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

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5xou
TitleCrystal structure of T. thermophilus Argonaute protein complexed with a bulge 7T8 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(P*TP*GP*AP*GP*GP*TP*AP*TP*GP*GP*TP*TP*GP*T)-3')
  • TtAgo (D546N)
KeywordsDNA BINDING PROTEIN / Argonaute / Bulge / miRNA / 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
Argonaute, PAZ domain / : / : / Argonaute PAZ domain / Argonaute, N-terminal domain / Argonaute, middle domain / Piwi domain profile. / Piwi domain / Piwi domain / Piwi ...Argonaute, PAZ domain / : / : / Argonaute PAZ domain / Argonaute, N-terminal domain / Argonaute, middle domain / Piwi domain profile. / Piwi domain / Piwi domain / Piwi / PAZ domain profile. / PAZ domain / Ribonuclease H superfamily / Ribonuclease H-like superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / Protein argonaute
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.63 Å
AuthorsSheng, G. / Wang, J. / Zhao, H. / 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
DepositionMay 31, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 4, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2017Group: Structure summary / Category: entity / entity_name_com / struct
Item: _entity.pdbx_description / _entity_name_com.name / _struct.pdbx_descriptor
Revision 1.2Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: TtAgo (D546N)
B: TtAgo (D546N)
C: DNA (5'-D(P*TP*GP*AP*GP*GP*TP*AP*TP*GP*GP*TP*TP*GP*T)-3')
D: DNA (5'-D(*AP*CP*AP*AP*CP*CP*TP*AP*CP*TP*AP*CP*CP*TP*CP*G)-3')
E: DNA (5'-D(P*TP*GP*AP*GP*GP*TP*AP*TP*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')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)178,7068
Polymers178,6586
Non-polymers492
Water34219
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16530 Å2
ΔGint-95 kcal/mol
Surface area49990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.747, 114.982, 160.441
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN 'A' AND (RESSEQ 5:37 OR RESSEQ 42:47 OR RESSEQ...
211CHAIN 'B' AND (RESSEQ 5:37 OR RESSEQ 42:47 OR RESSEQ...
112CHAIN 'D' AND (RESSEQ 5:18 )
212CHAIN 'F' AND (RESSEQ 5:18 )

NCS ensembles :
ID
1
2

-
Components

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


Mass: 6892.458 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: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 19 / 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: 2.91 Å3/Da / Density % sol: 57.74 %
Crystal growTemperature: 308 K / Method: vapor diffusion, hanging drop
Details: 3.0 M NaAc.3H2O, 100 mM Bis-Tris propane, pH 7.0-7.2

-
Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 60975 / % possible obs: 97.5 % / Redundancy: 4.9 % / Net I/σ(I): 17.7
Reflection shellResolution: 2.63→2.72 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 2 / % possible all: 95.3

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data processing
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4KPY

4kpy


Resolution: 2.63→43.17 Å / SU ML: 0.53 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 31.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.276 3091 5.07 %
Rwork0.235 --
obs0.237 60975 97.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.63→43.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8808 1267 2 19 10096
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01910435
X-RAY DIFFRACTIONf_angle_d2.44214426
X-RAY DIFFRACTIONf_dihedral_angle_d19.293951
X-RAY DIFFRACTIONf_chiral_restr0.1391600
X-RAY DIFFRACTIONf_plane_restr0.0161663
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A4067X-RAY DIFFRACTIONPOSITIONAL0.2
12B4067X-RAY DIFFRACTIONPOSITIONAL0.2
21D272X-RAY DIFFRACTIONPOSITIONAL0.038
22F272X-RAY DIFFRACTIONPOSITIONAL0.038
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.629-2.67010.46861340.48482335X-RAY DIFFRACTION88
2.6701-2.71390.42691250.43062532X-RAY DIFFRACTION95
2.7139-2.76070.40261320.36632648X-RAY DIFFRACTION98
2.7607-2.81080.37421690.35382624X-RAY DIFFRACTION98
2.8108-2.86490.36861430.32462605X-RAY DIFFRACTION99
2.8649-2.92340.37771210.30312663X-RAY DIFFRACTION98
2.9234-2.98690.3291410.28442652X-RAY DIFFRACTION99
2.9869-3.05640.30151570.26672610X-RAY DIFFRACTION99
3.0564-3.13280.31681360.24822676X-RAY DIFFRACTION99
3.1328-3.21750.26931290.23672685X-RAY DIFFRACTION99
3.2175-3.31210.29131570.22242642X-RAY DIFFRACTION99
3.3121-3.4190.26151430.22832627X-RAY DIFFRACTION98
3.419-3.54110.30121150.25062606X-RAY DIFFRACTION97
3.5411-3.68280.29771350.2632647X-RAY DIFFRACTION97
3.6828-3.85030.24451480.22032614X-RAY DIFFRACTION97
3.8503-4.05320.28061430.22642619X-RAY DIFFRACTION97
4.0532-4.30690.20761510.17292693X-RAY DIFFRACTION100
4.3069-4.63910.24081460.1612708X-RAY DIFFRACTION100
4.6391-5.10530.21851510.1682730X-RAY DIFFRACTION100
5.1053-5.84250.2391390.20142760X-RAY DIFFRACTION100
5.8425-7.3550.25971330.22972781X-RAY DIFFRACTION99
7.355-43.17460.27821430.24712427X-RAY DIFFRACTION84
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)
10.725-0.1974-0.31810.309-0.09870.1645-0.0756-0.1735-0.1873-0.151-0.05990.24970.03410.0639-0.10170.73510.3495-0.12880.097-0.17910.3272-3.174430.455249.5413
20.50850.08450.11650.4453-0.14681.3471-0.0662-0.0358-0.12410.0123-0.0046-0.022-0.09820.06920.00010.21390.02660.02980.20410.06890.277429.32518.815238.906
30.1359-0.2061-0.14970.3050.19210.105-0.0944-0.03870.25810.0441-0.0321-0.32660.06850.1235-0.00010.40380.1766-0.00230.68450.05260.50173.698340.6577-6.0818
40.6374-0.12140.17230.8376-0.33161.30290.03240.2069-0.0428-0.117-0.047-0.0535-0.1494-0.03520.00280.2020.07150.06090.2305-0.01060.185819.64564.4106-0.9012
50.0397-0.074-0.09710.18920.18440.1688-0.09210.22040.1487-0.00060.16980.1097-0.2175-0.09180.00020.4773-0.00390.05850.51930.10210.636719.065223.38938.9794
60.1346-0.0384-0.09980.13270.21880.41-0.1195-0.0449-0.0414-0.02410.05730.02690.00390.0621-0.19860.93490.3408-0.11520.6046-0.32760.51592.092325.325638.8807
70.00050.00490.00140.0340.02680.01870.0586-0.09910.03340.04540.341-0.2133-0.14920.15430.00350.64530.03550.15110.99180.17770.707421.065624.942836.0475
80.01190.0036-0.01160.0114-0.01760.02470.14830.1986-0.05260.53950.1584-0.10910.3957-0.0163-0.00030.6078-0.0702-0.05020.79860.08460.662433.760826.481950.271
90.0009-0.0008-0.00360.03080.05020.0768-0.0074-0.05250.04770.20610.11180.346-0.0818-0.7503-0.00150.44480.11030.04490.6110.07660.66336.34393.07-2.4535
100.4630.27220.00710.4855-0.34270.3759-0.22360.33190.0457-0.0649-0.55520.1755-0.20360.3062-0.03260.830.04310.11970.8591-0.12650.75917.969422.2447.8362
110.9977-0.0264-0.11840.08550.02780.03080.05240.6392-0.2820.1848-0.25390.0312-0.4186-0.90160.02651.01050.17-0.0350.84120.09780.5266.657111.1266-1.1541
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 4 THROUGH 319 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 320 THROUGH 685 )
3X-RAY DIFFRACTION3CHAIN 'B' AND (RESID 4 THROUGH 123 )
4X-RAY DIFFRACTION4CHAIN 'B' AND (RESID 124 THROUGH 685 )
5X-RAY DIFFRACTION5CHAIN 'C' AND (RESID 1 THROUGH 17 )
6X-RAY DIFFRACTION6CHAIN 'D' AND (RESID 4 THROUGH 8 )
7X-RAY DIFFRACTION7CHAIN 'D' AND (RESID 9 THROUGH 13 )
8X-RAY DIFFRACTION8CHAIN 'D' AND (RESID 14 THROUGH 19 )
9X-RAY DIFFRACTION9CHAIN 'E' AND (RESID 1 THROUGH 10 )
10X-RAY DIFFRACTION10CHAIN 'E' AND (RESID 11 THROUGH 16 )
11X-RAY DIFFRACTION11CHAIN 'F' AND (RESID 4 THROUGH 18 )

+
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