[English] 日本語
Yorodumi
- PDB-7mpt: Brucella melitensis NrnC with bound Mg2+ -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7mpt
TitleBrucella melitensis NrnC with bound Mg2+
ComponentsNanoRNase C
KeywordsRNA BINDING PROTEIN / RNase / bacteria / enzyme
Function / homology
Function and homology information


ribonuclease D activity / 3'-5' exonuclease activity / nucleic acid binding
Similarity search - Function
3'-5' exonuclease / 3'-5' exonuclease / 3'-5' exonuclease domain / Ribonuclease H superfamily / Ribonuclease H-like superfamily
Similarity search - Domain/homology
PHOSPHATE ION / Ribonuclease D
Similarity search - Component
Biological speciesBrucella melitensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsLormand, J.D. / Sondermann, H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI142400 United States
CitationJournal: Elife / Year: 2021
Title: Structural characterization of NrnC identifies unifying features of dinucleotidases.
Authors: Justin D Lormand / Soo-Kyoung Kim / George A Walters-Marrah / Bryce A Brownfield / J Christopher Fromme / Wade C Winkler / Jonathan R Goodson / Vincent T Lee / Holger Sondermann /
Abstract: RNA degradation is fundamental for cellular homeostasis. The process is carried out by various classes of endolytic and exolytic enzymes that together degrade an RNA polymer to mono-ribonucleotides. ...RNA degradation is fundamental for cellular homeostasis. The process is carried out by various classes of endolytic and exolytic enzymes that together degrade an RNA polymer to mono-ribonucleotides. Within the exoribonucleases, nano-RNases play a unique role as they act on the smallest breakdown products and hence catalyze the final steps in the process. We recently showed that oligoribonuclease (Orn) acts as a dedicated diribonucleotidase, defining the ultimate step in RNA degradation that is crucial for cellular fitness (Kim et al., 2019). Whether such a specific activity exists in organisms that lack Orn-type exoribonucleases remained unclear. Through quantitative structure-function analyses, we show here that NrnC-type RNases share this narrow substrate length preference with Orn. Although NrnC and Orn employ similar structural features that distinguish these two classes of dinucleotidases from other exonucleases, the key determinants for dinucleotidase activity are realized through distinct structural scaffolds. The structures, together with comparative genomic analyses of the phylogeny of DEDD-type exoribonucleases, indicate convergent evolution as the mechanism of how dinucleotidase activity emerged repeatedly in various organisms. The evolutionary pressure to maintain dinucleotidase activity further underlines the important role these analogous proteins play for cell growth.
History
DepositionMay 4, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 15, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 29, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: NanoRNase C
B: NanoRNase C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6537
Polymers46,4612
Non-polymers1925
Water10,088560
1
A: NanoRNase C
hetero molecules

A: NanoRNase C
hetero molecules

A: NanoRNase C
hetero molecules

A: NanoRNase C
hetero molecules

A: NanoRNase C
hetero molecules

A: NanoRNase C
hetero molecules

A: NanoRNase C
hetero molecules

A: NanoRNase C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)186,23324
Polymers185,8448
Non-polymers38916
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation4_565y,-x+1,z1
crystal symmetry operation5_656-x+1,y,-z+11
crystal symmetry operation6_566x,-y+1,-z+11
crystal symmetry operation7_556y,x,-z+11
crystal symmetry operation8_666-y+1,-x+1,-z+11
2
B: NanoRNase C
hetero molecules

B: NanoRNase C
hetero molecules

B: NanoRNase C
hetero molecules

B: NanoRNase C
hetero molecules

B: NanoRNase C
hetero molecules

B: NanoRNase C
hetero molecules

B: NanoRNase C
hetero molecules

B: NanoRNase C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)186,99332
Polymers185,8448
Non-polymers1,14924
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
crystal symmetry operation5_555-x,y,-z1
crystal symmetry operation6_555x,-y,-z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation8_555-y,-x,-z1
Unit cell
Length a, b, c (Å)93.314, 93.314, 123.962
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number89
Space group name H-MP422
Space group name HallP42
Components on special symmetry positions
IDModelComponents
11A-670-

HOH

-
Components

#1: Protein NanoRNase C


Mass: 23230.486 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella melitensis (bacteria) / Gene: rnd_2, CUC12_07925, NCTC8223_00749 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2X1C2S7, ribonuclease D
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 560 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.9 Å3/Da / Density % sol: 57.65 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop
Details: 0.06 M sodium-potassium-monophosphate monohydrate, 1.2 M potassium phosphate dibasic, 20 % xylitol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Mar 26, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.75→61.98 Å / Num. obs: 55765 / % possible obs: 99.77 % / Redundancy: 15.9 % / Biso Wilson estimate: 24.88 Å2 / CC1/2: 0.999 / CC star: 1 / Net I/σ(I): 26.42
Reflection shellResolution: 1.75→1.813 Å / Redundancy: 15 % / Mean I/σ(I) obs: 2.03 / Num. unique obs: 5452 / CC1/2: 0.754 / CC star: 0.927 / % possible all: 99.27

-
Processing

Software
NameVersionClassification
PHENIX1.18rc6_3830refinement
XDSdata reduction
Aimless3.3.22data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1yt3

1yt3


Resolution: 1.75→61.98 Å / SU ML: 0.1567 / Cross valid method: FREE R-VALUE / Phase error: 19.0959
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1819 1998 -
Rwork0.1691 53768 -
obs-55765 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.35 Å2
Refinement stepCycle: LAST / Resolution: 1.75→61.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3215 0 9 560 3784
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00543323
X-RAY DIFFRACTIONf_angle_d0.76114505
X-RAY DIFFRACTIONf_chiral_restr0.0534513
X-RAY DIFFRACTIONf_plane_restr0.0044585
X-RAY DIFFRACTIONf_dihedral_angle_d18.72261243
LS refinement shellResolution: 1.75→1.813 Å
RfactorNum. reflection% reflection
Rfree0.291 195 -
Rwork0.281 5452 -
obs--99.27 %
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)
11.15918642894-0.3693674914680.5419843850212.54907425694-0.3270992575791.931381186510.05909146958750.00470261278732-0.0971682512088-0.08661828487590.02065163058890.365061506469-0.00890285305063-0.268321584334-0.06785199378050.137131462374-0.0163325448885-0.0208687816850.1970955632540.01312397504060.2083284693213.4635557834.178573451744.7910591398
23.12514585776-1.198412543920.4402707788062.78671069205-1.057397820384.187790728410.02983050311460.4536719381640.483591253075-0.278419455103-0.11393643606-0.293893736019-0.2522451835510.1071015633720.1312777653830.222323979409-0.01091772578550.001505729635960.2300481755830.03970795143190.26947958582534.365710924630.12409756341.6516385816
30.810803477585-0.4128287882430.1009606342831.46804668387-0.2480083630051.701759179850.001796926362980.03011393845090.0134285808606-0.0266175548284-0.00863203765374-0.0240195735746-0.047169766123-0.04158440928560.01383252917650.127990791465-0.0354126646812-0.01631889073510.166820481439-0.0005442682903840.19222557236724.975890579631.482802758648.6847665302
42.54273114201-0.884353849454-0.2216143210792.435524281020.872737825661.698066143450.03163322413440.006412720969840.04115635707570.1623902446250.0435057275009-0.35018465943-0.09018724363850.145149083283-0.08253253126860.242692306623-0.00900584516488-0.05929921585490.1676070879140.003862607855020.22432917420132.67651246616.829907538618.486474967
50.7366741307670.1943974891790.5912623467044.08906248506-0.03002832827391.00781015543-0.0265641059339-0.139615638357-0.01347543762330.4508988203380.1099660477180.218774087217-0.0337746464412-0.173687455752-0.0673300392690.2384100417360.0440138020509-0.002083126161730.2073972059620.01066142070830.17446604733225.31395543592.5927290312515.4338189744
60.467714429086-0.110891129701-0.2257140872822.248878368260.7377425156480.582745551356-0.02731022780510.00483662652264-0.004434684946150.2124489782030.0102981235848-0.0546388635117-0.0136525825172-0.03861463215560.02680837110980.2014561381020.00717206471939-0.02927545262790.1794692761020.01166434462490.1915921673626.45179668334.5341262603913.0743357887
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain A and resid 0:100)AA0 - 1001 - 102
22(chain A and resid 101:133)AA101 - 133103 - 137
33(chain A and resid 134:205)AA134 - 205138 - 211
44(chain B and resid 1:73)BB1 - 731 - 77
55(chain B and resid 74:130)BB74 - 13078 - 134
66(chain B and resid 135:205)BB135 - 205135 - 207

+
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