[English] 日本語
Yorodumi
- PDB-3nmu: Crystal Structure of substrate-bound halfmer box C/D RNP -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3nmu
TitleCrystal Structure of substrate-bound halfmer box C/D RNP
Components
  • 50S ribosomal protein L7Ae
  • Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase
  • NOP5/NOP56 related protein
  • RNA (34-MER)
  • RNA (5'-R(*GP*AP*GP*CP*UP*UP*CP*AP*AP*CP*GP*GP*C)-3')
KeywordsTransferase/RNA / Kink-turn motif / RNA assembly motif / 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 / tRNA processing / snoRNA binding / Transferases; Transferring one-carbon groups; Methyltransferases / rRNA processing ...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 / tRNA processing / snoRNA binding / Transferases; Transferring one-carbon groups; Methyltransferases / rRNA processing / 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 / : / Helix hairpin bin domain superfamily / Nucleolar protein Nop56/Nop58 / rRNA 2'-O-methyltransferase fibrillarin-like / Fibrillarin, conserved site ...Nucleotidyltransferase; domain 5 - #220 / Helix Hairpins - #4070 / Nop domain / : / Archaeal Nop5/56-rel, N-terminal domain / : / Helix hairpin bin domain superfamily / 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-ADENOSYLMETHIONINE / RNA / RNA (> 10) / Large ribosomal subunit protein eL8 / NOP5/NOP56 related protein / Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.729 Å
AuthorsLi, H. / Xue, S. / Wang, R.
CitationJournal: Mol.Cell / Year: 2010
Title: Structural basis for substrate placement by an archaeal box C/D ribonucleoprotein particle.
Authors: Xue, S. / Wang, R. / Yang, F. / Terns, R.M. / Terns, M.P. / Zhang, X. / Maxwell, E.S. / Li, H.
History
DepositionJun 22, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: NOP5/NOP56 related protein
B: NOP5/NOP56 related protein
C: 50S ribosomal protein L7Ae
D: RNA (34-MER)
E: RNA (34-MER)
F: Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase
G: 50S ribosomal protein L7Ae
J: Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase
I: RNA (5'-R(*GP*AP*GP*CP*UP*UP*CP*AP*AP*CP*GP*GP*C)-3')
K: RNA (5'-R(*GP*AP*GP*CP*UP*UP*CP*AP*AP*CP*GP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)201,01312
Polymers200,21610
Non-polymers7972
Water48627
1
A: NOP5/NOP56 related protein
D: RNA (34-MER)
F: Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase
G: 50S ribosomal protein L7Ae
I: RNA (5'-R(*GP*AP*GP*CP*UP*UP*CP*AP*AP*CP*GP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,5076
Polymers100,1085
Non-polymers3981
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10320 Å2
ΔGint-60 kcal/mol
Surface area37820 Å2
MethodPISA
2
B: NOP5/NOP56 related protein
C: 50S ribosomal protein L7Ae
E: RNA (34-MER)
J: Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase
K: RNA (5'-R(*GP*AP*GP*CP*UP*UP*CP*AP*AP*CP*GP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,5076
Polymers100,1085
Non-polymers3981
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10300 Å2
ΔGint-65 kcal/mol
Surface area37440 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24320 Å2
ΔGint-152 kcal/mol
Surface area71560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)293.506, 94.054, 96.810
Angle α, β, γ (deg.)90.00, 101.47, 90.00
Int Tables number5
Space group name H-MC121

-
Components

-
Protein , 3 types, 6 molecules ABCGFJ

#1: Protein NOP5/NOP56 related protein


Mass: 43937.555 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Gene: PF0060 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8U4M1
#2: Protein 50S ribosomal protein L7Ae


Mass: 14243.545 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Gene: rpl7ae, PF1367 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8U160
#4: Protein Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase


Mass: 26760.844 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Gene: flpA, PF0059 / Production host: Escherichia coli (E. coli)
References: UniProt: Q8U4M2, Transferases; Transferring one-carbon groups; Methyltransferases

-
RNA chain , 2 types, 4 molecules DEIK

#3: RNA chain RNA (34-MER)


Mass: 11009.606 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: box C/D RNA / Source: (gene. exp.) Pyrococcus furiosus (archaea)
#5: RNA chain RNA (5'-R(*GP*AP*GP*CP*UP*UP*CP*AP*AP*CP*GP*GP*C)-3')


Mass: 4156.542 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: The RNA was chemically synthesized

-
Non-polymers , 2 types, 29 molecules

#6: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H22N6O5S
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 3.4 Å3/Da / Density % sol: 63.86 %
Crystal growTemperature: 303 K / Method: vapor diffusion, hanging drop / pH: 7
Details: The complex was equilibrated with reservoir solutions containing 0-400 mM potassium chloride, 200 mM-1.5 M sodium chloride, 150-250 mM magnesium acetate, 200 mM ammonium acetate, 50 mM HEPES- ...Details: The complex was equilibrated with reservoir solutions containing 0-400 mM potassium chloride, 200 mM-1.5 M sodium chloride, 150-250 mM magnesium acetate, 200 mM ammonium acetate, 50 mM HEPES-NaOH (pH 7.0), and 0 5% PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 303K

-
Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. all: 63177 / Num. obs: 61445 / % possible obs: 89.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 3 / Redundancy: 5.8 % / Biso Wilson estimate: 56.33 Å2 / Rsym value: 0.074
Reflection shellResolution: 2.7→2.8 Å / % possible all: 58.1

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
PHENIX(phenix.refine: 1.5_2)refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.729→33.572 Å / SU ML: 0.34 / σ(F): 0 / Phase error: 34.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2845 1789 3.26 %
Rwork0.2218 --
obs0.2238 54883 79.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.602 Å2 / ksol: 0.297 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-50.8446 Å20 Å217.4718 Å2
2---26.8336 Å2-0 Å2
3----24.011 Å2
Refinement stepCycle: LAST / Resolution: 2.729→33.572 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11458 1994 52 27 13531
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113955
X-RAY DIFFRACTIONf_angle_d1.49119289
X-RAY DIFFRACTIONf_dihedral_angle_d19.1025661
X-RAY DIFFRACTIONf_chiral_restr0.12214
X-RAY DIFFRACTIONf_plane_restr0.0082127
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.729-2.80310.4137760.32682307X-RAY DIFFRACTION45
2.8031-2.88560.3698900.3262642X-RAY DIFFRACTION52
2.8856-2.97870.3908950.30592998X-RAY DIFFRACTION59
2.9787-3.0850.35821160.30023481X-RAY DIFFRACTION68
3.085-3.20850.40071300.29523845X-RAY DIFFRACTION76
3.2085-3.35440.32421420.28394220X-RAY DIFFRACTION83
3.3544-3.5310.35581520.25724454X-RAY DIFFRACTION87
3.531-3.7520.29181580.23384559X-RAY DIFFRACTION89
3.752-4.04120.31351580.20984650X-RAY DIFFRACTION91
4.0412-4.44710.23311620.18664793X-RAY DIFFRACTION94
4.4471-5.08870.23921670.19084902X-RAY DIFFRACTION95
5.0887-6.40390.27221700.23175056X-RAY DIFFRACTION98
6.4039-33.57420.2371730.17975187X-RAY DIFFRACTION99

+
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