[English] 日本語
Yorodumi
- PDB-7ndj: Crystal structure of ZC3H12C PIN-CCCH Zn Finger domain with RNA h... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7ndj
TitleCrystal structure of ZC3H12C PIN-CCCH Zn Finger domain with RNA heptamer
Components
  • Probable ribonuclease ZC3H12C
  • RNA (5'-R(*UP*UP*AP*UP*UP*AP*U)-3')
KeywordsRNA BINDING PROTEIN / Endo-ribonuclease / Regnase
Function / homology
Function and homology information


RNA endonuclease activity / cytoplasmic ribonucleoprotein granule / Hydrolases; Acting on ester bonds / mRNA binding / nucleus / metal 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 / Zinc finger, CCCH-type / Zinc finger C3H1-type profile.
Similarity search - Domain/homology
RNA / Probable ribonuclease ZC3H12C
Similarity search - Component
Biological speciesMus musculus (house mouse)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.649 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 1.1May 26, 2021Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details
Revision 1.2Jun 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 1.3Jan 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: RNA (5'-R(*UP*UP*AP*UP*UP*AP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,72814
Polymers47,1203
Non-polymers60811
Water6,774376
1
A: Probable ribonuclease ZC3H12C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6975
Polymers22,4881
Non-polymers2094
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Probable ribonuclease ZC3H12C
C: RNA (5'-R(*UP*UP*AP*UP*UP*AP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0319
Polymers24,6322
Non-polymers3997
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.248, 63.248, 114.544
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41

-
Components

-
Protein / RNA chain , 2 types, 3 molecules ABC

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


Mass: 22488.010 Da / Num. of mol.: 2
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: RNA chain RNA (5'-R(*UP*UP*AP*UP*UP*AP*U)-3')


Mass: 2144.283 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

-
Non-polymers , 4 types, 387 molecules

#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 376 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.43 Å3/Da / Density % sol: 49.41 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 18% PEG 3350 and 0.2 M NaF pH 6.9

-
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 3, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.649→44.723 Å / Num. obs: 53908 / % possible obs: 99.5 % / Redundancy: 4.6 % / CC1/2: 0.998 / Net I/σ(I): 11.04
Reflection shellResolution: 1.649→1.75 Å / Num. unique obs: 8680 / CC1/2: 0.758

-
Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.24data extraction
XDSdata scaling
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7NDI

7ndi


Resolution: 1.649→44.723 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 24.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2082 2097 3.9 %
Rwork0.175 51736 -
obs0.1763 53833 99.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 128.66 Å2 / Biso mean: 36.1081 Å2 / Biso min: 15.21 Å2
Refinement stepCycle: final / Resolution: 1.649→44.723 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2891 121 35 376 3423
Biso mean--37.53 43.94 -
Num. residues----364
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.649-1.68720.32231380.3312339198
1.6872-1.72930.35821390.291343699
1.7293-1.77610.30431390.27413424100
1.7761-1.82840.27111390.2424344799
1.8284-1.88740.27471400.2316343199
1.8874-1.95480.25151390.2219344999
1.9548-2.03310.25811400.21083450100
2.0331-2.12560.21851400.18583458100
2.1256-2.23770.19861400.17463451100
2.2377-2.37790.22531400.17163447100
2.3779-2.56150.21181410.17163474100
2.5615-2.81920.19281390.1739342399
2.8192-3.22710.19061400.16933472100
3.2271-4.06530.21111420.14543486100
4.0653-44.7230.1531410.1426349799
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.1399-0.48570.42072.277-0.11824.32690.05110.08540.2387-0.0439-0.08770.0325-0.7204-0.1910.03340.28470.0197-0.00350.13250.00470.168463.27495.2984124.9211
24.288-0.43373.37660.8777-0.56213.55220.0898-0.1584-0.24720.03740.05790.12970.0466-0.0905-0.13520.19820.02530.03550.18540.00630.171560.0149-4.6428115.791
31.3479-0.5533-0.05782.95420.873.5976-0.0165-0.0222-0.09490.07210.0095-0.1520.04290.327-0.00360.15410.0078-0.01170.19960.02860.190171.9778-7.5211132.35
42.686-0.0320.32994.1850.17734.50360.21420.0201-0.24670.0023-0.0716-0.05610.76310.319-0.05990.25220.0584-0.02270.14210.0030.187399.5045-34.0494118.8056
51.1229-0.9434-0.04072.416-0.89014.08780.0996-0.0847-0.08130.07040.07190.34250.4665-0.4988-0.19260.2089-0.05090.01660.1960.00660.206689.9808-29.6718124.9981
65.03482.0518-1.8855.33542.21655.20440.2277-0.13370.291-0.1049-0.26750.4967-0.3617-0.58490.02530.20080.10120.02310.26520.03020.28683.3969-18.0922118.0763
72.17750.85550.88357.80460.8182.48430.21730.24380.3907-0.2335-0.2058-0.0461-0.34570.14750.03430.25760.03940.0820.2050.04470.220999.0766-18.2752108.6034
84.903-2.5486-0.62264.00651.00911.90960.1258-0.4757-0.72010.1091-0.4719-0.20621.95191.09810.23470.85030.23870.03370.48570.14040.4551103.040512.5738105.1933
92.1209-0.5364-0.24860.14390.06470.0357-0.2059-0.32051.23210.0730.33520.4308-1.1333-0.6897-0.04410.72380.1547-0.01450.434-0.02430.6945113.445813.7292106.8168
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 132 through 204 )A132 - 204
2X-RAY DIFFRACTION2chain 'A' and (resid 205 through 236 )A205 - 236
3X-RAY DIFFRACTION3chain 'A' and (resid 237 through 297 )A237 - 297
4X-RAY DIFFRACTION4chain 'B' and (resid 132 through 204 )B132 - 204
5X-RAY DIFFRACTION5chain 'B' and (resid 205 through 246 )B205 - 246
6X-RAY DIFFRACTION6chain 'B' and (resid 247 through 263 )B247 - 263
7X-RAY DIFFRACTION7chain 'B' and (resid 264 through 300 )B264 - 300
8X-RAY DIFFRACTION8chain 'B' and (resid 301 through 323 )B301 - 323
9X-RAY DIFFRACTION9chain 'C' and (resid 1 through 7 )C1 - 7

+
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