[English] 日本語
Yorodumi
- PDB-5xq2: Crystal structure of T. thermophilus Argonaute protein complexed ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5xq2
TitleCrystal structure of T. thermophilus Argonaute protein complexed with a bulge 5A6 on the guide strand
Components
  • DNA (5'-D(*AP*CP*AP*AP*CP*CP*TP*AP*CP*TP*AP*CP*CP*TP*CP*G)-3')
  • DNA (5'-D(*AP*GP*T)-3')
  • DNA (5'-D(P*TP*GP*AP*AP*GP*AP*TP*AP*GP*TP*AP*GP*GP*TP*TP*GP*T)-3')
  • TtAgo (D546N)
KeywordsDNA BINDING PROTEIN / Argonaute / miRNA / bulge / mismatch
Function / homology
Function and homology information


Hydrolases; Acting on ester bonds; Site specific endodeoxyribonucleases: cleavage is not sequence specific (deleted sub-subclass) / clearance of foreign intracellular DNA / DNA endonuclease activity / manganese ion binding / DNA replication / DNA binding / RNA binding
Similarity search - Function
paz domain - #50 / Argonaute, PAZ domain / : / : / Argonaute PAZ domain / Argonaute, N-terminal domain / Argonaute, middle domain / paz domain / Piwi domain profile. / Piwi domain ...paz domain - #50 / Argonaute, PAZ domain / : / : / Argonaute PAZ domain / Argonaute, N-terminal domain / Argonaute, middle domain / paz domain / Piwi domain profile. / Piwi domain / Piwi domain / Piwi / PAZ domain profile. / PAZ domain / Response regulator / Ribonuclease H-like superfamily/Ribonuclease H / Beta Complex / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Protein argonaute
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.33 Å
AuthorsSheng, G. / Gogakos, T. / Wang, J. / Zhao, H. / Serganov, A. / Juranek, S. / Tuschl, T. / Patel, D. / Wang, Y.
Funding support China, 4items
OrganizationGrant numberCountry
Natural Science Foundation of China31571335 China
Natural Science Foundation of China31630015 China
Natural Science Foundation of China91440201 China
Chinese Ministry of Science and Technology2014CB910102 China
CitationJournal: Nucleic Acids Res. / Year: 2017
Title: Structure/cleavage-based insights into helical perturbations at bulge sites within T. thermophilus Argonaute silencing complexes
Authors: Sheng, G. / Gogakos, T. / Wang, J. / Zhao, H. / Serganov, A. / Juranek, S. / Tuschl, T. / Patel, D.J. / Wang, Y.
History
DepositionJun 6, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 4, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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: TtAgo (D546N)
X: DNA (5'-D(P*TP*GP*AP*AP*GP*AP*TP*AP*GP*TP*AP*GP*GP*TP*TP*GP*T)-3')
Y: DNA (5'-D(*AP*CP*AP*AP*CP*CP*TP*AP*CP*TP*AP*CP*CP*TP*CP*G)-3')
C: DNA (5'-D(*AP*GP*T)-3')
B: TtAgo (D546N)
E: DNA (5'-D(P*TP*GP*AP*AP*GP*AP*TP*AP*GP*TP*AP*GP*GP*TP*TP*GP*T)-3')
F: DNA (5'-D(*AP*CP*AP*AP*CP*CP*TP*AP*CP*TP*AP*CP*CP*TP*CP*G)-3')
D: DNA (5'-D(*AP*GP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,52810
Polymers180,4798
Non-polymers492
Water543
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20150 Å2
ΔGint-103 kcal/mol
Surface area62210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)201.843, 201.843, 201.843
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein TtAgo (D546N) / Uncharacterized protein


Mass: 76727.750 Da / Num. of mol.: 2 / Mutation: D546N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039) (bacteria)
Strain: HB27 / ATCC BAA-163 / DSM 7039 / Gene: TT_P0026 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q746M7

-
DNA chain , 3 types, 6 molecules XEYFCD

#2: DNA chain DNA (5'-D(P*TP*GP*AP*AP*GP*AP*TP*AP*GP*TP*AP*GP*GP*TP*TP*GP*T)-3')


Mass: 6901.473 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Thermus thermophilus (bacteria)
#3: DNA chain DNA (5'-D(*AP*CP*AP*AP*CP*CP*TP*AP*CP*TP*AP*CP*CP*TP*CP*G)-3')


Mass: 5708.726 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Thermus thermophilus (bacteria)
#4: DNA chain DNA (5'-D(*AP*GP*T)-3')


Mass: 901.648 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Thermus thermophilus (bacteria)

-
Non-polymers , 2 types, 5 molecules

#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 3.8 Å3/Da / Density % sol: 67.61 %
Crystal growTemperature: 308 K / Method: vapor diffusion, hanging drop
Details: 2.8 M Na-acetate, pH7.0, 0.1M Tris-Cl, pH 8.0 and 0.15 M glycine

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97852 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jan 4, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97852 Å / Relative weight: 1
ReflectionResolution: 3.32→50 Å / Num. obs: 40665 / % possible obs: 100 % / Redundancy: 33.8 % / Rmerge(I) obs: 0.106 / Net I/σ(I): 45.5
Reflection shellResolution: 3.32→3.38 Å / Redundancy: 26.4 % / Rmerge(I) obs: 0.908 / Mean I/σ(I) obs: 4.2 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-2000data processing
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4KPY

4kpy


Resolution: 3.33→48.95 Å / SU ML: 0.48 / Cross valid method: FREE R-VALUE / σ(F): 2.15 / Phase error: 28.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.294 1846 4.95 %
Rwork0.252 --
obs0.254 37315 92.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.33→48.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10369 1470 2 3 11844
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01312268
X-RAY DIFFRACTIONf_angle_d1.70316996
X-RAY DIFFRACTIONf_dihedral_angle_d24.6894590
X-RAY DIFFRACTIONf_chiral_restr0.1441881
X-RAY DIFFRACTIONf_plane_restr0.0091968
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3246-3.41440.2925180.2578366X-RAY DIFFRACTION13
3.4144-3.51490.36481270.29422501X-RAY DIFFRACTION85
3.5149-3.62830.32951400.2782923X-RAY DIFFRACTION100
3.6283-3.75790.30541560.28722968X-RAY DIFFRACTION100
3.7579-3.90830.34351450.26932907X-RAY DIFFRACTION100
3.9083-4.08610.28831420.27072974X-RAY DIFFRACTION100
4.0861-4.30140.2751560.25262926X-RAY DIFFRACTION100
4.3014-4.57080.30581570.24942926X-RAY DIFFRACTION100
4.5708-4.92340.32171800.23692979X-RAY DIFFRACTION100
4.9234-5.41820.30481650.2442918X-RAY DIFFRACTION100
5.4182-6.20090.31381390.26343009X-RAY DIFFRACTION100
6.2009-7.80740.32411310.23463021X-RAY DIFFRACTION100
7.8074-48.95940.20271900.20593051X-RAY DIFFRACTION99

+
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