[English] 日本語
Yorodumi
- PDB-1e7k: Crystal structure of the spliceosomal 15.5kD protein bound to a U... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1e7k
TitleCrystal structure of the spliceosomal 15.5kD protein bound to a U4 snRNA fragment
Components
  • 15.5 KD RNA BINDING PROTEIN
  • RNA (5'-R(*GP*CP*CP*AP*AP*UP*GP*AP*GP*GP*UP*UP*UP* AP*UP*CP*CP*GP*AP*GP*G*C(-3')
KeywordsRNA BINDING PROTEIN / RNA-BINDING PROTEIN / SPLICING / RNA RECOGNITION MOTIF / U4 SNRNA
Function / homology
Function and homology information


U4atac snRNP / U4atac snRNA binding / box C/D sno(s)RNA binding / dense fibrillar component / U4 snRNA binding / box C/D methylation guide snoRNP complex / U2-type precatalytic spliceosome / box C/D snoRNP assembly / rRNA modification in the nucleus and cytosol / U3 snoRNA binding ...U4atac snRNP / U4atac snRNA binding / box C/D sno(s)RNA binding / dense fibrillar component / U4 snRNA binding / box C/D methylation guide snoRNP complex / U2-type precatalytic spliceosome / box C/D snoRNP assembly / rRNA modification in the nucleus and cytosol / U3 snoRNA binding / precatalytic spliceosome / single fertilization / Major pathway of rRNA processing in the nucleolus and cytosol / U4/U6 x U5 tri-snRNP complex / mRNA Splicing - Major Pathway / maturation of LSU-rRNA / maturation of SSU-rRNA / small-subunit processome / mRNA splicing, via spliceosome / ribosomal small subunit biogenesis / ATPase binding / cytosolic large ribosomal subunit / nucleolus / protein-containing complex / RNA binding / nucleoplasm / nucleus
Similarity search - Function
H/ACA ribonucleoprotein complex, subunit Nhp2-like / Ribosomal protein L30/S12 / 60s Ribosomal Protein L30; Chain: A; / Ribosomal protein L7Ae conserved site / Ribosomal protein L7Ae signature. / Ribosomal protein L7Ae/L8/Nhp2 family / Ribosomal protein L7Ae/L30e/S12e/Gadd45 / Ribosomal protein L7Ae/L30e/S12e/Gadd45 family / 50S ribosomal protein L30e-like / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
RNA / RNA (> 10) / NHP2-like protein 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.9 Å
AuthorsVidovic, I. / Nottrott, S. / Harthmuth, K. / Luhrmann, R. / Ficner, R.
Citation
Journal: Mol.Cell / Year: 2000
Title: Crystal Structure of the Spliceosomal 15.5Kd Protein Bound to a U4 Snrna Fragment
Authors: Vidovic, I. / Nottrott, S. / Hartmuth, K. / Luhrmann, R. / Ficner, R.
#1: Journal: Embo J. / Year: 1999
Title: Functional Interaction of a Novel 15.5Kd [U4/U6.U5] Tri-Snrnp Protein with the 5' Stem-Loop of U4 Snrna
Authors: Nottrott, S. / Hartmuth, K. / Fabrizio, P. / Urlaub, H. / Vidovic, I. / Ficner, R. / Luhrmann, R.
History
DepositionAug 29, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 19, 2001Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 15.5 KD RNA BINDING PROTEIN
B: 15.5 KD RNA BINDING PROTEIN
C: RNA (5'-R(*GP*CP*CP*AP*AP*UP*GP*AP*GP*GP*UP*UP*UP* AP*UP*CP*CP*GP*AP*GP*G*C(-3')
D: RNA (5'-R(*GP*CP*CP*AP*AP*UP*GP*AP*GP*GP*UP*UP*UP* AP*UP*CP*CP*GP*AP*GP*G*C(-3')


Theoretical massNumber of molelcules
Total (without water)42,5324
Polymers42,5324
Non-polymers00
Water00
1
A: 15.5 KD RNA BINDING PROTEIN
C: RNA (5'-R(*GP*CP*CP*AP*AP*UP*GP*AP*GP*GP*UP*UP*UP* AP*UP*CP*CP*GP*AP*GP*G*C(-3')


Theoretical massNumber of molelcules
Total (without water)21,2662
Polymers21,2662
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1510 Å2
ΔGint2.1 kcal/mol
Surface area10620 Å2
MethodPQS
2
B: 15.5 KD RNA BINDING PROTEIN
D: RNA (5'-R(*GP*CP*CP*AP*AP*UP*GP*AP*GP*GP*UP*UP*UP* AP*UP*CP*CP*GP*AP*GP*G*C(-3')


Theoretical massNumber of molelcules
Total (without water)21,2662
Polymers21,2662
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1530 Å2
ΔGint2.1 kcal/mol
Surface area10510 Å2
MethodPQS
Unit cell
Length a, b, c (Å)45.756, 55.287, 146.735
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.057157, 0.330472, -0.942084), (0.008778, 0.943423, 0.331474), (0.998327, -0.027216, 0.051022)
Vector: 95.2612, -21.8777, 15.7786)

-
Components

#1: Protein 15.5 KD RNA BINDING PROTEIN / NHP2/RS6 FAMILY PROTEIN YEL026W HOMOLOG / HIGH MOBILITY GROUP-LIKE NUCLEAR PROTEIN 2 HOMOLOG / OTK27


Mass: 14191.524 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P55769
#2: RNA chain RNA (5'-R(*GP*CP*CP*AP*AP*UP*GP*AP*GP*GP*UP*UP*UP* AP*UP*CP*CP*GP*AP*GP*G*C(-3') / U4 SNRNA


Mass: 7074.250 Da / Num. of mol.: 2 / Fragment: 26-47 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human)
Sequence detailsTHE SWISSPROT ENTRY P55769 IS IDENTICAL TO THE SWISSPROT ENTRY AAF06959 REPORTED IN, S.NOTTROTT,K. ...THE SWISSPROT ENTRY P55769 IS IDENTICAL TO THE SWISSPROT ENTRY AAF06959 REPORTED IN, S.NOTTROTT,K.HARTMUTH,P.FABRIZIO,H.URLAUB,I.VIDOVIC, R.FICNER,R.LUHRMANN FUNCTIONAL INTERACTION OF A NOVEL 15.5KD [U4/U6.U5] TRI-SNRNP PROTEIN WITH THE 5' STEM-LOOP OF U4 SNRNA EMBO J. 18, 6119-6133 (1999).

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.18 Å3/Da / Density % sol: 37 %
Crystal growpH: 7.6 / Details: pH 7.60
Crystal grow
*PLUS
Temperature: 21 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15 mg/mlprotein1drop
20.1 MHEPES-NaOH1reservoir
316.5 %PEG20001reservoir
430 mM1reservoirMgCl2
55 mMdithiothreitol1reservoir
60.04 %(w/v)sodium azide1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9184, 0.9790, 0.9791, 0.9919
DetectorDate: Mar 15, 1999
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.91841
20.9791
30.97911
40.99191
ReflectionResolution: 2.9→30 Å / Num. obs: 8125 / % possible obs: 93.2 % / Redundancy: 3.5 % / Rsym value: 0.055
Reflection shellResolution: 2.9→3 Å / Rsym value: 0.118 / % possible all: 89.3
Reflection
*PLUS
Num. measured all: 28438 / Rmerge(I) obs: 0.055
Reflection shell
*PLUS
% possible obs: 89.3 % / Rmerge(I) obs: 0.118

-
Processing

Software
NameVersionClassification
X-PLOR3.851refinement
SHARPphasing
SOLOMONphasing
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.9→30 Å / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.302 --RANDOM
Rwork0.216 ---
obs0.216 7948 92.99 %-
Displacement parametersBiso mean: 15.192 Å2
Refinement stepCycle: LAST / Resolution: 2.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1923 732 0 0 2655
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.21
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refine LS restraints NCSNCS model details: RESTRAINTS
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
% reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
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://pdbjlvh1.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