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- PDB-7mpo: Bartonella henselae NrnC bound to pAp -

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Basic information

Entry
Database: PDB / ID: 7mpo
TitleBartonella henselae NrnC bound to pAp
ComponentsNanoRNase C
KeywordsRNA BINDING PROTEIN / RNase / bacteria / enzyme
Function / homology
Function and homology information


nucleobase-containing compound metabolic process / 3'-5' exonuclease activity / nucleic acid binding / metal ion 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
ADENOSINE-3'-5'-DIPHOSPHATE / 3'-5' exonuclease
Similarity search - Component
Biological speciesBartonella henselae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NanoRNase C
B: NanoRNase C
C: NanoRNase C
D: NanoRNase C
E: NanoRNase C
F: NanoRNase C
G: NanoRNase C
H: NanoRNase C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)190,99116
Polymers187,5748
Non-polymers3,4188
Water32,2651791
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25090 Å2
ΔGint-142 kcal/mol
Surface area64380 Å2
Unit cell
Length a, b, c (Å)99.676, 141.688, 147.920
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein
NanoRNase C


Mass: 23446.725 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bartonella henselae (bacteria) / Gene: BM1374165_00260 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: X5MEI1
#2: Chemical
ChemComp-A3P / ADENOSINE-3'-5'-DIPHOSPHATE


Type: RNA linking / Mass: 427.201 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H15N5O10P2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1791 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.79 Å3/Da / Density % sol: 55.99 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1 M Succinic acid; 10% PEG 3,350; 20% xylitol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 1.0001 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0001 Å / Relative weight: 1
ReflectionResolution: 1.95→47.23 Å / Num. obs: 153174 / % possible obs: 99.89 % / Redundancy: 7.4 % / Biso Wilson estimate: 25.11 Å2 / CC1/2: 0.999 / Net I/σ(I): 14.04
Reflection shellResolution: 1.95→2.02 Å / Num. unique obs: 15073 / CC1/2: 0.877 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3471refinement
XDSdata reduction
Aimlessdata scaling
pointlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1yt3

1yt3


Resolution: 1.95→47.23 Å / SU ML: 0.1631 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.2415
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1881 2000 1.31 %
Rwork0.1643 151174 -
obs0.1646 153174 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.31 Å2
Refinement stepCycle: LAST / Resolution: 1.95→47.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13089 0 216 1791 15096
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005913796
X-RAY DIFFRACTIONf_angle_d0.792118762
X-RAY DIFFRACTIONf_chiral_restr0.05482131
X-RAY DIFFRACTIONf_plane_restr0.00482420
X-RAY DIFFRACTIONf_dihedral_angle_d19.91715140
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-20.26641450.220410651X-RAY DIFFRACTION99.5
2-2.050.25961400.206810688X-RAY DIFFRACTION99.99
2.05-2.110.22331380.193710709X-RAY DIFFRACTION99.94
2.11-2.180.21591430.178710730X-RAY DIFFRACTION99.92
2.18-2.260.18641500.176810694X-RAY DIFFRACTION99.92
2.26-2.350.22671340.17710733X-RAY DIFFRACTION99.92
2.35-2.450.22951450.177910718X-RAY DIFFRACTION99.91
2.45-2.580.18741400.172610768X-RAY DIFFRACTION99.95
2.58-2.740.20681460.171410793X-RAY DIFFRACTION99.94
2.74-2.960.20831390.171810788X-RAY DIFFRACTION99.98
2.96-3.250.15411470.158910826X-RAY DIFFRACTION99.91
3.25-3.720.15091420.141610874X-RAY DIFFRACTION99.94
3.72-4.690.1481390.129610964X-RAY DIFFRACTION99.93
4.69-47.230.20191520.174711238X-RAY DIFFRACTION99.5
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)
12.64568207350.460689560789-0.9122942231760.724897060627-0.2694232989220.777755214729-0.127789801247-0.188976803336-0.213303474610.005515123069440.038657796582-0.0182493713770.1173434931040.07717981978760.07071358201780.2053933782420.01113349224120.003159251121350.1777873200240.02297187842020.202387210462-2.1324472056-17.096769944617.6141106424
24.12977685117-0.666927197812-0.5938922567781.804991360510.1145401529561.73059732331-0.1089460249950.195490469993-0.328913380673-0.2829078500190.0260615344536-0.07595252236430.307196210282-0.03057420510520.1003531593680.276451987236-0.02828298072740.05942102075120.20230652354-0.01208316820330.313697195791-11.1121611419-24.89951895558.18203239827
31.174876313810.494718465213-0.3199214818551.000231529160.01678346149790.762473289354-0.0330863072907-0.143700620884-0.08906376442890.06868666323270.005379512737110.01671443810180.04406012853010.1342672568120.01935379468090.180549033744-0.00116686778290.01497966079420.191127508730.01012966995070.1670881402937.38676460351-8.7391738306114.0612136049
42.30153204529-0.476572448847-0.7740567426370.978633023080.1458989916350.381220051807-0.09707400991290.0980221401049-0.0873804059558-0.04592629566610.051828406895-0.00345440371570.0681128514424-0.05093919582490.03859160068740.18443409333-0.0151453087867-0.00528128914570.174014776415-0.02396116585860.1596145155452.12317870819-16.7439760984-43.632706447
54.000078715291.18211450785-0.6219016663912.58150306168-0.2546581687522.497231354910.0706527940084-0.213857377572-0.08177222795780.276594124674-0.1147219701670.05264319971170.1114849955460.02232234000060.08196950700920.2395076847680.01946347596240.008810437156380.170312401518-0.002510738351490.25652899459411.6348368173-25.068307352-34.3563185768
60.848069361754-0.3072867794-0.4093319535860.951257335781-0.05133228831160.470848878485-0.04212015263690.0683355054359-0.01567422953230.01688478851780.01618870238730.01094137328880.0112271785286-0.1004897478570.02308838079930.1785542912680.00605699507749-0.005077094848330.190774454426-0.01800623878960.167296386942-7.37894701016-8.43123186002-39.9811157596
70.855151886999-0.07027089967220.8495849869231.02995106783-0.5204252985032.61451869955-0.01929867208790.07046179334580.124787525614-0.0259000600909-0.0173964621836-0.0627433652261-0.3220818965560.2267111438340.02454842590040.232544443989-0.05482515867380.01683132485050.216443812839-0.01591259180380.22563830365525.691286468819.1489253115-30.1052339954
83.280763191480.5324051408741.534228606453.271070274130.9692023073923.23095792359-0.193613912788-0.1383219682640.508003675664-0.0620509986578-0.1828863363970.313818467749-0.539982655097-0.2159133910530.3409018395870.344700007660.000649097327064-0.00780345149560.214624715044-0.001863283923790.36266437365713.674230570826.8010520084-33.7167819143
90.6758411752750.0631241503427-0.007735209624941.46074688924-0.373799348211.02984886866-0.0222542530188-0.07316092545880.0455976663587-0.100754976847-0.0406834707625-0.010066535944-0.1180051849470.2080019808140.0580709461730.190457588287-0.01892269228397.32005813273E-50.235375982443-0.02577729042480.19222701387927.478268386810.0655301047-19.6140948023
101.14904686181-0.006605124608980.6277700513541.483183818830.1692334501362.138196905120.000965287354379-0.1553143697010.06972496888230.1549501036330.01213667797870.0617840344621-0.198079328233-0.291949051581-0.01137028071410.2189896730910.05170074090890.02701491472420.218842698078-0.007667323625450.177174783643-27.231855319318.22693017378.87381304007
111.057777540750.3070926207221.001688191721.02072656726-0.1473781450491.78825685606-0.1108843460750.1538637048530.1082175326590.004926329180390.0972770068194-0.176809874276-0.2426130279960.310140916725-0.02116263924140.245639459950.02803812710240.007830584249840.213554341555-0.006766521449920.211450931549-17.104286850422.9150909203-4.0396275902
120.530953655420.1886332947780.00916685562190.9180269248640.3843782707821.010141938330.005434974104820.07761904644880.008788793610490.0339702044017-0.009618411617890.0320439939599-0.100516634843-0.1710620336050.007151320651230.1900145643730.03139436452678.4254720587E-50.21975666885-0.001409245682570.185586529657-26.672614585811.8740952256-5.23793327769
132.181422237570.6900739545320.1312267291711.00976978185-0.1990014791090.37129409884-0.0570087550315-0.03920744069130.01262143594890.01492054678193.17152919297E-5-0.0501124564988-0.1054422821090.01896814897360.05481704515820.215446757956-0.020377694301-0.02345771939970.156143945972-0.001987957307120.13782501892821.093853069318.26062142614.1323402212
142.009144256220.668339102244-0.6840319729930.757492213028-0.1269791002220.715120780181-0.05378407860440.3963626162080.327386623778-0.1064017362140.1271373390680.158094385034-0.144943763784-0.100673593378-0.06516399473750.300816332057-0.019763274369-0.0486001091010.2206005992760.03937773439530.2061619941918.7528879709323.02646266083.9627608633
151.155388047420.5165481904750.1894560271120.921992401404-0.01120491904630.335085915102-0.0658493467137-0.0682732732231-0.0250777443822-0.01717124656670.0154585911304-0.0235909699086-0.070213781261-0.01656296710750.03473093832130.201709472524-0.0055680378434-0.01935831282650.1763821135750.0124640915090.16170603357.6067033145311.390003585913.8640612139
161.87428936637-0.612317635808-0.1426708015370.7946429245850.3342063673810.138321606043-0.0464410417679-0.03854869995710.148048487056-0.02532192067270.0208514976752-0.0496546754043-0.02298594467770.02535940644560.03629944107780.2044086807460.00437016644068-0.009698440582230.1650328366450.007974120413750.164717630089-16.980906095518.9910628475-38.6288903931
173.421655316870.930762092115-1.460118791322.79633533606-0.6212399706232.404078690150.0911227450053-0.8769882720140.3593991383590.3709890075890.0226379171003-0.185436686724-0.2757821845340.592327015152-0.09974013494630.351097444795-0.0150916615514-0.05482952612570.397566316145-0.07309486511530.308167187228-19.248646566527.4681036239-26.9334565281
181.130600070950.1938077213360.1321515586651.29899638395-0.2189107982220.336019969166-0.02774288324860.07435462624990.116709563092-0.001972033025510.0585718539710.11357663803-0.06626498970450.06032425467-0.03653653993960.199547145660.024783360438-0.003585813721080.188548462836-0.01549424948690.174988354789-6.673937052969.90277716996-40.4803165642
191.351206024910.103619484108-0.2528391160471.637277014790.1232361523472.14715321657-0.02256335229850.0715204867566-0.171405874037-0.0346169399365-0.0227687149630.1702756370170.17965560486-0.4746170620740.03327345301680.192752761204-0.03917560123310.005127431084040.310174117629-0.03186719659750.255415866249-35.3556740141-18.5343928789-19.4258880478
200.4896270767410.03564500417320.4175147172130.651098011210.1581936513982.31779167912-0.02151460017280.0295022793703-0.132096914903-0.02130347222290.0210486274841-0.03232884581170.191796857034-0.08906845628940.01434586642140.127925680689-0.02454020284690.03208572366080.152854747586-0.01087893154780.174247993926-24.2531352704-18.2641379146-12.0773162455
210.707470420084-0.5168977376740.3943888933091.49483643281-0.4187846974361.57252827324-0.00705377688298-0.0238545232195-0.005073854189-0.04647519417920.009510191642870.106017526449-0.0633273230201-0.217790034487-0.004162469888740.1789573449060.03265557674330.005949991345260.223434364975-0.01770995567020.185815000066-26.6656695249-3.07258801836-5.19440302031
220.7630917500080.01919969452110.3150291551861.29294540286-0.2953162740272.31449711302-0.0190416370170.0191639946558-0.1322343231420.07480059986450.00890949825323-0.1179099542640.07256821848760.505312176824-0.005057171892730.1522410086310.0376097769832-0.008492790452550.27718500191-0.01684017448650.23154059979934.2489081311-16.2825343413-7.93927418258
230.5804248002340.2944417263660.1330047385290.918117224241-0.2979026022782.631759763980.0059693928107-0.0452356023788-0.1899959625430.05546093824550.1252185215190.1514995861360.352528235887-0.31776858096-0.1284052937390.2068360901540.02202590248880.007240147607130.226574697671-0.006451955589140.25726908763419.4755670398-21.4515168765-13.0256438991
240.525061580560.1483451679320.3978906431671.0745082272-0.3646669951881.0264762208-0.02568996411350.0678360737355-0.0673222600910.009812824150540.0381756468796-0.0717821947561-0.005174522176570.224700426718-0.01790164226850.1625115636020.004162364400110.01007625141920.243595179268-0.03260641284780.22182698949727.1616506711-8.54500410672-20.3531357414
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 1:129)
2X-RAY DIFFRACTION2(chain A and resid 130:151)
3X-RAY DIFFRACTION3(chain A and resid 152:206)
4X-RAY DIFFRACTION4(chain B and resid 1:130)
5X-RAY DIFFRACTION5(chain B and resid 131:151)
6X-RAY DIFFRACTION6(chain B and resid 152:206)
7X-RAY DIFFRACTION7(chain C and resid 1:131)
8X-RAY DIFFRACTION8(chain C and resid 132:154)
9X-RAY DIFFRACTION9(chain C and resid 155:206)
10X-RAY DIFFRACTION10(chain D and resid 1:103)
11X-RAY DIFFRACTION11(chain D and resid 104:148)
12X-RAY DIFFRACTION12(chain D and resid 149:206)
13X-RAY DIFFRACTION13(chain E and resid 1:105)
14X-RAY DIFFRACTION14(chain E and resid 106:148)
15X-RAY DIFFRACTION15(chain E and resid 149:206)
16X-RAY DIFFRACTION16(chain F and resid 1:128)
17X-RAY DIFFRACTION17(chain F and resid 129:154)
18X-RAY DIFFRACTION18(chain F and resid 155:206)
19X-RAY DIFFRACTION19(chain G and resid 1:78)
20X-RAY DIFFRACTION20(chain G and resid 79:167)
21X-RAY DIFFRACTION21(chain G and resid 168:206)
22X-RAY DIFFRACTION22(chain H and resid 1:104)
23X-RAY DIFFRACTION23(chain H and resid 105:151)
24X-RAY DIFFRACTION24(chain H and resid 152:206)

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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

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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

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