[English] 日本語
Yorodumi
- PDB-2f9d: 2.5 angstrom resolution structure of the spliceosomal protein p14... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2f9d
Title2.5 angstrom resolution structure of the spliceosomal protein p14 bound to region of SF3b155
Components
  • Pre-mRNA branch site protein p14
  • Splicing factor 3B subunit 1
KeywordsRNA BINDING PROTEIN / p14 SF3bp14 SF3b155 SAP155 RRM
Function / homology
Function and homology information


U11/U12 snRNP / B-WICH complex / splicing factor binding / U12-type spliceosomal complex / blastocyst formation / RNA splicing, via transesterification reactions / : / U2-type spliceosomal complex / U2-type precatalytic spliceosome / U2-type prespliceosome assembly ...U11/U12 snRNP / B-WICH complex / splicing factor binding / U12-type spliceosomal complex / blastocyst formation / RNA splicing, via transesterification reactions / : / U2-type spliceosomal complex / U2-type precatalytic spliceosome / U2-type prespliceosome assembly / U2 snRNP / positive regulation of transcription by RNA polymerase III / U2-type prespliceosome / precatalytic spliceosome / spliceosomal complex assembly / positive regulation of transcription by RNA polymerase I / mRNA Splicing - Minor Pathway / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / RNA splicing / spliceosomal complex / B-WICH complex positively regulates rRNA expression / mRNA splicing, via spliceosome / 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 / 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 ...SF3B6, RNA recognition motif / Splicing factor 3B subunit 1 / Splicing factor 3B subunit 1 / Splicing factor 3B subunit 1-like / 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
Splicing factor 3B subunit 1 / Splicing factor 3B subunit 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsSchellenberg, M.J. / Edwards, R.A. / Ritchie, D.B. / Glover, J.N.M. / Macmillan, A.M.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2006
Title: Crystal structure of a core spliceosomal protein interface
Authors: Schellenberg, M.J. / Edwards, R.A. / Ritchie, D.B. / Kent, O.A. / Golas, M.M. / Stark, H. / Glover, J.N.M. / Macmillan, A.M.
History
DepositionDec 5, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 24, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version

-
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


Theoretical massNumber of molelcules
Total (without water)39,9174
Polymers39,9174
Non-polymers00
Water1,20767
1
A: Pre-mRNA branch site protein p14
P: Splicing factor 3B subunit 1


Theoretical massNumber of molelcules
Total (without water)19,9582
Polymers19,9582
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2670 Å2
ΔGint-10 kcal/mol
Surface area9480 Å2
MethodPISA
2
B: Pre-mRNA branch site protein p14
Q: Splicing factor 3B subunit 1


Theoretical massNumber of molelcules
Total (without water)19,9582
Polymers19,9582
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2700 Å2
ΔGint-10 kcal/mol
Surface area9500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.870, 115.227, 82.536
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B
13P
23Q

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg label comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ILEPHE2AA20 - 8020 - 80
21ILEPHE2BB20 - 8020 - 80
12ASNLEU2AA84 - 11284 - 112
22ASNLEU2BB84 - 11284 - 112
13ARGLEU4PC390 - 41518 - 43
23ARGLEU4QD390 - 41518 - 43

NCS ensembles :
ID
1
2
3
Details2 biological units per ASU. Biological unit consists of 1 p14 molecule bound to one SF3b155 molecule

-
Components

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


Mass: 14606.900 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SF3B14 / Plasmid: pMALc2x / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q9Y3B4
#2: Protein/peptide Splicing factor 3B subunit 1 / Spliceosome associated protein 155 / SAP 155 / SF3b155 / Pre-mRNA splicing factor SF3b 155 kDa subunit


Mass: 5351.517 Da / Num. of mol.: 2 / Fragment: Residues: 373-415
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SF3B1, SAP155 / Plasmid: pGEX6P1 / Production host: Escherichia coli (E. coli) / References: UniProt: O75533
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 67 / 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: 3.03 Å3/Da / Density % sol: 59.36 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 14-18% PEG3350, MOPS buffer, 0.2M sodium formate selenomethionine derivatized SF3b155 protein, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 0.979547, 1.019859
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Aug 25, 2004
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9795471
21.0198591
ReflectionNumber: 17097 / Rmerge(I) obs: 0.076 / Χ2: 1.033 / D res high: 2.5 Å / D res low: 100 Å / % possible obs: 99.5
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squared
5.3910099.710.0310.971
4.275.3910010.0381.02
3.734.2710010.0491.002
3.393.7310010.0721.066
3.153.3910010.1161.068
2.963.1510010.1821.042
2.822.9610010.3221.067
2.692.8210010.4171.041
2.592.6999.910.5521.015
2.52.5995.610.3991.028
ReflectionResolution: 2.5→100 Å / Num. obs: 17097 / % possible obs: 99.5 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 25.5
Reflection shellResolution: 2.5→2.59 Å / Rmerge(I) obs: 0.399 / Mean I/σ(I) obs: 2.4 / % possible all: 95.6

-
Phasing

PhasingMethod: MAD
Phasing set
ID
1
2
Phasing MAD set
Clust-IDExpt-IDSet-IDWavelength (Å)F double prime refinedF prime refined
12 wavelength10.97950.5-8.06
12 wavelength21.01990.54-2.84
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Se19.6220.880.0680.0890.831
2Se600.0110.1290.0491.314
3Se16.3270.3990.1380.090.934
4Se30.5640.7610.2870.1690.988
Phasing dmFOM : 0.62 / FOM acentric: 0.62 / FOM centric: 0.67 / Reflection: 16104 / Reflection acentric: 14438 / Reflection centric: 1666
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
7.1-56.0420.910.920.88811592219
4.5-7.10.860.870.7923251976349
3.6-4.50.830.840.7828892562327
3.1-3.60.710.710.6828652591274
2.7-3.10.450.450.4648444488356
2.5-2.70.30.30.323702229141

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVE2.08phasing
RESOLVE2.08phasing
REFMACrefinement
PDB_EXTRACT1.701data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: MAD / Resolution: 2.5→76.25 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.918 / SU B: 16.022 / SU ML: 0.218 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.382 / ESU R Free: 0.283 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27562 858 5 %RANDOM
Rwork0.2214 ---
obs0.22403 16225 99.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.447 Å2
Baniso -1Baniso -2Baniso -3
1--4.8 Å20 Å20 Å2
2--4.63 Å20 Å2
3---0.17 Å2
Refinement stepCycle: LAST / Resolution: 2.5→76.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2560 0 0 67 2627
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222618
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6081.9793538
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1965302
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.32523.857140
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.12415476
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.4681524
X-RAY DIFFRACTIONr_chiral_restr0.1340.2366
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022034
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2250.21213
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3140.21788
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.2112
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.210.235
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1470.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6441.51570
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.18222494
X-RAY DIFFRACTIONr_scbond_it1.74531194
X-RAY DIFFRACTIONr_scangle_it2.7184.51044
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A244tight positional0.050.05
2A116tight positional0.050.05
1A253medium positional0.530.5
2A137medium positional0.710.5
3P219medium positional0.70.5
1A244tight thermal0.110.5
2A116tight thermal0.170.5
1A253medium thermal0.672
2A137medium thermal0.532
3P219medium thermal1.382
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.487 47 -
Rwork0.33 1155 -
obs--95.02 %
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)
16.2341-1.01452.68582.0953-0.64613.9171-0.03230.15930.2839-0.0286-0.05570.02210.07230.10850.088-0.1581-0.0478-0.0127-0.09860.0268-0.113329.206131.55434.891
26.69091.2784-0.52232.63930.87232.8078-0.2129-0.1068-0.52340.14460.0317-0.27940.20950.3420.1812-0.13580.04090.02850.03310.02-0.03633.651122.211938.5014
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A13 - 125
2X-RAY DIFFRACTION2B13 - 125

+
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