[English] 日本語
Yorodumi
- PDB-7ndk: Crystal structure of ZC3H12C PIN catalytic mutant -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7ndk
TitleCrystal structure of ZC3H12C PIN catalytic mutant
ComponentsProbable ribonuclease ZC3H12C
KeywordsRNA BINDING PROTEIN / Endo-ribonuclease / Regnase
Function / homology
Function and homology information


endonuclease activity / Hydrolases; Acting on ester bonds / zinc ion binding
Similarity search - Function
Rege-1, UBA-like domain / Endoribonuclease Regnase 1/ZC3H12, C-terminal domain / UBA-like domain / Endoribonuclease Regnase 1/ ZC3H12 C-terminal domain / Ribonuclease Zc3h12a-like, NYN domain / : / Zc3h12a-like Ribonuclease NYN domain / Rossmann fold - #11980 / Zinc finger, CCCH-type / Zinc finger C3H1-type profile. ...Rege-1, UBA-like domain / Endoribonuclease Regnase 1/ZC3H12, C-terminal domain / UBA-like domain / Endoribonuclease Regnase 1/ ZC3H12 C-terminal domain / Ribonuclease Zc3h12a-like, NYN domain / : / Zc3h12a-like Ribonuclease NYN domain / Rossmann fold - #11980 / Zinc finger, CCCH-type / Zinc finger C3H1-type profile. / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Probable ribonuclease ZC3H12C
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.34 Å
AuthorsGarg, A. / Heinemann, U.
CitationJournal: Nucleic Acids Res. / Year: 2021
Title: PIN and CCCH Zn-finger domains coordinate RNA targeting in ZC3H12 family endoribonucleases.
Authors: Garg, A. / Roske, Y. / Yamada, S. / Uehata, T. / Takeuchi, O. / Heinemann, U.
History
DepositionFeb 1, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 19, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 2, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Probable ribonuclease ZC3H12C
B: Probable ribonuclease ZC3H12C
C: Probable ribonuclease ZC3H12C
D: Probable ribonuclease ZC3H12C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,6546
Polymers76,6084
Non-polymers462
Water1,69394
1
A: Probable ribonuclease ZC3H12C


Theoretical massNumber of molelcules
Total (without water)19,1521
Polymers19,1521
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Probable ribonuclease ZC3H12C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,1752
Polymers19,1521
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Probable ribonuclease ZC3H12C


Theoretical massNumber of molelcules
Total (without water)19,1521
Polymers19,1521
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Probable ribonuclease ZC3H12C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,1752
Polymers19,1521
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.753, 61.475, 111.620
Angle α, β, γ (deg.)90.000, 90.060, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Probable ribonuclease ZC3H12C / Zinc finger CCCH domain-containing protein 12C


Mass: 19151.951 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Zc3h12c, Kiaa1726 / Production host: Escherichia coli (E. coli)
References: UniProt: Q5DTV4, Hydrolases; Acting on ester bonds
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M KSCN, 20% PEG 3350 and 0.1 M Bis-Tris propane pH 6.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 2, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.521
11-h,-k,l20.479
ReflectionResolution: 2.34→38.75 Å / Num. obs: 21746 / % possible obs: 97 % / Redundancy: 2.25 % / CC1/2: 0.998 / Net I/σ(I): 10.19
Reflection shellResolution: 2.34→2.39 Å / Num. unique obs: 1417 / CC1/2: 0.629

-
Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
PDB_EXTRACT3.24data extraction
XDSdata scaling
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7NDI

7ndi


Resolution: 2.34→38.75 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.921 / SU B: 7.299 / SU ML: 0.189 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.07 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2748 1082 5 %RANDOM
Rwork0.2292 ---
obs0.2314 20656 96.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 141.13 Å2 / Biso mean: 61.591 Å2 / Biso min: 27.73 Å2
Baniso -1Baniso -2Baniso -3
1-35.81 Å20 Å24.11 Å2
2--22.95 Å2-0 Å2
3----58.76 Å2
Refinement stepCycle: final / Resolution: 2.34→38.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5130 0 2 94 5226
Biso mean--41.29 54.07 -
Num. residues----623
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0195241
X-RAY DIFFRACTIONr_bond_other_d0.0020.024994
X-RAY DIFFRACTIONr_angle_refined_deg1.2691.9617057
X-RAY DIFFRACTIONr_angle_other_deg0.938311550
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1065612
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.34423.258267
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.76115964
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1141552
X-RAY DIFFRACTIONr_chiral_restr0.0690.2756
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215702
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021130
LS refinement shellResolution: 2.34→2.398 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.411 76 -
Rwork0.319 1470 -
obs--94.21 %

+
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