[English] 日本語
Yorodumi
- PDB-3plv: Structure of Hub-1 protein in complex with Snu66 peptide (HINDII) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3plv
TitleStructure of Hub-1 protein in complex with Snu66 peptide (HINDII)
Components
  • 66 kDa U4/U6.U5 small nuclear ribonucleoprotein component
  • Ubiquitin-like modifier HUB1
KeywordsPEPTIDE BINDING PROTEIN / Ubiquitin-like
Function / homology
Function and homology information


cell morphogenesis involved in conjugation with cellular fusion / maturation of 5S rRNA / mRNA cis splicing, via spliceosome / U4/U6 x U5 tri-snRNP complex / post-translational protein modification / positive regulation of RNA splicing / spliceosomal complex / mRNA splicing, via spliceosome / protein modification process / protein tag activity ...cell morphogenesis involved in conjugation with cellular fusion / maturation of 5S rRNA / mRNA cis splicing, via spliceosome / U4/U6 x U5 tri-snRNP complex / post-translational protein modification / positive regulation of RNA splicing / spliceosomal complex / mRNA splicing, via spliceosome / protein modification process / protein tag activity / nucleus / cytoplasm
Similarity search - Function
Ubiquitin-like modifier Hub1/Ubl5 / SNU66/SART1 family / HIND motif / SART-1 family / HIND motif / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin domain profile. / Ubiquitin-like domain ...Ubiquitin-like modifier Hub1/Ubl5 / SNU66/SART1 family / HIND motif / SART-1 family / HIND motif / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
66 kDa U4/U6.U5 small nuclear ribonucleoprotein component / Ubiquitin-like modifier HUB1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsMishra, S.K. / Ammon, T. / Popowicz, G.M. / Krajewski, M. / Nagel, R.J. / Ares, M. / Holak, T.A. / Jentsch, S.
CitationJournal: Nature / Year: 2011
Title: Role of the ubiquitin-like protein Hub1 in splice-site usage and alternative splicing.
Authors: Mishra, S.K. / Ammon, T. / Popowicz, G.M. / Krajewski, M. / Nagel, R.J. / Ares, M. / Holak, T.A. / Jentsch, S.
History
DepositionNov 15, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 1, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: 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_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ubiquitin-like modifier HUB1
C: 66 kDa U4/U6.U5 small nuclear ribonucleoprotein component


Theoretical massNumber of molelcules
Total (without water)12,7242
Polymers12,7242
Non-polymers00
Water2,828157
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1130 Å2
ΔGint-8 kcal/mol
Surface area5910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.720, 83.570, 35.110
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein Ubiquitin-like modifier HUB1


Mass: 10440.913 Da / Num. of mol.: 1 / Mutation: A20G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: HUB1, YNR032C-A / Plasmid: pET-28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 / References: UniProt: Q6Q546
#2: Protein/peptide 66 kDa U4/U6.U5 small nuclear ribonucleoprotein component


Mass: 2282.634 Da / Num. of mol.: 1 / Fragment: HINDII domain / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q12420
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / 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: 2.12 Å3/Da / Density % sol: 41.9 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.9
Details: 0.2M Ammonium Iodide, 20% PEG 3350, pH 6.9, VAPOR DIFFUSION, SITTING DROP, temperature 290K

-
Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.05 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: May 9, 2006 / Details: mirrors
RadiationMonochromator: Si-111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.05 Å / Relative weight: 1
ReflectionResolution: 1.9→45 Å / Num. all: 9009 / Num. obs: 8959 / % possible obs: 99.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 1.9→2 Å / Rmerge(I) obs: 0.136 / Mean I/σ(I) obs: 9.96 / % possible all: 97.8

-
Processing

Software
NameVersionClassification
MAR345dtbdata collection
MOLREPphasing
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1UBI

1ubi


Resolution: 1.9→41.78 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.891 / SU B: 3.91 / SU ML: 0.116 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R Free: 0.155 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24177 425 4.7 %RANDOM
Rwork0.20099 ---
obs0.20301 8559 99.66 %-
all-8559 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.774 Å2
Baniso -1Baniso -2Baniso -3
1--0.49 Å20 Å20 Å2
2---0.18 Å20 Å2
3---0.67 Å2
Refinement stepCycle: LAST / Resolution: 1.9→41.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms780 0 0 157 937
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.022790
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1912.0081066
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.544599
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.81625.31232
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.05115151
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.214154
X-RAY DIFFRACTIONr_chiral_restr0.0880.2129
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02565
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1820.2347
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2940.2533
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1280.2103
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1660.240
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1240.223
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 32 -
Rwork0.283 624 -
obs--97.76 %

+
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