[English] 日本語
Yorodumi
- PDB-8px5: Structure of the RNA recognition motif (RRM) of Seb1 from S. pomb... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8px5
TitleStructure of the RNA recognition motif (RRM) of Seb1 from S. pombe., solved at wavelength 2.75 A
ComponentsRpb7-binding protein seb1
KeywordsTRANSCRIPTION / RRM / RNA binding protein
Function / homology
Function and homology information


Mei2 nuclear dot complex / sno(s)RNA 3'-end processing / co-transcriptional mRNA 3'-end processing, cleavage and polyadenylation pathway / regulatory ncRNA 3'-end processing / mRNA 3'-end processing / lncRNA binding / RNA polymerase II C-terminal domain binding / RNA binding / nucleus
Similarity search - Function
: / Nrd1/Seb1, domain 2 / Nrd1/Seb1, RNA recognition motif / CID domain / RPR / CID domain / CID domain profile. / ENTH/VHS / RNA recognition motif / RNA recognition motif ...: / Nrd1/Seb1, domain 2 / Nrd1/Seb1, RNA recognition motif / CID domain / RPR / CID domain / CID domain profile. / ENTH/VHS / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily
Similarity search - Domain/homology
Rpb7-binding protein seb1
Similarity search - Component
Biological speciesSchizosaccharomyces pombe 972h- (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.77 Å
AuthorsEl Omari, K. / Duman, R. / Mykhaylyk, V. / Orr, C. / Wittmann, S. / Renner, M. / Grimes, J.M. / Wagner, A.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Diamond Light Source United Kingdom
CitationJournal: Commun Chem / Year: 2023
Title: Experimental phasing opportunities for macromolecular crystallography at very long wavelengths.
Authors: El Omari, K. / Duman, R. / Mykhaylyk, V. / Orr, C.M. / Latimer-Smith, M. / Winter, G. / Grama, V. / Qu, F. / Bountra, K. / Kwong, H.S. / Romano, M. / Reis, R.I. / Vogeley, L. / Vecchia, L. / ...Authors: El Omari, K. / Duman, R. / Mykhaylyk, V. / Orr, C.M. / Latimer-Smith, M. / Winter, G. / Grama, V. / Qu, F. / Bountra, K. / Kwong, H.S. / Romano, M. / Reis, R.I. / Vogeley, L. / Vecchia, L. / Owen, C.D. / Wittmann, S. / Renner, M. / Senda, M. / Matsugaki, N. / Kawano, Y. / Bowden, T.A. / Moraes, I. / Grimes, J.M. / Mancini, E.J. / Walsh, M.A. / Guzzo, C.R. / Owens, R.J. / Jones, E.Y. / Brown, D.G. / Stuart, D.I. / Beis, K. / Wagner, A.
History
DepositionJul 22, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 25, 2023Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Rpb7-binding protein seb1


Theoretical massNumber of molelcules
Total (without water)17,3781
Polymers17,3781
Non-polymers00
Water1,53185
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.100, 46.900, 32.300
Angle α, β, γ (deg.)90.00, 99.00, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Rpb7-binding protein seb1


Mass: 17377.832 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe 972h- (yeast)
Gene: seb1, SPAC222.09 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UTE3
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 85 / 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: 2.39 Å3/Da / Density % sol: 48.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 1 M ammonium formate, 100 mM sodium cacodylate, 8% (w/v) poly-gamma-glutamic acid polymer (PGA-LM, 200-400 kDa low molecular weight polymer)

-
Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I23 / Wavelength: 2.7552 Å
DetectorType: DECTRIS PILATUS 12M / Detector: PIXEL / Date: Jul 4, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 2.7552 Å / Relative weight: 1
ReflectionResolution: 1.775→54.87 Å / Num. obs: 10445 / % possible obs: 64.89 % / Redundancy: 6.1 % / Biso Wilson estimate: 23.2 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.04513 / Rpim(I) all: 0.01897 / Rrim(I) all: 0.04915 / Net I/σ(I): 22.91
Reflection shellResolution: 1.775→1.838 Å / Rmerge(I) obs: 0.2519 / Mean I/σ(I) obs: 3.26 / Num. unique obs: 653 / CC1/2: 0.919

-
Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSdata reduction
Aimlessdata scaling
HKL2Mapphasing
RefinementMethod to determine structure: SAD / Resolution: 1.77→54.87 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.956 / SU B: 1.928 / SU ML: 0.061 / Cross valid method: THROUGHOUT / ESU R: 0.168 / ESU R Free: 0.141 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18829 545 5.2 %RANDOM
Rwork0.15472 ---
obs0.15652 9850 64.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.71 Å2
Baniso -1Baniso -2Baniso -3
1--0.86 Å2-0 Å20.61 Å2
2--1.63 Å2-0 Å2
3----0.92 Å2
Refinement stepCycle: 1 / Resolution: 1.77→54.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1192 0 0 85 1277
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0131219
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171158
X-RAY DIFFRACTIONr_angle_refined_deg1.0941.6551651
X-RAY DIFFRACTIONr_angle_other_deg1.0861.5762668
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0285151
X-RAY DIFFRACTIONr_dihedral_angle_2_deg24.52218.98669
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.915203
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0751515
X-RAY DIFFRACTIONr_chiral_restr0.0620.2162
X-RAY DIFFRACTIONr_gen_planes_refined0.0260.021368
X-RAY DIFFRACTIONr_gen_planes_other0.0170.02289
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.4352.161607
X-RAY DIFFRACTIONr_mcbond_other2.4162.155606
X-RAY DIFFRACTIONr_mcangle_it3.2543.23757
X-RAY DIFFRACTIONr_mcangle_other3.2523.236758
X-RAY DIFFRACTIONr_scbond_it3.3082.524612
X-RAY DIFFRACTIONr_scbond_other3.2582.525612
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.6673.657895
X-RAY DIFFRACTIONr_long_range_B_refined5.63725.7971333
X-RAY DIFFRACTIONr_long_range_B_other5.59825.7031324
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.775→1.821 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 16 -
Rwork0.225 434 -
obs--38.66 %

+
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