[English] 日本語
Yorodumi
- PDB-6cih: Crystal structure of a group II intron lariat in the post-catalyt... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6cih
TitleCrystal structure of a group II intron lariat in the post-catalytic state
Components
  • RNA (5'-R(P*UP*GP*UP*UP*UP*AP*UP*UP*AP*AP*AP*AP*AP*C*-3')
  • RNA (696-MER)
KeywordsRNA / group II intron / RNA splicing / spliceosome / lariat
Function / homologyIRIDIUM HEXAMMINE ION / RNA / RNA (> 10) / RNA (> 100)
Function and homology information
Biological speciesPylaiella littoralis (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.676 Å
AuthorsChan, R.T. / Peters, J.K. / Robart, A.R. / Wiryaman, T. / Rajashankar, K.R. / Toor, N.
Funding support United States, 5items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5R01GM102216 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01GM123275 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5P41GM103403 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5T32GM007240 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5T32GM008326 United States
CitationJournal: Nat Commun / Year: 2018
Title: Structural basis for the second step of group II intron splicing.
Authors: Chan, R.T. / Peters, J.K. / Robart, A.R. / Wiryaman, T. / Rajashankar, K.R. / Toor, N.
History
DepositionFeb 23, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 21, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Mar 13, 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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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.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.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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: RNA (696-MER)
B: RNA (5'-R(P*UP*GP*UP*UP*UP*AP*UP*UP*AP*AP*AP*AP*AP*C*-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)219,637138
Polymers205,2702
Non-polymers14,368136
Water4,432246
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: Lariat intron and ligated exons show up as separate bands with denaturing gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15090 Å2
ΔGint-170 kcal/mol
Surface area97630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)163.639, 255.361, 136.786
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-745-

MG

21A-760-

MG

-
Components

-
RNA chain , 2 types, 2 molecules AB

#1: RNA chain RNA (696-MER)


Mass: 200851.984 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Pylaiella littoralis (eukaryote)
#2: RNA chain RNA (5'-R(P*UP*GP*UP*UP*UP*AP*UP*UP*AP*AP*AP*AP*AP*C*-3')


Mass: 4417.659 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Pylaiella littoralis (eukaryote)

-
Non-polymers , 4 types, 382 molecules

#3: Chemical...
ChemComp-IRI / IRIDIUM HEXAMMINE ION


Mass: 294.400 Da / Num. of mol.: 41 / Source method: obtained synthetically / Formula: H18IrN6
#4: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 86 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 246 / Source method: obtained synthetically / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.51 Å3/Da / Density % sol: 64.91 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.4 mM spermine, 21% 2-Methyl-2,4-pentanediol, 175 mM magnesium acetate tetrahydrate, and 90 mM MES monohydrate, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 303K, soaked in 3mM iridium hexammine

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.1052 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 12, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1052 Å / Relative weight: 1
ReflectionResolution: 3.676→81.83 Å / Num. obs: 31107 / % possible obs: 99.9 % / Redundancy: 6.8 % / Rsym value: 0.149 / Net I/σ(I): 6.4
Reflection shellResolution: 3.676→3.74 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 0.6 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXDEphasing
RefinementMethod to determine structure: MAD / Resolution: 3.676→81.82 Å / SU ML: 0.53 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 32.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2552 1994 6.41 %
Rwork0.2081 --
obs0.2112 31107 98.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.676→81.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 13479 628 0 14107
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0115587
X-RAY DIFFRACTIONf_angle_d1.16524728
X-RAY DIFFRACTIONf_dihedral_angle_d18.6237550
X-RAY DIFFRACTIONf_chiral_restr0.0493149
X-RAY DIFFRACTIONf_plane_restr0.005629
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.6761-3.7680.41491160.36721730X-RAY DIFFRACTION83
3.768-3.86990.37151410.35352045X-RAY DIFFRACTION99
3.8699-3.98380.35751430.32622088X-RAY DIFFRACTION100
3.9838-4.11240.32031430.30362088X-RAY DIFFRACTION100
4.1124-4.25940.32041430.29412091X-RAY DIFFRACTION100
4.2594-4.42990.37791430.27162077X-RAY DIFFRACTION100
4.4299-4.63150.31791430.25132083X-RAY DIFFRACTION100
4.6315-4.87560.291440.24532101X-RAY DIFFRACTION100
4.8756-5.18110.28851420.21282086X-RAY DIFFRACTION100
5.1811-5.5810.24161450.19682108X-RAY DIFFRACTION100
5.581-6.14250.26341460.18982120X-RAY DIFFRACTION100
6.1425-7.03090.25451450.18462132X-RAY DIFFRACTION100
7.0309-8.85650.22311470.1952144X-RAY DIFFRACTION100
8.8565-81.83970.19811530.15942220X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 24.7218 Å / Origin y: 32.5209 Å / Origin z: -10.4659 Å
111213212223313233
T0.9382 Å2-0.1736 Å2-0.1605 Å2-0.9865 Å20.0915 Å2--0.8467 Å2
L0.5484 °2-0.0014 °2-0.4226 °2-0.6782 °20.1263 °2--1.4995 °2
S-0.0981 Å °-0.2122 Å °-0.111 Å °-0.042 Å °0.104 Å °-0.1585 Å °-0.1411 Å °0.5864 Å °-0.036 Å °
Refinement TLS groupSelection details: all

+
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