[English] 日本語
Yorodumi
- PDB-1hc8: CRYSTAL STRUCTURE OF A CONSERVED RIBOSOMAL PROTEIN-RNA COMPLEX -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1hc8
TitleCRYSTAL STRUCTURE OF A CONSERVED RIBOSOMAL PROTEIN-RNA COMPLEX
Components
  • 58 NUCLEOTIDE RIBOSOMAL 23S RNA DOMAIN
  • RIBOSOMAL PROTEIN L11
KeywordsRIBOSOME / RIBOSOMAL RNA / TERTIARY STRUCTURE / RNA-PROTEIN
Function / homology
Function and homology information


large ribosomal subunit rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / DNA binding
Similarity search - Function
Ribosomal protein L11/L12, C-terminal domain / Ribosomal protein L11, bacterial-type / Ribosomal protein L11, conserved site / Ribosomal protein L11 signature. / Ribosomal protein L11, N-terminal / Ribosomal protein L11, N-terminal domain / Ribosomal protein L11/L12 / Ribosomal protein L11, C-terminal / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein L11/L12, N-terminal domain superfamily ...Ribosomal protein L11/L12, C-terminal domain / Ribosomal protein L11, bacterial-type / Ribosomal protein L11, conserved site / Ribosomal protein L11 signature. / Ribosomal protein L11, N-terminal / Ribosomal protein L11, N-terminal domain / Ribosomal protein L11/L12 / Ribosomal protein L11, C-terminal / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein L11/L12 / Ribosomal protein L11, RNA binding domain / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
: / OSMIUM ION / RNA / RNA (> 10) / Large ribosomal subunit protein uL11
Similarity search - Component
Biological speciesBACILLUS STEAROTHERMOPHILUS (bacteria)
ESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.8 Å
AuthorsConn, G.L. / Draper, D.E. / Lattman, E.E. / Gittis, A.G.
Citation
Journal: J.Mol.Biol. / Year: 2002
Title: A Compact RNA Tertiary Structure Contains a Buried Backbone-K+ Complex
Authors: Conn, G.L. / Gittis, A.G. / Lattman, E.E. / Misra, V.K. / Draper, D.E.
#1: Journal: Science / Year: 1999
Title: Crystal Structure of a Conserved Ribosomal Protein-RNA Complex
Authors: Conn, G.L. / Draper, D.E. / Lattman, E.E. / Gittis, A.G.
History
DepositionApr 27, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 23, 2002Provider: 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 / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: RIBOSOMAL PROTEIN L11
B: RIBOSOMAL PROTEIN L11
C: 58 NUCLEOTIDE RIBOSOMAL 23S RNA DOMAIN
D: 58 NUCLEOTIDE RIBOSOMAL 23S RNA DOMAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,45531
Polymers54,1054
Non-polymers1,35027
Water23413
1
A: RIBOSOMAL PROTEIN L11
C: 58 NUCLEOTIDE RIBOSOMAL 23S RNA DOMAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,71515
Polymers27,0532
Non-polymers66313
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: RIBOSOMAL PROTEIN L11
D: 58 NUCLEOTIDE RIBOSOMAL 23S RNA DOMAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,74016
Polymers27,0532
Non-polymers68714
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)150.675, 150.675, 63.841
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.043157, -0.998994, -0.012207), (-0.392208, -0.005704, -0.919859), (0.918863, 0.044486, -0.39206)
Vector: 166.83, 180.4792, -58.8074)
DetailsCOMPLEX OF THE RIBOSOMAL PROTEIN L11 AND THERIBOSOMAL 23S RNA FRAGMENT

-
Components

-
Protein / RNA chain , 2 types, 4 molecules ABCD

#1: Protein RIBOSOMAL PROTEIN L11


Mass: 8167.547 Da / Num. of mol.: 2 / Fragment: C-TERMINAL DOMAIN OF RIBOSOMAL PROTEIN L11
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACILLUS STEAROTHERMOPHILUS (bacteria) / Plasmid: PET11 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P56210
#2: RNA chain 58 NUCLEOTIDE RIBOSOMAL 23S RNA DOMAIN


Mass: 18885.150 Da / Num. of mol.: 2 / Fragment: NTS 1051-1108 FROM E. COLI 23S RRNA / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli)
Description: RNA SYNTHESIZED BY IN VITRO TRANSCRIPTION USING T7 RNA POLYMERASE
Production host: ESCHERICHIA COLI (E. coli)

-
Non-polymers , 4 types, 40 molecules

#3: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#5: Chemical
ChemComp-OS / OSMIUM ION


Mass: 190.230 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Os
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Formula: H2O

-
Details

Compound detailsCHAIN C, D ENGINEERED MUTATION U1601A

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.35 Å3/Da / Density % sol: 70 %
Crystal growpH: 6.5
Details: PEG 600, MAGNESIUM ACETATE, COBALT HEXAMINE CHLORIDE, SODIUM CACODYLATE, KCL, pH 6.50
Crystal grow
*PLUS
Temperature: 37 ℃ / pH: 6.5 / Method: vapor diffusion, sitting drop / Details: Conn, G.L., (1999) Science, 284, 1171.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
150 mMsodium cacodylate1reservoir
215 %PEG6001reservoir
380 mM1reservoirMg(OAc)2
4100 mM1reservoirKCl
50.2 mM1reservoirCo(NH3)6Cl3

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 1.13951
DetectorType: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: Sep 9, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.13951 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. obs: 17542 / % possible obs: 94.5 % / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 75.5 Å2 / Rmerge(I) obs: 0.24 / Net I/σ(I): 5.9
Reflection shellResolution: 2.8→2.93 Å / Redundancy: 4 % / Rmerge(I) obs: 0.27 / % possible all: 88.7
Reflection
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 20 Å / Num. measured all: 89078 / Rmerge(I) obs: 0.55
Reflection shell
*PLUS
% possible obs: 88.7 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 5.9

-
Processing

Software
NameVersionClassification
CNS0.9refinement
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
RefinementMethod to determine structure: MAD / Resolution: 2.8→20 Å / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0
Stereochemistry target values: MAXIMUM LIKELIHOOD USING AMPLITUDES
RfactorNum. reflection% reflectionSelection details
Rfree0.253 1373 7.8 %RANDOM
Rwork0.217 ---
obs0.217 17542 94.5 %-
Solvent computationSolvent model: CNS
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1063 2504 27 13 3607
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.03
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.8→2.84 Å / Total num. of bins used: 27
RfactorNum. reflection% reflection
Rfree0.425 48 7.8 %
Rwork0.368 525 -
obs--88.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
LS refinement shell
*PLUS
Rfactor obs: 0.368

+
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