[English] 日本語
Yorodumi
- PDB-5gip: Crystal structure of box C/D RNP with 13 nt guide regions and 11 ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5gip
TitleCrystal structure of box C/D RNP with 13 nt guide regions and 11 nt substrates
Components
  • 50S ribosomal protein L7Ae
  • C/D RNA
  • C/D box methylation guide ribonucleoprotein complex aNOP56 subunit
  • Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase
  • substrate
KeywordsTRANSFERASE/RNA / 2'-O-methylation / guide RNA / RNP / TRANSFERASE-RNA complex
Function / homology
Function and homology information


histone H2AQ104 methyltransferase activity / box C/D sno(s)RNA 3'-end processing / rRNA methyltransferase activity / box C/D methylation guide snoRNP complex / ribonuclease P activity / tRNA 5'-leader removal / rRNA methylation / tRNA processing / snoRNA binding / Transferases; Transferring one-carbon groups; Methyltransferases ...histone H2AQ104 methyltransferase activity / box C/D sno(s)RNA 3'-end processing / rRNA methyltransferase activity / box C/D methylation guide snoRNP complex / ribonuclease P activity / tRNA 5'-leader removal / rRNA methylation / tRNA processing / snoRNA binding / Transferases; Transferring one-carbon groups; Methyltransferases / ribosome biogenesis / rRNA binding / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / RNA binding / cytoplasm
Similarity search - Function
Nucleotidyltransferase; domain 5 - #220 / Helix Hairpins - #4070 / Nop domain / : / Archaeal Nop5/56-rel, N-terminal domain / : / Nucleolar protein Nop56/Nop58 / rRNA 2'-O-methyltransferase fibrillarin-like / Fibrillarin, conserved site / Fibrillarin ...Nucleotidyltransferase; domain 5 - #220 / Helix Hairpins - #4070 / Nop domain / : / Archaeal Nop5/56-rel, N-terminal domain / : / Nucleolar protein Nop56/Nop58 / rRNA 2'-O-methyltransferase fibrillarin-like / Fibrillarin, conserved site / Fibrillarin / Fibrillarin signature. / Fibrillarin / Ribosomal protein L30/S12 / NOSIC / NOSIC (NUC001) domain / Nop domain / Nop domain superfamily / Nop, C-terminal domain / snoRNA binding domain, fibrillarin / Nop domain profile. / Ribosomal protein L7Ae, archaea / Serum Albumin; Chain A, Domain 1 / 60s Ribosomal Protein L30; Chain: A; / Ribosomal protein L7Ae conserved site / Ribosomal protein L7Ae signature. / Vaccinia Virus protein VP39 / Ribosomal protein L7Ae/L8/Nhp2 family / : / Ribosomal protein L7Ae/L30e/S12e/Gadd45 / Ribosomal protein L7Ae/L30e/S12e/Gadd45 family / 50S ribosomal protein L30e-like / Nucleotidyltransferase; domain 5 / Helix Hairpins / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / RNA / RNA (> 10) / Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase / Large ribosomal subunit protein eL8 / C/D box methylation guide ribonucleoprotein complex aNOP56 subunit / Large ribosomal subunit protein eL8 / Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase / Pre mRNA splicing protein
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.129 Å
AuthorsYang, Z. / Lin, J. / Ye, K.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Box C/D guide RNAs recognize a maximum of 10 nt of substrates
Authors: Yang, Z. / Lin, J. / Ye, K.
History
DepositionJun 24, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 14, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 12, 2016Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: C/D box methylation guide ribonucleoprotein complex aNOP56 subunit
B: C/D box methylation guide ribonucleoprotein complex aNOP56 subunit
C: 50S ribosomal protein L7Ae
D: 50S ribosomal protein L7Ae
E: Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase
F: Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase
G: C/D RNA
H: C/D RNA
I: substrate
J: substrate
K: C/D box methylation guide ribonucleoprotein complex aNOP56 subunit
L: C/D box methylation guide ribonucleoprotein complex aNOP56 subunit
M: 50S ribosomal protein L7Ae
N: 50S ribosomal protein L7Ae
O: Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase
P: Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase
Q: C/D RNA
R: C/D RNA
S: substrate
T: substrate
hetero molecules


Theoretical massNumber of molelcules
Total (without water)406,99824
Polymers405,46120
Non-polymers1,5384
Water00
1
A: C/D box methylation guide ribonucleoprotein complex aNOP56 subunit
B: C/D box methylation guide ribonucleoprotein complex aNOP56 subunit
C: 50S ribosomal protein L7Ae
D: 50S ribosomal protein L7Ae
E: Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase
F: Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase
G: C/D RNA
H: C/D RNA
I: substrate
J: substrate
hetero molecules


Theoretical massNumber of molelcules
Total (without water)203,49912
Polymers202,73010
Non-polymers7692
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area33550 Å2
ΔGint-203 kcal/mol
Surface area62380 Å2
MethodPISA
2
K: C/D box methylation guide ribonucleoprotein complex aNOP56 subunit
L: C/D box methylation guide ribonucleoprotein complex aNOP56 subunit
M: 50S ribosomal protein L7Ae
N: 50S ribosomal protein L7Ae
O: Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase
P: Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase
Q: C/D RNA
R: C/D RNA
S: substrate
T: substrate
hetero molecules


Theoretical massNumber of molelcules
Total (without water)203,49912
Polymers202,73010
Non-polymers7692
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area33820 Å2
ΔGint-195 kcal/mol
Surface area62210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.916, 97.718, 128.793
Angle α, β, γ (deg.)108.98, 104.42, 89.86
Int Tables number1
Space group name H-MP1

-
Components

-
Protein , 3 types, 12 molecules ABKLCDMNEFOP

#1: Protein
C/D box methylation guide ribonucleoprotein complex aNOP56 subunit


Mass: 44168.531 Da / Num. of mol.: 4 / Fragment: UNP residues 3-379
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Gene: SULA_1947, SULB_1948, SULC_1946 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0E3MJI1, UniProt: Q97ZH3*PLUS
#2: Protein
50S ribosomal protein L7Ae / Ribosomal protein L8e


Mass: 14075.301 Da / Num. of mol.: 4 / Fragment: UNP residues 3-127
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Gene: rpl7ae, SULA_1106, SULB_1107, SULC_1105 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0E3JZF7, UniProt: P55858*PLUS
#3: Protein
Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase


Mass: 26439.375 Da / Num. of mol.: 4 / Fragment: UNP residues 3-232
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Gene: flpA, SSOP1_0970, SULA_1948, SULB_1949, SULC_1947 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A0E3JUC9, UniProt: P58032*PLUS, Transferases; Transferring one-carbon groups; Methyltransferases

-
RNA chain , 2 types, 8 molecules GHQRIJST

#4: RNA chain
C/D RNA


Mass: 13197.862 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Sulfolobus solfataricus (archaea)
#5: RNA chain
substrate


Mass: 3484.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Sulfolobus solfataricus (archaea)

-
Non-polymers , 1 types, 4 molecules

#6: Chemical
ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H20N6O5S

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.76 Å3/Da / Density % sol: 55.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 1.7M DL-malic acid, 0.1M potassium sodium tartrate tetrahydrate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 11, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 3.12→25 Å / Num. obs: 74336 / % possible obs: 97.3 % / Redundancy: 2.3 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 22.5
Reflection shellResolution: 3.13→3.21 Å

-
Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PLA

3pla


Resolution: 3.129→24.859 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 25.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2338 2002 2.7 %
Rwork0.178 --
obs0.1796 74281 96.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.129→24.859 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23100 3508 0 0 26608
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01327398
X-RAY DIFFRACTIONf_angle_d1.47937798
X-RAY DIFFRACTIONf_dihedral_angle_d18.83216452
X-RAY DIFFRACTIONf_chiral_restr0.1734441
X-RAY DIFFRACTIONf_plane_restr0.0064241
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1292-3.20730.31851310.24534930X-RAY DIFFRACTION93
3.2073-3.29380.29561520.2355201X-RAY DIFFRACTION98
3.2938-3.39050.31471440.22775220X-RAY DIFFRACTION98
3.3905-3.49970.27531510.21685235X-RAY DIFFRACTION98
3.4997-3.62440.26991290.20025224X-RAY DIFFRACTION98
3.6244-3.7690.291610.19975198X-RAY DIFFRACTION98
3.769-3.93990.23491380.18565200X-RAY DIFFRACTION97
3.9399-4.14680.25921430.17515147X-RAY DIFFRACTION97
4.1468-4.40520.18251460.15955209X-RAY DIFFRACTION97
4.4052-4.74320.19961360.15425180X-RAY DIFFRACTION97
4.7432-5.21650.20391410.16045176X-RAY DIFFRACTION97
5.2165-5.96230.25141470.17185169X-RAY DIFFRACTION97
5.9623-7.47780.20871430.17265145X-RAY DIFFRACTION96
7.4778-24.85930.19411400.14925045X-RAY DIFFRACTION95

+
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