[English] 日本語
Yorodumi
- PDB-3lqv: Branch Recognition by SF3b14 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3lqv
TitleBranch Recognition by SF3b14
Components
  • Pre-mRNA branch site protein p14
  • Splicing factor 3B subunit 1
KeywordsPROTEIN BINDING / Cysless mutant / pre-mRNA splicing / adenine / mRNA processing / mRNA splicing / Nucleus / Phosphoprotein / RNA-binding / Spliceosome
Function / homology
Function and homology information


U11/U12 snRNP / B-WICH complex / splicing factor binding / U12-type spliceosomal complex / RNA splicing, via transesterification reactions / blastocyst formation / U2-type precatalytic spliceosome / U2-type spliceosomal complex / U2-type prespliceosome assembly / U2 snRNP ...U11/U12 snRNP / B-WICH complex / splicing factor binding / U12-type spliceosomal complex / RNA splicing, via transesterification reactions / blastocyst formation / U2-type precatalytic spliceosome / U2-type spliceosomal complex / U2-type prespliceosome assembly / U2 snRNP / U2-type prespliceosome / positive regulation of transcription by RNA polymerase III / positive regulation of transcription by RNA polymerase I / spliceosomal complex assembly / mRNA Splicing - Minor Pathway / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / RNA splicing / spliceosomal complex / mRNA splicing, via spliceosome / B-WICH complex positively regulates rRNA expression / nuclear speck / chromatin remodeling / mRNA binding / nucleolus / positive regulation of transcription by RNA polymerase II / RNA binding / nucleoplasm / nucleus
Similarity search - Function
SF3B6, RNA recognition motif / Splicing factor 3B subunit 1 / Splicing factor 3B subunit 1 / : / Splicing factor 3B subunit 1-like / : / PPP2R1A-like HEAT repeat / RRM (RNA recognition motif) domain / RNA recognition motif / RNA recognition motif ...SF3B6, RNA recognition motif / Splicing factor 3B subunit 1 / Splicing factor 3B subunit 1 / : / Splicing factor 3B subunit 1-like / : / PPP2R1A-like HEAT repeat / RRM (RNA recognition motif) domain / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Armadillo-like helical / Armadillo-type fold / Nucleotide-binding alpha-beta plait domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENINE / Splicing factor 3B subunit 1 / Splicing factor 3B subunit 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.38 Å
AuthorsSchellenberg, M.J. / MacMillan, A.M.
CitationJournal: Rna / Year: 2011
Title: Branch Recognition by SF3b14
Authors: Schellenberg, M.J. / Dul, E.L. / MacMillan, A.M.
History
DepositionFeb 10, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 26, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 branch site protein p14
B: Pre-mRNA branch site protein p14
P: Splicing factor 3B subunit 1
Q: Splicing factor 3B subunit 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8366
Polymers36,5664
Non-polymers2702
Water1,44180
1
A: Pre-mRNA branch site protein p14
P: Splicing factor 3B subunit 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,4183
Polymers18,2832
Non-polymers1351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2950 Å2
ΔGint-5 kcal/mol
Surface area9590 Å2
MethodPISA
2
B: Pre-mRNA branch site protein p14
Q: Splicing factor 3B subunit 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,4183
Polymers18,2832
Non-polymers1351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3170 Å2
ΔGint-8 kcal/mol
Surface area9400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.848, 112.702, 82.163
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein Pre-mRNA branch site protein p14 / SF3B 14 kDa subunit


Mass: 13511.514 Da / Num. of mol.: 2 / Fragment: UNP residues 11-125
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CGI-110, HSPC175, HT006, SF3B14 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9Y3B4
#2: Protein/peptide Splicing factor 3B subunit 1 / Pre-mRNA-splicing factor SF3b 155 kDa subunit / SF3b155 / Spliceosome-associated protein 155 / SAP 155


Mass: 4771.279 Da / Num. of mol.: 2 / Fragment: UNP residues 377-415
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SAP155, SF3B1, SF3b155 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O75533
#3: Chemical ChemComp-ADE / ADENINE


Mass: 135.127 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H5N5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / 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: 3.22 Å3/Da / Density % sol: 61.85 %
Crystal growTemperature: 298 K / pH: 6
Details: PEG3350, 0.2M NaCl, 20mM Adenine, pH 6, vapor diffusion, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11586 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 1, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11586 Å / Relative weight: 1
ReflectionResolution: 2.38→50 Å / Num. obs: 18348 / % possible obs: 95.9 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.055 / Χ2: 0.997 / Net I/σ(I): 15.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.38-2.493.10.30115880.99584
2.49-2.593.40.30816171.00186.4
2.59-2.73.60.317801.0294
2.7-2.853.90.21618620.98898.2
2.85-3.024.10.17218580.99598.9
3.02-3.264.10.09818810.97599.3
3.26-3.584.10.06318971.00899.3
3.58-4.14.10.04819060.99199.2
4.1-5.1740.03319401.00799.6
5.17-503.90.02420190.99499.6

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0005refinement
PDB_EXTRACT3.005data extraction
REFMAC5.2.0005phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.38→46.47 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.92 / Occupancy max: 1 / Occupancy min: 1 / SU B: 13.1 / SU ML: 0.196 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.329 / ESU R Free: 0.248 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.258 945 5.2 %RANDOM
Rwork0.214 ---
obs0.216 18329 95.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 90.1 Å2 / Biso mean: 49.856 Å2 / Biso min: 27.22 Å2
Baniso -1Baniso -2Baniso -3
1--2.04 Å20 Å20 Å2
2--1.25 Å20 Å2
3---0.8 Å2
Refinement stepCycle: LAST / Resolution: 2.38→46.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2545 0 20 80 2645
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222625
X-RAY DIFFRACTIONr_angle_refined_deg1.5511.9873551
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1415300
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.25523.957139
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.04615471
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.2161523
X-RAY DIFFRACTIONr_chiral_restr0.1030.2367
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022041
X-RAY DIFFRACTIONr_nbd_refined0.2040.21137
X-RAY DIFFRACTIONr_nbtor_refined0.3050.21753
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1730.2115
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1840.231
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0860.25
X-RAY DIFFRACTIONr_mcbond_it0.8531.51573
X-RAY DIFFRACTIONr_mcangle_it1.37122481
X-RAY DIFFRACTIONr_scbond_it2.15931222
X-RAY DIFFRACTIONr_scangle_it3.3344.51070
LS refinement shellResolution: 2.38→2.449 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 69 -
Rwork0.282 1054 -
all-1123 -
obs--81.2 %
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)
14.9803-0.96281.97481.944-0.16952.9919-0.01890.21270.2703-0.077-0.0793-0.0401-0.03390.10650.0982-0.2991-0.0470.00140.14170.013-0.08429.21231.55934.887
25.8831.0655-0.52622.30080.36911.5566-0.1288-0.1151-0.3903-0.0039-0.0103-0.22180.08250.22350.1392-0.29580.02170.0180.18730.0214-0.02843.64422.21138.505
34.2767-1.98254.91021.5665-2.21026.91360.1415-0.01170.1208-0.0402-0.1709-0.11380.01130.14820.0295-0.0943-0.05370.0461-0.0668-0.0356-0.102119.92631.37622.596
42.98482.8872.43356.37581.39365.29550.1251-0.2631-0.5420.48810.01380.15651.17650.4066-0.139-0.02490.15450.0707-0.110.0630.1069-5.0479.73440.31
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A13 - 125
2X-RAY DIFFRACTION2B13 - 125
3X-RAY DIFFRACTION3P6 - 43
4X-RAY DIFFRACTION4Q6 - 43

+
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