[English] 日本語
Yorodumi
- PDB-6ozp: Crystal structure of Mus musculus (Mm) Endonuclease V in complex ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ozp
TitleCrystal structure of Mus musculus (Mm) Endonuclease V in complex with a 23mer RNA oligo containing an inosine after a 180 min soak in 10 mM Mn2+
Components
  • DNA/RNA (5'-R(*CP*GP*GP*UP*AP*AP*CP*CP*C)-D(P*I)-R(P*A)-3')
  • Endonuclease V
  • RNA (5'-R(P*UP*AP*UP*GP*CP*AP*UP*GP*CP*AP*UP*U)-3')
KeywordsHYDROLASE/RNA / Nucleic acid hydrolysis / RNA recognition / metal ion dependent catalysis / DNA damage / adenosine deamination / HYDROLASE-RNA complex
Function / homology
Function and homology information


RNA endonuclease activity, producing 5'-phosphomonoesters / endodeoxyribonuclease activity, producing 5'-phosphomonoesters / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / cytoplasmic stress granule / single-stranded RNA binding / DNA repair / nucleolus / magnesium ion binding / DNA binding / cytoplasm
Similarity search - Function
Endonuclease V / Endonuclease V / archaeoglobus fulgidus dsm 4304 fold / archaeoglobus fulgidus dsm 4304 superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / TRIETHYLENE GLYCOL / DNA/RNA hybrid / DNA/RNA hybrid (> 10) / RNA / RNA (> 10) / Endonuclease V
Similarity search - Component
Biological speciesMus musculus (house mouse)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsSamara, N.L. / Yang, W.
CitationJournal: Mol.Cell / Year: 2019
Title: Evolution of Inosine-Specific Endonuclease V from Bacterial DNase to Eukaryotic RNase.
Authors: Wu, J. / Samara, N.L. / Kuraoka, I. / Yang, W.
History
DepositionMay 15, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2019Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_alt_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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 / _struct_conn.ptnr2_symmetry

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Endonuclease V
B: Endonuclease V
c: DNA/RNA (5'-R(*CP*GP*GP*UP*AP*AP*CP*CP*C)-D(P*I)-R(P*A)-3')
C: RNA (5'-R(P*UP*AP*UP*GP*CP*AP*UP*GP*CP*AP*UP*U)-3')
d: DNA/RNA (5'-R(*CP*GP*GP*UP*AP*AP*CP*CP*C)-D(P*I)-R(P*A)-3')
D: RNA (5'-R(P*UP*AP*UP*GP*CP*AP*UP*GP*CP*AP*UP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,91230
Polymers68,9126
Non-polymers2,00024
Water5,765320
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10680 Å2
ΔGint-84 kcal/mol
Surface area25190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.031, 73.006, 155.760
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein / DNA/RNA hybrid / RNA chain , 3 types, 6 molecules ABcdCD

#1: Protein Endonuclease V /


Mass: 27207.539 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Endov / Production host: Escherichia coli (E. coli)
References: UniProt: Q8C9A2, Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters
#2: DNA/RNA hybrid DNA/RNA (5'-R(*CP*GP*GP*UP*AP*AP*CP*CP*C)-D(P*I)-R(P*A)-3')


Mass: 3474.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: RNA chain RNA (5'-R(P*UP*AP*UP*GP*CP*AP*UP*GP*CP*AP*UP*U)-3')


Mass: 3774.264 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

-
Non-polymers , 6 types, 344 molecules

#4: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#7: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#8: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O4
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 320 / 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: 3.18 Å3/Da / Density % sol: 61.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M potassium sodium tartrate, 20-25% w/v PEG3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Mar 17, 2016
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.96→38.94 Å / Num. obs: 56317 / % possible obs: 94.2 % / Redundancy: 1 % / Biso Wilson estimate: 26.67 Å2 / Net I/σ(I): 10.1 / Num. measured all: 56317
Reflection shellResolution: 1.96→2.01 Å / Redundancy: 1 % / Num. unique obs: 2410 / % possible all: 58

-
Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
Aimless0.5.31data scaling
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.96→36.483 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 22.39
RfactorNum. reflection% reflection
Rfree0.2013 2848 5.07 %
Rwork0.1749 --
obs0.1763 56185 94.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.96→36.483 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3776 672 103 320 4871
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074768
X-RAY DIFFRACTIONf_angle_d0.936570
X-RAY DIFFRACTIONf_dihedral_angle_d15.872815
X-RAY DIFFRACTIONf_chiral_restr0.057772
X-RAY DIFFRACTIONf_plane_restr0.006726
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9604-1.99420.2949600.28061394X-RAY DIFFRACTION49
1.9942-2.03050.41831040.31442302X-RAY DIFFRACTION82
2.0305-2.06950.32831300.29652384X-RAY DIFFRACTION86
2.0695-2.11180.30381430.28072499X-RAY DIFFRACTION90
2.1118-2.15770.26361400.2412542X-RAY DIFFRACTION91
2.1577-2.20790.24911430.21872630X-RAY DIFFRACTION94
2.2079-2.26310.2451480.21412650X-RAY DIFFRACTION95
2.2631-2.32430.23661310.20352742X-RAY DIFFRACTION97
2.3243-2.39270.24631630.19052741X-RAY DIFFRACTION98
2.3927-2.46990.23281590.18852779X-RAY DIFFRACTION100
2.4699-2.55810.20951350.17882844X-RAY DIFFRACTION100
2.5581-2.66050.23491850.16922770X-RAY DIFFRACTION100
2.6605-2.78160.20811550.16652852X-RAY DIFFRACTION100
2.7816-2.92810.19531380.18092844X-RAY DIFFRACTION100
2.9281-3.11150.18931230.17542856X-RAY DIFFRACTION100
3.1115-3.35160.18921440.1682836X-RAY DIFFRACTION100
3.3516-3.68860.15371430.14992875X-RAY DIFFRACTION100
3.6886-4.22170.15781730.1362860X-RAY DIFFRACTION100
4.2217-5.31620.15611440.12842925X-RAY DIFFRACTION100
5.3162-36.4890.19871870.17643012X-RAY DIFFRACTION100
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)
15.93474.093-3.15275.3245-2.99963.3871-0.1108-0.211-0.39530.0017-0.1542-0.49190.08170.11970.28120.15470.0352-0.00330.1312-0.06790.147836.31911.19445.3732
22.62970.016-0.88632.179-0.04882.0904-0.05820.0980.2365-0.11290.05680.0568-0.2286-0.212-0.01370.20510.0195-0.02320.19670.00510.195126.75367.187640.3091
31.9238-0.60530.62823.3957-0.32553.79430.03140.1972-0.13-0.50090.01160.00280.4365-0.0098-0.03870.3089-0.02330.01450.14080.00450.195430.222-11.485334.2019
47.35130.0624-0.60767.6497-3.23297.6058-0.11290.31590.6887-0.87860.37140.2786-0.1663-0.3353-0.2830.31780.0043-0.07950.28490.02340.288216.6188.152731.1517
56.8614-4.6527-2.63626.63283.50074.6303-0.0750.1971-0.15460.1281-0.24320.5525-0.0516-0.45610.32370.2597-0.0219-0.04250.1980.06310.2105-0.28062.6145-10.9745
63.2921-0.5322-0.25291.99240.14893.2387-0.0954-0.14710.31050.24530.0479-0.0092-0.3460.08390.0060.29410.0059-0.05430.175-0.00260.20739.32767.5393-4.8362
73.6491-0.2143-0.41854.0519-0.62784.6134-0.0181-0.4656-0.53230.73630.11110.36530.7173-0.3566-0.0470.4616-0.06960.04560.26660.0480.30193.1798-10.87831.1238
85.08440.56550.85916.38121.36995.2156-0.0050.11440.34190.7387-0.03820.0031-0.27660.3485-0.06210.382-0.0124-0.11290.2760.02040.210219.2367.42064.9314
94.81641.11662.47845.0852-2.4623.2862-0.28491.1868-0.3346-1.55310.4474-1.88640.52381.78550.03140.368-0.0440.21860.6513-0.11080.567338.95480.880227.4814
100.7490.40680.23873.21330.11554.767-0.13380.03110.1312-0.11340.00910.5215-0.3096-0.33650.11180.30350.031-0.07460.34340.02130.312515.06810.043517.4544
111.3756-2.67591.30095.222-2.51571.2298-0.3945-1.27070.14381.720.09172.26070.356-2.2619-0.03690.56240.02360.22881.0507-0.10260.749-4.51662.56467.1837
121.4656-0.9826-0.39243.83490.32314.68290.1976-0.11890.058-0.2633-0.1076-0.1415-0.32050.245-0.06890.2886-0.0389-0.03970.3150.00450.23119.112-0.08818.3793
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 8 through 46 )
2X-RAY DIFFRACTION2chain 'A' and (resid 47 through 154 )
3X-RAY DIFFRACTION3chain 'A' and (resid 155 through 233 )
4X-RAY DIFFRACTION4chain 'A' and (resid 234 through 252 )
5X-RAY DIFFRACTION5chain 'B' and (resid 8 through 46 )
6X-RAY DIFFRACTION6chain 'B' and (resid 47 through 154 )
7X-RAY DIFFRACTION7chain 'B' and (resid 155 through 233 )
8X-RAY DIFFRACTION8chain 'B' and (resid 234 through 251 )
9X-RAY DIFFRACTION9chain 'C' and (resid 8 through 11 )
10X-RAY DIFFRACTION10chain 'C' and (resid 12 through 23 )
11X-RAY DIFFRACTION11chain 'D' and (resid 8 through 11 )
12X-RAY DIFFRACTION12chain 'D' and (resid 12 through 23 )

+
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