[English] 日本語
Yorodumi
- PDB-6oze: Crystal structure of the catalytic domain of human Endonuclease V... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6oze
TitleCrystal structure of the catalytic domain of human Endonuclease V (C140S/C225S/C226A/C228S)
ComponentsEndonuclease V
KeywordsHYDROLASE / Nucleic acid hydrolysis / RNA recognition / metal ion dependent catalysis / DNA damage / adenosine deamination
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
ACETATE ION / Endonuclease V
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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 1.2Oct 11, 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 / 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Endonuclease V
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5067
Polymers27,1571
Non-polymers3486
Water2,630146
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area940 Å2
ΔGint-21 kcal/mol
Surface area11570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.949, 50.949, 102.978
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31

-
Components

#1: Protein Endonuclease V / / hEndoV / Inosine-specific endoribonuclease


Mass: 27157.359 Da / Num. of mol.: 1 / Mutation: C140S/C225S/C226A/C228S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ENDOV / Production host: Escherichia coli (E. coli)
References: UniProt: Q8N8Q3, Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters
#2: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: 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
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 146 / 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: 2.84 Å3/Da / Density % sol: 56.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 3.6 M sodium acetate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 7, 2013
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: 1.5→24.73 Å / Num. obs: 47096 / % possible obs: 98.2 % / Redundancy: 1 % / Biso Wilson estimate: 21.1 Å2 / Net I/σ(I): 9.9 / Num. measured all: 47096
Reflection shell
Resolution (Å)Redundancy (%)Num. measured allNum. unique obsDiffraction-IDNet I/σ(I) obs% possible all
1.5-1.521207320731288.3
8.21-24.731131131121.444.9

-
Processing

Software
NameVersionClassification
Aimless0.5.21data scaling
PHENIX1.12_2829refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2W35

2w35


Resolution: 1.5→24.729 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 22.84
RfactorNum. reflection% reflection
Rfree0.191 2240 4.76 %
Rwork0.1719 --
obs0.1729 47020 98.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 110.49 Å2 / Biso mean: 37.4917 Å2 / Biso min: 14.73 Å2
Refinement stepCycle: final / Resolution: 1.5→24.729 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1908 0 22 146 2076
Biso mean--57.87 48 -
Num. residues----246
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062088
X-RAY DIFFRACTIONf_angle_d0.8232853
X-RAY DIFFRACTIONf_chiral_restr0.079328
X-RAY DIFFRACTIONf_plane_restr0.005375
X-RAY DIFFRACTIONf_dihedral_angle_d21.283822
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.499-1.53160.29581160.28222515263189
1.5316-1.56720.26411100.25462767287796
1.5672-1.60640.256880.25229012989100
1.6064-1.64980.23531880.231727952983100
1.6498-1.69830.25161580.216828953053100
1.6983-1.75310.21761380.202628262964100
1.7531-1.81580.23271450.202628442989100
1.8158-1.88850.24211480.193228523000100
1.8885-1.97440.20861330.177128292962100
1.9744-2.07840.1991780.164628112989100
2.0784-2.20860.16251690.156128643033100
2.2086-2.3790.16971440.162728252969100
2.379-2.61810.20171160.167628682984100
2.6181-2.99640.21281400.182928953035100
2.9964-3.7730.1571470.147428122959100
3.773-24.73240.17911220.16062481260387
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)
13.7143-1.7459-3.60583.20921.70273.4534-0.0237-0.33450.63770.15280.25650.385-0.7966-0.1087-0.3020.53120.0678-0.00440.2489-0.01070.3381.60323.229311.1857
21.8420.4379-1.59842.27030.21516.20290.10790.17680.1029-0.02710.1529-0.1016-0.20450.1361-0.26610.16850.0241-0.01640.1279-0.00480.13796.1869-17.2432-0.5097
31.18060.2811-0.64811.6419-0.06925.7619-0.1743-0.0783-0.06190.37240.12690.14270.3516-0.15390.11550.1392-0.0159-0.03450.1628-0.00410.16450.3164-18.73836.7052
41.2697-0.0512-0.71753.56882.30275.84090.0215-0.1186-0.00290.08320.10390.0436-0.34370.1922-0.09590.2101-0.0097-0.00330.1273-0.01190.17215.628-12.47454.9739
55.3003-1.0891.12583.1292-0.41766.03360.0741-0.110.19280.1064-0.0660.1364-0.3674-0.36040.00110.30620.09970.00920.24690.03030.1624-6.7804-9.3223-14.9825
65.17591.08341.05943.34291.02835.6534-0.06320.1451-0.0425-0.34220.1284-0.0541-0.23880.1173-0.08830.22470.01330.00550.15430.01860.09523.5112-15.2744-9.636
78.72744.1686-6.46924.8842-4.11055.2134-0.150.1663-0.1721-0.04180.12760.08360.5018-0.49030.00720.2874-0.0415-0.01870.20510.01030.1814-5.9542-26.97785.0061
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 9 through 27 )A9 - 27
2X-RAY DIFFRACTION2chain 'A' and (resid 28 through 71 )A28 - 71
3X-RAY DIFFRACTION3chain 'A' and (resid 72 through 95 )A72 - 95
4X-RAY DIFFRACTION4chain 'A' and (resid 96 through 154 )A96 - 154
5X-RAY DIFFRACTION5chain 'A' and (resid 155 through 206 )A155 - 206
6X-RAY DIFFRACTION6chain 'A' and (resid 207 through 233 )A207 - 233
7X-RAY DIFFRACTION7chain 'A' and (resid 234 through 254 )A234 - 254

+
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