[English] 日本語
Yorodumi
- PDB-5w0o: Structure of human TUT7 catalytic module (CM) in complex with dsRNA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5w0o
TitleStructure of human TUT7 catalytic module (CM) in complex with dsRNA
Components
  • Terminal uridylyltransferase 7
  • double-stranded RNA
KeywordsTRANSFERASE/RNA / terminal uridyltransferase / TUTase / TRANSFERASE-RNA complex
Function / homology
Function and homology information


polyuridylation-dependent mRNA catabolic process / uridylyltransferase activity / transposable element silencing by mRNA destabilization / RNA uridylyltransferase / RNA 3'-end processing / RNA uridylyltransferase activity / Z-decay: degradation of maternal mRNAs by zygotically expressed factors / miRNA metabolic process / Deadenylation of mRNA / pre-miRNA processing ...polyuridylation-dependent mRNA catabolic process / uridylyltransferase activity / transposable element silencing by mRNA destabilization / RNA uridylyltransferase / RNA 3'-end processing / RNA uridylyltransferase activity / Z-decay: degradation of maternal mRNAs by zygotically expressed factors / miRNA metabolic process / Deadenylation of mRNA / pre-miRNA processing / oocyte maturation / miRNA binding / Zygotic genome activation (ZGA) / RNA binding / zinc ion binding / nucleoplasm / cytosol / cytoplasm
Similarity search - Function
Unstructured region 4 on terminal uridylyltransferase 7 / TUTase nucleotidyltransferase domain / TUTase nucleotidyltransferase domain / PAP/25A-associated / Cid1 family poly A polymerase / : / Poly(A) RNA polymerase, mitochondrial-like, central palm domain / Matrin/U1-C-like, C2H2-type zinc finger / U1-like zinc finger / Nucleotidyltransferase superfamily ...Unstructured region 4 on terminal uridylyltransferase 7 / TUTase nucleotidyltransferase domain / TUTase nucleotidyltransferase domain / PAP/25A-associated / Cid1 family poly A polymerase / : / Poly(A) RNA polymerase, mitochondrial-like, central palm domain / Matrin/U1-C-like, C2H2-type zinc finger / U1-like zinc finger / Nucleotidyltransferase superfamily / Zinc finger C2H2 type domain signature. / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile.
Similarity search - Domain/homology
URIDINE 5'-TRIPHOSPHATE / RNA / RNA (> 10) / Terminal uridylyltransferase 7
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.488 Å
AuthorsFaehnle, C.R. / Walleshauser, J. / Joshua-Tor, L.
CitationJournal: Nat. Struct. Mol. Biol. / Year: 2017
Title: Multi-domain utilization by TUT4 and TUT7 in control of let-7 biogenesis.
Authors: Faehnle, C.R. / Walleshauser, J. / Joshua-Tor, L.
History
DepositionMay 31, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 28, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 19, 2017Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Aug 16, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 4, 2023Group: 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: Terminal uridylyltransferase 7
B: Terminal uridylyltransferase 7
C: double-stranded RNA
D: double-stranded RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,0686
Polymers99,0994
Non-polymers9682
Water90150
1
A: Terminal uridylyltransferase 7
C: double-stranded RNA
D: double-stranded RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,8184
Polymers54,3343
Non-polymers4841
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3630 Å2
ΔGint-28 kcal/mol
Surface area20690 Å2
MethodPISA
2
B: Terminal uridylyltransferase 7
C: double-stranded RNA
D: double-stranded RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,8184
Polymers54,3343
Non-polymers4841
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3910 Å2
ΔGint-31 kcal/mol
Surface area20040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.825, 80.851, 181.830
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Terminal uridylyltransferase 7 / TUT7 / TUTase 7 / Zinc finger CCHC domain-containing protein 6


Mass: 44765.824 Da / Num. of mol.: 2
Fragment: nucleotidyltransferase domain (UNP residues 983-1365)
Mutation: D1160A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ZCCHC6, HS2, KIAA1711, TUT7 / Plasmid: Multi-Bac, pFL / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf9 / References: UniProt: Q5VYS8, RNA uridylyltransferase
#2: RNA chain double-stranded RNA


Mass: 4783.889 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-UTP / URIDINE 5'-TRIPHOSPHATE


Mass: 484.141 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H15N2O15P3 / Comment: UTP*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / 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: 2.48 Å3/Da / Density % sol: 50.37 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2 M ammonium acetate, 0.1 M trisodium citrate, pH 5.5, 14% PEG400

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 6, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.488→181.832 Å / Num. obs: 35240 / % possible obs: 99.5 % / Redundancy: 4.7 % / Biso Wilson estimate: 61.69 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.049 / Net I/σ(I): 19.4
Reflection shellResolution: 2.488→2.51 Å / Rmerge(I) obs: 0.734 / CC1/2: 0.733

-
Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
SCALAdata scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5W0M

5w0m


Resolution: 2.488→45.458 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2542 1774 5.05 %
Rwork0.2054 33375 -
obs0.2079 35149 99.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 171.04 Å2 / Biso mean: 78.5625 Å2 / Biso min: 36.58 Å2
Refinement stepCycle: final / Resolution: 2.488→45.458 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5337 640 58 50 6085
Biso mean--62.53 61.76 -
Num. residues----685
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066236
X-RAY DIFFRACTIONf_angle_d0.98584
X-RAY DIFFRACTIONf_chiral_restr0.049978
X-RAY DIFFRACTIONf_plane_restr0.005961
X-RAY DIFFRACTIONf_dihedral_angle_d14.7273645
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4881-2.55540.31931250.271225292654100
2.5554-2.63060.33711600.267925112671100
2.6306-2.71550.3441410.270325432684100
2.7155-2.81250.32741320.255125282660100
2.8125-2.92510.3461240.257925982722100
2.9251-3.05820.24631220.249325572679100
3.0582-3.21940.30841210.245625842705100
3.2194-3.4210.28411190.227225672686100
3.421-3.6850.2571340.208525882722100
3.685-4.05570.2251630.186225662729100
4.0557-4.6420.22211200.160126062726100
4.642-5.84650.22221690.180926322801100
5.8465-45.46510.24431440.1992566271093
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)
13.93091.6158-2.0883.6757-1.9582.7936-0.00770.67450.21760.0980.08620.3346-0.0906-0.2051-0.07290.3658-0.0903-0.05770.60970.02020.4752-46.365593.69.954
24.26681.0309-2.78983.683-0.68952.625-0.21890.51350.1425-0.29760.09610.0230.03850.02980.15460.2624-0.0439-0.08740.57570.07150.359-36.737294.49067.7353
34.55430.2767-1.90782.74350.56112.6948-0.4920.9291-1.0252-0.14070.03190.20770.7506-0.69590.31270.5775-0.22320.10980.5908-0.18470.736-48.269376.20829.8848
45.27120.0116-3.70242.0874-0.48196.7148-0.25570-1.4648-0.1027-0.2971-0.13220.44210.56060.46540.6146-0.0350.06860.46950.03470.9564-39.570473.422718.3325
57.5408-5.3002-0.49653.78370.8675.464-0.4444-0.90990.62440.68190.417-0.0037-0.9070.09470.18620.9134-0.09190.01520.5367-0.01690.6175-54.026588.832333.4984
62.8431-1.50090.50843.62051.42121.7301-0.0168-0.2371-0.37580.542-0.0830.41920.4354-0.23020.13030.76450.0050.0710.47470.04370.5605-15.03967.485863.6873
74.76971.18521.96426.95271.89216.71-0.00940.96260.3944-0.84410.1047-0.1945-0.0630.5316-0.16530.61420.03190.09910.4930.10860.4871-2.079369.633950.5413
83.20970.16750.41172.73730.04543.16960.0201-0.37270.40130.3944-0.20030.5195-0.4884-0.36880.18870.7280.12440.12320.4683-0.05740.5929-18.79385.000270.3375
97.7244-5.8756-3.00775.4482.82123.78390.86751.04962.6488-1.3524-0.58430.4727-1.577-0.3061-0.40681.27980.1492-0.05830.44820.04421.2456-12.7292100.693559.792
106.56051.73860.13443.46721.34882.413-0.08770.73390.5459-0.3326-0.10950.6696-0.5353-0.37240.15630.6420.2129-0.09540.45980.0030.6905-24.806385.969956.9022
112.2933-0.9644.11370.1482-1.74786.12250.10690.7052-0.05850.1657-0.1230.11920.35070.8324-0.00950.8172-0.0122-0.12191.0070.33350.7666-15.777188.199228.4932
121.5038-0.38353.68511.41-1.83186.88620.1310.825-0.0845-0.5420.0950.21960.08810.6705-0.10190.8590.0307-0.16411.0690.29890.7984-13.365588.187134.3499
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resseq 987:1074)A987 - 1074
2X-RAY DIFFRACTION2(chain A and resseq 1075:1153)A1075 - 1153
3X-RAY DIFFRACTION3(chain A and resseq 1154:1248)A1154 - 1248
4X-RAY DIFFRACTION4(chain A and resseq 1249:1318)A1249 - 1318
5X-RAY DIFFRACTION5(chain A and resseq 1319:1336)A1319 - 1336
6X-RAY DIFFRACTION6(chain B and resseq 992:1067)B992 - 1067
7X-RAY DIFFRACTION7(chain B and resseq 1068:1123)B1068 - 1123
8X-RAY DIFFRACTION8(chain B and resseq 1124:1266)B1124 - 1266
9X-RAY DIFFRACTION9(chain B and resseq 1267:1273)B1267 - 1273
10X-RAY DIFFRACTION10(chain B and resseq 1276:1332)B1276 - 1332
11X-RAY DIFFRACTION11(chain C and resseq 1:15)C1 - 15
12X-RAY DIFFRACTION12(chain D and resseq 1:15)D1 - 15

+
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