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

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ozs
TitleCrystal structure of Mus musculus (Mm) Endonuclease V in complex with a 23mer RNA oligo containing an inosine after a 90 min soak in 10 mM Mg2+
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


endodeoxyribonuclease activity, producing 5'-phosphomonoesters / RNA endonuclease 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: 2.41 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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _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.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: 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)70,87223
Polymers69,3126
Non-polymers1,55917
Water64936
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10160 Å2
ΔGint-115 kcal/mol
Surface area24890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.086, 73.257, 155.704
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain D
21chain C
12(chain A and (resseq 9:11 or resseq 13:15 or resseq...
22(chain B and (resseq 9:11 or resseq 13:15 or resseq...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain DD8 - 11
211chain CC8 - 11
112(chain A and (resseq 9:11 or resseq 13:15 or resseq...A9 - 11
122(chain A and (resseq 9:11 or resseq 13:15 or resseq...A13 - 15
132(chain A and (resseq 9:11 or resseq 13:15 or resseq...A0
142(chain A and (resseq 9:11 or resseq 13:15 or resseq...A54
152(chain A and (resseq 9:11 or resseq 13:15 or resseq...A6 - 252
162(chain A and (resseq 9:11 or resseq 13:15 or resseq...A6 - 252
172(chain A and (resseq 9:11 or resseq 13:15 or resseq...A6 - 252
182(chain A and (resseq 9:11 or resseq 13:15 or resseq...A6 - 252
212(chain B and (resseq 9:11 or resseq 13:15 or resseq...B9 - 11
222(chain B and (resseq 9:11 or resseq 13:15 or resseq...B13 - 15
232(chain B and (resseq 9:11 or resseq 13:15 or resseq...B0
242(chain B and (resseq 9:11 or resseq 13:15 or resseq...B54
252(chain B and (resseq 9:11 or resseq 13:15 or resseq...B8 - 251
262(chain B and (resseq 9:11 or resseq 13:15 or resseq...B8 - 251
272(chain B and (resseq 9:11 or resseq 13:15 or resseq...B8 - 251
282(chain B and (resseq 9:11 or resseq 13:15 or resseq...B8 - 251

NCS ensembles :
ID
1
2

-
Components

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

#1: Protein Endonuclease V


Mass: 27407.730 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 , 8 types, 53 molecules

#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#6: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#9: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#10: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 2.88 Å3/Da / Density % sol: 61.62 %
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: Jun 13, 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: 2.41→41.71 Å / Num. obs: 30469 / % possible obs: 95.6 % / Redundancy: 1 % / Biso Wilson estimate: 48.74 Å2 / Net I/σ(I): 11 / Num. measured all: 30469
Reflection shellResolution: 2.41→2.5 Å / Redundancy: 1 % / Num. unique obs: 2341 / % possible all: 71.4

-
Processing

Software
NameVersionClassification
Aimless0.5.31data scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.41→36.246 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.99 / Phase error: 29.73
RfactorNum. reflection% reflection
Rfree0.236 1530 5.05 %
Rwork0.1909 --
obs0.1932 30306 95.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 199.49 Å2 / Biso mean: 39 Å2 / Biso min: 31.01 Å2
Refinement stepCycle: final / Resolution: 2.41→36.246 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3785 506 265 36 4592
Biso mean--97.79 59.27 -
Num. residues----512
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074729
X-RAY DIFFRACTIONf_angle_d1.0126508
X-RAY DIFFRACTIONf_chiral_restr0.053763
X-RAY DIFFRACTIONf_plane_restr0.006716
X-RAY DIFFRACTIONf_dihedral_angle_d16.432774
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11D342X-RAY DIFFRACTION7.501TORSIONAL
12C342X-RAY DIFFRACTION7.501TORSIONAL
21A1975X-RAY DIFFRACTION7.501TORSIONAL
22B1975X-RAY DIFFRACTION7.501TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4067-2.48440.343920.28751871196369
2.4844-2.57320.32711160.27612309242585
2.5732-2.67610.30331370.26052609274696
2.6761-2.79790.24331490.25542686283599
2.7979-2.94530.3151400.235827112851100
2.9453-3.12980.30721510.219527072858100
3.1298-3.37130.27281310.200327502881100
3.3713-3.71020.22331480.182927362884100
3.7102-4.24640.22751480.166327422890100
4.2464-5.34730.21061460.15022783292999
5.3473-36.25050.19591720.18272872304499
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)
19.63136.5301-4.99457.982-4.56786.543-0.2735-0.6061-0.5127-0.1273-0.3491-0.69920.55730.34460.62810.30740.1116-0.00120.2865-0.13560.319935.47641.700144.7803
24.80470.0758-1.8573.2249-0.094.5675-0.05590.21520.3889-0.25090.07150.2733-0.2226-0.3467-0.0210.31960.0002-0.0340.371-0.01490.364225.69886.9740.9176
32.1978-0.737-0.29484.50020.70655.41840.0280.2367-0.1671-0.35630.06920.07930.2612-0.1649-0.11140.4274-0.0425-0.01140.31390.00350.379329.9316-11.381834.0808
43.103-0.47180.35674.9079-4.94454.9188-0.32330.01070.5558-1.05380.39770.72790.0165-0.9324-0.14330.6047-0.0461-0.11250.61520.00680.627915.42188.185131.389
57.80211.85631.23226.30371.69298.7392-0.1442-0.48231.308-0.0586-0.26990.7612-2.2294-1.34770.43191.15660.41-0.16480.9478-0.08480.9264-8.974612.9421-4.9748
63.9751-0.54410.39663.29190.2957.464-0.2929-0.24270.44020.83990.15110.073-1.0203-0.19290.09440.77960.061-0.05880.42620.04630.38688.79084.8077-6.9257
73.57010.2637-0.54816.9754-2.44555.05760.1402-0.7405-0.32260.91430.23290.55180.8096-0.4907-0.36010.7869-0.04630.03480.63560.02190.49332.8922-10.72421.1478
85.88571.40570.61963.44395.22998.372-0.448-0.22490.95611.34510.02-0.3662-1.11430.77030.41621.5026-0.082-0.26740.79180.03420.580318.50447.28654.744
98.80094.0016-2.88482.047-2.06273.6114-1.11140.836-0.0988-2.47611.2635-3.06521.25131.73550.13590.847-0.13110.41520.9305-0.15961.215738.0520.996727.5931
100.30250.51680.24224.4551-0.45476.5162-0.868-0.15710.8844-0.48280.06720.92-1.271-0.64440.67680.72310.1089-0.20490.8865-0.03290.700114.46670.064717.4443
112.892-2.15341.85163.02150.9314.9932-0.2991-0.70510.10752.8106-0.24032.56462.4454-1.16620.79751.77430.40040.63811.4137-0.04841.2926-4.65072.31847.3301
123.1403-0.6419-3.09876.38791.63478.92340.23290.14910.2894-0.6254-0.2253-0.0993-1.58480.2986-0.0220.707-0.0513-0.15140.6521-0.01640.455818.7179-0.118.4295
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 46 )A6 - 46
2X-RAY DIFFRACTION2chain 'A' and (resid 47 through 154 )A47 - 154
3X-RAY DIFFRACTION3chain 'A' and (resid 155 through 233 )A155 - 233
4X-RAY DIFFRACTION4chain 'A' and (resid 234 through 251 )A234 - 251
5X-RAY DIFFRACTION5chain 'B' and (resid 8 through 27 )B8 - 27
6X-RAY DIFFRACTION6chain 'B' and (resid 28 through 154 )B28 - 154
7X-RAY DIFFRACTION7chain 'B' and (resid 155 through 233 )B155 - 233
8X-RAY DIFFRACTION8chain 'B' and (resid 234 through 251 )B234 - 251
9X-RAY DIFFRACTION9chain 'C' and (resid 12 through 23 )C12 - 23
10X-RAY DIFFRACTION10chain 'D' and (resid 12 through 23 )D12 - 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