[English] 日本語
Yorodumi
- PDB-7mpu: Brucella melitensis NrnC bound to pGG -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7mpu
TitleBrucella melitensis NrnC bound to pGG
Components
  • 5'-phosphorylated GG
  • NanoRNase C
KeywordsRNA BINDING PROTEIN/RNA / RNase / bacteria / enzyme / RNA BINDING PROTEIN / RNA BINDING PROTEIN-RNA complex
Function / homologyRNA / :
Function and homology information
Biological speciesBrucella melitensis (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 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
D: 5'-phosphorylated GG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6839
Polymers47,1063
Non-polymers5766
Water10,935607
1
B: NanoRNase C
D: 5'-phosphorylated GG
hetero molecules

B: NanoRNase C
D: 5'-phosphorylated GG
hetero molecules

B: NanoRNase C
D: 5'-phosphorylated GG
hetero molecules

B: NanoRNase C
D: 5'-phosphorylated GG
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)190,73136
Polymers188,42612
Non-polymers2,30624
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_544y+1/2,x-1/2,-z-1/21
crystal symmetry operation10_655-x+1,-y,z1
crystal symmetry operation16_554-y+1/2,-x+1/2,-z-1/21
crystal symmetry operation4_554y+1/2,-x,z-1/41
crystal symmetry operation5_554-x+1/2,y,-z-1/41
crystal symmetry operation11_554-y+1/2,x,z-1/41
crystal symmetry operation14_554x+1/2,-y,-z-1/41
Buried area27280 Å2
ΔGint-403 kcal/mol
Surface area65850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)170.922, 170.922, 85.297
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Space group name HallI4bw2bw
Symmetry operation#1: x,y,z
#2: -y+1/2,x,z+3/4
#3: y+1/2,-x,z+3/4
#4: x+1/2,-y,-z+3/4
#5: -x+1/2,y,-z+3/4
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
#9: x+1/2,y+1/2,z+1/2
#10: -y+1,x+1/2,z+5/4
#11: y+1,-x+1/2,z+5/4
#12: x+1,-y+1/2,-z+5/4
#13: -x+1,y+1/2,-z+5/4
#14: -x+1/2,-y+1/2,z+1/2
#15: y+1/2,x+1/2,-z+1/2
#16: -y+1/2,-x+1/2,-z+1/2

-
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: F6Y32_00630 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A5P3L1U6
#2: RNA chain 5'-phosphorylated GG


Mass: 645.454 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 607 / 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: 3.31 Å3/Da / Density % sol: 62.8 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1 M HEPES; 2.0 M Amonium sulfate; 20 % xylitol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 20, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.718→54.05 Å / Num. obs: 66925 / % possible obs: 99.92 % / Redundancy: 16.4 % / Biso Wilson estimate: 21.79 Å2 / CC1/2: 0.999 / Net I/σ(I): 22.49
Reflection shellResolution: 1.718→1.78 Å / Mean I/σ(I) obs: 3.04 / Num. unique obs: 6617 / CC1/2: 0.878 / % possible all: 99.43

-
Processing

Software
NameVersionClassification
XDSdata reduction
PHENIX1.15.2_3472refinement
Aimlessdata scaling
pointlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1yt3

1yt3


Resolution: 1.72→54.05 Å / SU ML: 0.1815 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.2791
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1838 2000 2.99 %
Rwork0.1551 64918 -
obs0.1559 66918 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.69 Å2
Refinement stepCycle: LAST / Resolution: 1.72→54.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3240 47 30 607 3924
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00573452
X-RAY DIFFRACTIONf_angle_d0.79994698
X-RAY DIFFRACTIONf_chiral_restr0.0547531
X-RAY DIFFRACTIONf_plane_restr0.005600
X-RAY DIFFRACTIONf_dihedral_angle_d16.6212108
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.72-1.760.28091400.23774549X-RAY DIFFRACTION99.2
1.76-1.810.23771410.20744578X-RAY DIFFRACTION100
1.81-1.860.22611420.19194596X-RAY DIFFRACTION100
1.86-1.920.20521410.16974583X-RAY DIFFRACTION99.98
1.92-1.990.18661410.16114602X-RAY DIFFRACTION100
1.99-2.070.19621420.15974597X-RAY DIFFRACTION100
2.07-2.160.20911420.15924606X-RAY DIFFRACTION100
2.16-2.280.1591430.15334625X-RAY DIFFRACTION100
2.28-2.420.20751420.15984618X-RAY DIFFRACTION100
2.42-2.610.19411420.1614626X-RAY DIFFRACTION100
2.61-2.870.20631440.1714650X-RAY DIFFRACTION100
2.87-3.290.20281440.16024694X-RAY DIFFRACTION100
3.29-4.140.16851450.12734700X-RAY DIFFRACTION100
4.14-54.050.1351510.14034894X-RAY DIFFRACTION99.88
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)
12.18309310319-1.24668618437-0.6563017248481.595493724010.04628511783671.245033051680.1273146487170.2066851228980.211683011517-0.155378674287-0.143321733496-0.0920797435074-0.06992804328920.06047874882830.02489103806380.1600436647910.01600367446670.01806445080610.1887968977220.03101292300830.17189965535121.62492353035.64987445742-34.0802761383
21.18918373157-0.1198631670041.065313139940.619671386171-0.6469012993622.00757415167-0.00799183967391-0.07312288453910.06330368133920.1338744207360.01306338960550.0530313439167-0.2760707063720.083290634024-0.02142677592090.191096951186-0.01591246749780.04189230529520.177598295855-0.008415424825080.1735216089222.66639874750.0589922507026-18.857272287
37.79954739273-1.263900813620.2003075574953.37185885186-0.1095177168962.02355419498-0.182871792355-0.3058338180451.231504436550.1421710213180.108945323576-0.385660260057-0.5092249036490.1269782177140.07655418992370.256970635206-0.02226643349580.0007772550522050.202976802724-0.02200466578740.37691606856418.811823007818.3853047178-26.7444077225
40.8914916224470.3512201841550.07724112393040.88901378954-0.284232100950.7491793624990.0310150194505-0.07208861659070.0676516428338-0.000245510468822-0.01815265790440.04338590095990.03735064211560.0758677125981-0.01588890983390.1491656088980.008226586237760.02643314701960.149960955876-0.002656415077630.14638792707121.2698720644-8.14535164989-19.5399639135
52.03644684542-0.283020419946-0.02996637910150.597706312079-0.09238168585821.77656560042-0.06527996075720.135637266655-0.1211027780170.04388813715670.05524963072130.09914285388130.0528839929234-0.0990695160580.007581809678340.1642611100680.001786070401490.03040295498630.212364494550.007130213368610.16539247414146.5181587852-9.63413132371-31.2047342389
62.448086870790.503379621674-1.314551684840.428286350125-0.7366195456481.352794199740.0162085720593-0.05536310638790.07731436750690.06387773649820.008646664329880.0695477511187-0.0326412364272-0.0136271237166-0.01021195896050.1496897942360.01684259749120.007185336051910.182674891164-0.007256521607950.1688852427257.4530688292-4.95062790013-35.4815464795
70.95486651486-0.305705168369-0.3479604232240.793255320331-0.1077452351510.836118629755-0.04954533084730.03699354234760.0497643639820.05208142889540.0727967423637-0.00298094508732-0.0216878426215-0.0485608249342-0.01949916156340.1589704587750.004966622298390.0001813306205550.182061021963-0.006193869020790.14411246969161.4964653436-6.52156738843-38.3842372861
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 0:75)
2X-RAY DIFFRACTION2(chain A and resid 76:132)
3X-RAY DIFFRACTION3(chain A and resid 135:151)
4X-RAY DIFFRACTION4(chain A and resid 152:205)
5X-RAY DIFFRACTION5(chain B and resid 0:60)
6X-RAY DIFFRACTION6(chain B and resid 61:140)
7X-RAY DIFFRACTION7(chain B and resid 141:205)

+
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://pdbjlvh1.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