-0.0783-0.0127-0.03150.12210.12580.0429-0.0896-0.01660.0164-0.0549-0.0387-0.020410.8562-44.6219-19.8992
82.38813.28022.224715.35857.51226.29470.0870.1243-0.1893-0.29820.082-0.4114-0.09620.5286-0.169-0.14830.00480.0177-0.0048-0.0139-0.067519.6238-45.381-21.5896
91.4282-0.0950.1031.7631-0.17270.56470.03370.00470.07590.1409-0.00620.0352-0.15180.0232-0.0275-0.036-0.04420.0198-0.0527-0.0076-0.077711.5723-31.6511-9.6883
105.32372.4688-2.18945.37710.03993.9954-0.12940.0429-0.1866-0.31710.1644-0.29270.10850.1495-0.035-0.09160.00460.0202-0.0782-0.0016-0.051210.2381-54.0417-1.8695
1113.12392.0707-3.25048.53761.40499.13740.4207-0.41260.5554-0.15670.03280.0016-0.26880.4746-0.4534-0.12830.00520.0473-0.0625-0.0211-0.08887.6275-52.31117.6816
127.6903-17.4891-15.201439.773534.570830.0487-1.0588-1.8497-0.66993.37011.6725-2.57563.09351.2376-0.61380.33310.1269-0.16030.34730.16740.157513.8188-59.620611.6596
131.6542-0.6503-0.356847.25852.77028.2002-0.4499-0.5131-0.71710.142-0.193-1.97640.71190.6130.6429-0.26030.07730.0552-0.0640.07120.129121.7183-58.96011.1441
144.5793-6.7112-1.461629.55611.99518.3374-0.3582-0.53530.37421.96820.3411-0.53540.1183-0.10040.01710.0972-0.0559-0.0071-0.05570.0279-0.22516.2303-31.92859.9857
158.2157-9.07791.450927.4071-2.45748.6672-0.3908-0.50621.130.02160.20470.0972-1.539-0.03610.18610.427-0.0987-0.1277-0.1483-0.19960.017613.4248-14.76819.7183
166.3452-4.1345-11.110225.184413.984921.4765-0.0942-1.2454-1.10632.3221.3402-1.18391.40052.6144-1.2460.28880.1574-0.27170.7098-0.07080.08827.3389-38.90648.5684
173.8292-3.043-0.88866.93982.38675.0990.0002-0.2127-0.04360.25770.0516-0.0618-0.13330.1209-0.0518-0.17-0.0954-0.0056-0.1220.0172-0.190216.4907-33.646-3.7492
1811.6193-11.10196.610818.0443-7.486312.6958-0.0269-0.22540.76160.7576-0.1108-1.1667-0.14910.52840.1377-0.0187-0.1635-0.0568-0.2089-0.1053-0.14119.5087-25.45031.5619
193.1384-1.5218-0.66785.68151.24554.447-0.2547-0.27080.32870.87890.206-0.0082-0.5746-0.06330.04860.1249-0.0194-0.0211-0.067-0.0569-0.149712.5085-23.75014.9144
203.9717-4.0719-1.46917.69934.06117.8504-0.2766-0.11520.04471.8292-0.13041.1482-0.761-0.80810.40690.28850.08380.12320.0064-0.0751-0.14355.9265-22.03679.6129
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1844 - 1856
2X-RAY DIFFRACTION2A1857 - 1880
3X-RAY DIFFRACTION3A1881 - 1889
4X-RAY DIFFRACTION4A1890 - 1900
5X-RAY DIFFRACTION5A1901 - 1914
6X-RAY DIFFRACTION6A1915 - 1921
7X-RAY DIFFRACTION7A1922 - 1938
8X-RAY DIFFRACTION8A1939 - 1955
9X-RAY DIFFRACTION9A1956 - 1990
10X-RAY DIFFRACTION10A1991 - 2006
11X-RAY DIFFRACTION11A2007 - 2020
12X-RAY DIFFRACTION12A2021 - 2031
13X-RAY DIFFRACTION13A2032 - 2043
14X-RAY DIFFRACTION14A2044 - 2060
15X-RAY DIFFRACTION15A2061 - 2076
16X-RAY DIFFRACTION16A2077 - 2084
17X-RAY DIFFRACTION17A2085 - 2110
18X-RAY DIFFRACTION18A2111 - 2121
19X-RAY DIFFRACTION19A2122 - 2151
20X-RAY DIFFRACTION20A2152 - 2163

+
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