[English] 日本語
Yorodumi
- PDB-1mzw: Crystal structure of a U4/U6 snRNP complex between human spliceos... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1mzw
TitleCrystal structure of a U4/U6 snRNP complex between human spliceosomal cyclophilin H and a U4/U6-60K peptide
Components
  • U-snRNP-associated cyclophilin
  • U4/U6 snrnp 60kDa protein
KeywordsISOMERASE / cyclophilin / peptidyl-prolyl-cis/trans isomerase / spliceosome / snRNP / U4/U6-60K protein / WD protein
Function / homology
Function and homology information


spliceosomal snRNP complex / U4/U6 snRNP / RNA splicing, via transesterification reactions / U4 snRNA binding / U2-type precatalytic spliceosome / cyclosporin A binding / U6 snRNA binding / ribonucleoprotein complex binding / RNA processing / Cajal body ...spliceosomal snRNP complex / U4/U6 snRNP / RNA splicing, via transesterification reactions / U4 snRNA binding / U2-type precatalytic spliceosome / cyclosporin A binding / U6 snRNA binding / ribonucleoprotein complex binding / RNA processing / Cajal body / positive regulation of viral genome replication / U4/U6 x U5 tri-snRNP complex / mRNA Splicing - Major Pathway / RNA splicing / peptidylprolyl isomerase / spliceosomal complex / peptidyl-prolyl cis-trans isomerase activity / mRNA splicing, via spliceosome / SARS-CoV-1 activates/modulates innate immune responses / protein folding / protein-containing complex assembly / nuclear speck / intracellular membrane-bounded organelle / nucleoplasm / nucleus / cytoplasm / cytosol
Similarity search - Function
PRP4-like superfamily / pre-mRNA processing factor 4 (PRP4) like / Pre-mRNA processing factor 4 (PRP4)-like / Splicing Factor Motif, present in Prp18 and Pr04 / Cyclophilin-like / Cyclophilin / Cyclophilin-type peptidyl-prolyl cis-trans isomerase / Cyclophilin-type peptidyl-prolyl cis-trans isomerase, conserved site / Cyclophilin-type peptidyl-prolyl cis-trans isomerase signature. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain profile. ...PRP4-like superfamily / pre-mRNA processing factor 4 (PRP4) like / Pre-mRNA processing factor 4 (PRP4)-like / Splicing Factor Motif, present in Prp18 and Pr04 / Cyclophilin-like / Cyclophilin / Cyclophilin-type peptidyl-prolyl cis-trans isomerase / Cyclophilin-type peptidyl-prolyl cis-trans isomerase, conserved site / Cyclophilin-type peptidyl-prolyl cis-trans isomerase signature. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain profile. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain / Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD / Cyclophilin-like domain superfamily / WD domain, G-beta repeat / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
U4/U6 small nuclear ribonucleoprotein Prp4 / Peptidyl-prolyl cis-trans isomerase H
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsReidt, U. / Wahl, M.C. / Horowitz, D.S. / Luehrmann, R. / Ficner, R.
CitationJournal: J.Mol.Biol. / Year: 2003
Title: Crystal structure of a complex between human spliceosomal cyclophilin H and a U4/U6 snRNP-60K peptide
Authors: Reidt, U. / Wahl, M.C. / Fasshauer, D. / Horowitz, D.S. / Luehrmann, R. / Ficner, R.
History
DepositionOct 10, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: 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: U-snRNP-associated cyclophilin
B: U4/U6 snrnp 60kDa protein


Theoretical massNumber of molelcules
Total (without water)22,7282
Polymers22,7282
Non-polymers00
Water4,684260
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.369, 59.526, 47.040
Angle α, β, γ (deg.)90.00, 110.65, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein U-snRNP-associated cyclophilin / cyclophilin H


Mass: 19230.117 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O43447
#2: Protein/peptide U4/U6 snrnp 60kDa protein / WD splicing factor Prp4 / hPrp4 / U4/U6 small nuclear ribonucleo protein Prp4


Mass: 3498.044 Da / Num. of mol.: 1 / Fragment: residues 107-137, internal domain / Source method: obtained synthetically / Details: peptide B106-B136 was chemically synthesized / References: UniProt: O43172
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 260 / 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: 2.56 Å3/Da / Density % sol: 51.88 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 8000, magnesium acetate, HEPES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 294.0K
Crystal grow
*PLUS
Temperature: 21 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
12 %(w/v)PEG80001reservoir
2200 mMmagnesium acetate1reservoir
30.1 MHEPES1reservoirpH6.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 10, 2001 / Details: Osmic Mirrors
RadiationMonochromator: Osmic Mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→100 Å / Num. obs: 55492 / % possible obs: 99.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rsym value: 0.063
Reflection shellResolution: 2→2.1 Å / Rsym value: 0.236 / % possible all: 99
Reflection
*PLUS
Highest resolution: 2.1 Å / Num. obs: 13762 / Num. measured all: 55492 / Rmerge(I) obs: 0.063
Reflection shell
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 2.2 Å / % possible obs: 99 % / Rmerge(I) obs: 0.236

-
Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QOI

1qoi


Resolution: 2→15 Å / Isotropic thermal model: ISOTROPIC / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.212 1344 -RANDOM
Rwork0.195 ---
all0.195 ---
obs0.195 13458 99.2 %-
Refinement stepCycle: LAST / Resolution: 2→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1565 0 0 260 1825
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.28
Refinement
*PLUS
Highest resolution: 2.1 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.257
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Rfactor Rfree: 0.275 / Rfactor Rwork: 0.212

+
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