[English] 日本語
Yorodumi
- PDB-7cqz: crystal structure of mouse FAM46C (TENT5C) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7cqz
Titlecrystal structure of mouse FAM46C (TENT5C)
ComponentsTerminal nucleotidyltransferase 5C
KeywordsGENE REGULATION / non-canonical poly(A) polymerase
Function / homology
Function and homology information


polynucleotide adenylyltransferase / poly(A) RNA polymerase activity / mRNA stabilization / negative regulation of cell differentiation / in utero embryonic development / centrosome / RNA binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Terminal nucleotidyltransferase / Nucleotidyltransferase / Domain of unknown function (DUF1693)
Similarity search - Domain/homology
Terminal nucleotidyltransferase 5C
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.34969764777 Å
AuthorsHu, J.L. / Zhang, H. / Gao, S.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31470729 China
National Natural Science Foundation of China (NSFC)31722016 China
National Natural Science Foundation of China (NSFC)81772977 China
CitationJournal: Cancer Commun (Lond) / Year: 2021
Title: Structural and functional characterization of multiple myeloma associated cytoplasmic poly(A) polymerase FAM46C.
Authors: Zhang, H. / Zhang, S.H. / Hu, J.L. / Wu, Y.T. / Ma, X.Y. / Chen, Y. / Yu, B. / Liao, S. / Huang, H. / Gao, S.
History
DepositionAug 12, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 9, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 4, 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 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Terminal nucleotidyltransferase 5C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,1453
Polymers40,0181
Non-polymers1282
Water43224
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-11 kcal/mol
Surface area16270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.827, 59.200, 173.432
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

#1: Protein Terminal nucleotidyltransferase 5C


Mass: 40017.539 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Tent5c, Fam46c / Production host: Escherichia coli (E. coli)
References: UniProt: Q5SSF7, polynucleotide adenylyltransferase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Cl
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / 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

CrystalDensity Matthews: 3.32 Å3/Da / Density % sol: 62.95 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.2 M sodium citrate tribasic pH 6.5, 16 % w/v PEG3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 5, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.34969764777→41.36 Å / Num. obs: 22719 / % possible obs: 98.7 % / Redundancy: 5.9 % / Biso Wilson estimate: 55.2759907965 Å2 / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.025 / Rrim(I) all: 0.061 / Net I/σ(I): 17.8
Reflection shellResolution: 2.35→2.48 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.572 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 3281 / Rpim(I) all: 0.252 / Rrim(I) all: 0.626 / % possible all: 99

-
Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.34969764777→26.34719568 Å / SU ML: 0.307589399968 / Cross valid method: FREE R-VALUE / σ(F): 1.33655770953 / Phase error: 27.477327327
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.246328775084 1999 8.82638643589 %
Rwork0.217499541187 20649 -
obs0.220033268159 22648 98.461003391 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 75.2816701509 Å2
Refinement stepCycle: LAST / Resolution: 2.34969764777→26.34719568 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2685 0 7 24 2716
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.001471733127452738
X-RAY DIFFRACTIONf_angle_d0.3781050308553698
X-RAY DIFFRACTIONf_chiral_restr0.0368522536114421
X-RAY DIFFRACTIONf_plane_restr0.00241683142825479
X-RAY DIFFRACTIONf_dihedral_angle_d17.96789525241660
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3497-2.40840.3314619263531360.3008929945891404X-RAY DIFFRACTION97.9020979021
2.4084-2.47350.3119412036031450.30202315811506X-RAY DIFFRACTION99.7583081571
2.4735-2.54620.3296110060461410.2759734542771449X-RAY DIFFRACTION99.8743718593
2.5462-2.62830.3247329734711420.2848390129491461X-RAY DIFFRACTION99.8753894081
2.6283-2.72220.3168364268431450.2733759473561493X-RAY DIFFRACTION100
2.7222-2.8310.3265009234831420.2753942716131471X-RAY DIFFRACTION99.7526283241
2.831-2.95970.3429959100161410.2822931538931471X-RAY DIFFRACTION99.7524752475
2.9597-3.11550.2731446948931450.2535948996991492X-RAY DIFFRACTION100
3.1155-3.31040.2780604536661440.2477104054221488X-RAY DIFFRACTION99.9387630129
3.3104-3.56540.2774853662211440.2398392303521486X-RAY DIFFRACTION99.8774509804
3.5654-3.92320.2451594669471460.2121256354291507X-RAY DIFFRACTION99.7585998793
3.9232-4.48850.1869784264431460.1771724667031509X-RAY DIFFRACTION99.6987951807
4.4885-5.64580.197333594951500.1662414393021541X-RAY DIFFRACTION99.7051886792
5.6458-26.347195680.215417470931320.1978799790041371X-RAY DIFFRACTION83.9195979899
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)
12.301846330941.478388160671.009444915984.982386002640.8991413797014.702026647320.222728732695-0.220450380295-0.1606762374410.0288258598842-0.282302527957-0.03365957336770.396246013058-0.2351628396730.08560826778760.4760972118340.0129076049754-0.09441364137640.413594835910.01065531633830.3571538853471.74951991368-22.9874802937-31.6552421992
23.5521722567-0.3441304682532.617805013776.527941255-0.769642404537.45243866434-0.135998154654-0.2739380120610.26746868591-0.546816231878-0.09996646398370.210362932206-1.43652567513-0.2712915346940.1721370139970.7097776111590.0181812313525-0.07632305234630.423791109119-0.02813513266710.4879596432164.9895396536-3.20035190823-22.1635018746
34.84301330053-1.94594516230.6686309057964.09901605712-0.6454085686486.31807723856-0.157920835861-0.508325118881-0.2993089310210.05685021771710.05687243604580.0736917983781-0.0584434294669-0.01746761056850.1231207906440.298935202108-0.138701820323-0.03431741727140.7921866370870.004396231721270.48807347376712.3292103776-14.6906579625-5.4070681882
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 10 through 210 )
2X-RAY DIFFRACTION2chain 'A' and (resid 211 through 240 )
3X-RAY DIFFRACTION3chain 'A' and (resid 241 through 343 )

+
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