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- PDB-9ftf: Crystal structure of the Connecting Domain of the Nipah virus Lar... -

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Entry
Database: PDB / ID: 9ftf
TitleCrystal structure of the Connecting Domain of the Nipah virus Large protein
ComponentsRNA-directed RNA polymerase L
KeywordsVIRAL PROTEIN / Nipah virus L / Connecting Domain
Function / homology
Function and homology information


negative stranded viral RNA transcription / NNS virus cap methyltransferase / GDP polyribonucleotidyltransferase / negative stranded viral RNA replication / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / virion component / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / host cell cytoplasm / RNA-directed RNA polymerase / RNA-dependent RNA polymerase activity ...negative stranded viral RNA transcription / NNS virus cap methyltransferase / GDP polyribonucleotidyltransferase / negative stranded viral RNA replication / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / virion component / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / host cell cytoplasm / RNA-directed RNA polymerase / RNA-dependent RNA polymerase activity / GTPase activity / ATP binding
Similarity search - Function
RNA-directed RNA polymerase, paramyxovirus / Mononegavirales RNA-directed RNA polymerase catalytic domain / Mononegavirus L protein 2-O-ribose methyltransferase / Mononegavirales mRNA-capping domain V / RNA-directed RNA polymerase L, C-terminal / Mononegavirales RNA dependent RNA polymerase / Mononegavirales mRNA-capping region V / RdRp of negative ssRNA viruses with non-segmented genomes catalytic domain profile. / Mononegavirus L protein 2'-O-ribose methyltransferase domain profile. / Ribosomal RNA methyltransferase, FtsJ domain / FtsJ-like methyltransferase
Similarity search - Domain/homology
RNA-directed RNA polymerase L
Similarity search - Component
Biological speciesHenipavirus nipahense
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsBalikci, E. / Gunl, F. / Carrique, L. / Keown, J.R. / Fodor, E. / Grimes, J.M.
Funding support United States, 1items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationINV-048922 United States
CitationJournal: EMBO J / Year: 2024
Title: Structure of the Nipah virus polymerase complex.
Authors: Esra Balıkçı / Franziska Günl / Loïc Carrique / Jeremy R Keown / Ervin Fodor / Jonathan M Grimes /
Abstract: Nipah virus is a highly virulent zoonotic paramyxovirus causing severe respiratory and neurological disease. Despite its lethality, there is no approved treatment for Nipah virus infection. The viral ...Nipah virus is a highly virulent zoonotic paramyxovirus causing severe respiratory and neurological disease. Despite its lethality, there is no approved treatment for Nipah virus infection. The viral polymerase complex, composed of the polymerase (L) and phosphoprotein (P), replicates and transcribes the viral RNA genome. Here, we describe structures of the Nipah virus L-P polymerase complex and the L-protein's Connecting Domain (CD). The cryo-electron microscopy L-P complex structure reveals the organization of the RNA-dependent RNA polymerase (RdRp) and polyribonucleotidyl transferase (PRNTase) domains of the L-protein, and shows how the P-protein, which forms a tetramer, interacts with the RdRp-domain of the L-protein. The crystal structure of the CD-domain alone reveals binding of three Mg ions. Modelling of this domain onto an AlphaFold 3 model of an RNA-L-P complex suggests a catalytic role for one Mg ion in mRNA capping. These findings offer insights into the structural details of the L-P polymerase complex and the molecular interactions between L-protein and P-protein, shedding light on the mechanisms of the replication machinery. This work will underpin efforts to develop antiviral drugs that target the polymerase complex of Nipah virus.
History
DepositionJun 24, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 8, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA-directed RNA polymerase L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,8914
Polymers30,8181
Non-polymers733
Water3,765209
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area260 Å2
ΔGint-17 kcal/mol
Surface area13270 Å2
Unit cell
Length a, b, c (Å)40.760, 50.540, 61.100
Angle α, β, γ (deg.)90.000, 95.710, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein RNA-directed RNA polymerase L / Protein L / Large structural protein / Replicase / Transcriptase


Mass: 30817.604 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Henipavirus nipahense / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q997F0, RNA-directed RNA polymerase, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides, GDP polyribonucleotidyltransferase, NNS virus cap methyltransferase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 209 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.03 Å3/Da / Density % sol: 39.47 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 5.6 / Details: 35% tert-Butanol 0.1M tri-Sodium Citrate pH 5.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.95373 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Sep 21, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 1.85→60.8 Å / Num. obs: 19413 / % possible obs: 91.3 % / Redundancy: 6 % / Biso Wilson estimate: 29.13 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.102 / Net I/σ(I): 10.3
Reflection shellResolution: 1.85→10 Å / Num. unique obs: 19413 / CC1/2: 0.998 / % possible all: 91.55

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
DIALSdata reduction
xia2data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→60.8 Å / SU ML: 0.2289 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.078
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2185 1002 5.16 %
Rwork0.1933 18411 -
obs0.1946 19413 91.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.93 Å2
Refinement stepCycle: LAST / Resolution: 1.85→60.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2133 0 3 209 2345
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00232198
X-RAY DIFFRACTIONf_angle_d0.55242987
X-RAY DIFFRACTIONf_chiral_restr0.0378347
X-RAY DIFFRACTIONf_plane_restr0.0056372
X-RAY DIFFRACTIONf_dihedral_angle_d4.4475284
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.950.3441880.3241670X-RAY DIFFRACTION58.48
1.95-2.070.3541340.28032352X-RAY DIFFRACTION82.7
2.07-2.230.25921380.22392830X-RAY DIFFRACTION98.18
2.23-2.450.24331570.21292850X-RAY DIFFRACTION99.6
2.45-2.810.21121640.19882885X-RAY DIFFRACTION99.9
2.81-3.540.20461680.17942860X-RAY DIFFRACTION99.97
3.54-60.80.19021530.16842964X-RAY DIFFRACTION99.78
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)
10.757068670701-0.0910831817665-1.011943352910.6729882973275.99402847642E-51.02824325121-0.0652763059215-0.280553234504-0.164246548452-0.01750380702150.3830928767540.423494505726-0.0416281583581-0.1936025420080.0004149528419630.1776112402760.00444278908668-0.02910896100430.224149302040.0134930213040.236353905517-6.422463704399.02453360799-23.1965580529
20.00678711008052-0.1059507104080.4651207566630.367932853339-0.3480406584960.714392571290.04254314545290.0604653894159-0.217995709723-0.2996273345010.02478145520040.03987319060260.1503819150380.0128661552752-5.46678605154E-50.3783856103820.006190793293650.03364797800960.469691767025-0.01350285683440.443642030273.752183284894.15961150143-28.3958098911
30.327677118503-0.170962932878-0.5637808352770.02663772681690.1559104393460.651156980610.05389368989370.0800946228161-0.0286254139830.160266831276-0.130763399328-0.2435602792690.07295880897920.281801291661-1.64581132552E-50.2039806477830.00387444467080.007128897789870.252476095831-0.02762333341980.23864133472-2.5648089634710.9977134327-13.3835472768
40.7922878874180.07815788114140.2662878632990.449642268273-0.43136940870.467562706526-0.0282855583191-0.385579837398-0.2514200262580.3204988855580.0354534110302-0.3038681279460.2713996160530.4140453119990.0003719605735380.3003337817980.034872567908-0.02608750792180.2794891323160.02320624753080.3225867240292.010928039884.255398305740.279496722845
50.488647772205-0.209109907658-0.08068471642370.2941293790470.140667115020.1952479970940.0261887093509-0.196078793386-0.5785744828290.03085123657690.08579406896170.1297308361870.1867022585770.5216384722550.004938025476920.3127869296920.03118602059430.004589214343770.492704068034-0.116410137170.46016676698111.62712933373.43461341197-17.7174784123
60.4976261087090.0378840550059-0.3840030045540.3246519645180.1802719982150.203768952131-0.1722848476230.387133508966-0.1240271402260.182150433442-0.110873453886-0.164424395972-0.1850803007340.275572578174-0.0003778417879080.239240544533-0.00241202333930.01634624491530.395077002935-0.04192537430050.33353790385414.324050097518.0043648317-19.2696965424
70.803533224222-0.332843948777-0.3777851059810.210464095183-0.6320322688510.8050227709830.0381714085924-0.0397161943769-0.07841308794020.0165774095173-0.0236952961167-0.0382963743118-0.08737166373350.1259075040549.63062520822E-50.190911544181-0.01177040067330.0004940458143870.16491773848-0.02329956743220.216264072358-2.0154124003610.772199255-10.8970257324
80.372248380714-0.328454194798-0.1160789341440.559166543749-0.09655896199260.150381886937-0.005557018093230.0137830899297-0.164785904608-0.1352056343420.06622461865380.1359049263780.154556085987-0.128899086098-2.85425359461E-50.257253517003-0.02253196081480.0006304293873750.1819414645110.03001588572080.242746617173-12.82065900241.62555473788-6.87692316932
91.195537888520.127113353148-1.048611436440.4278747658050.3714739974591.828350988060.02474561948630.0438568963047-0.6433712786590.1013566335580.2411915658860.06276739648431.120937015310.6056758983470.06553879391030.5034693107680.0441650773356-0.1235987930290.217776174093-0.01133634571430.35978973047-9.12403285165-1.712831566987.15732252186
100.1898691115910.3096564392750.612869263884-0.3188823514920.1290294735271.205688426280.0401127738838-0.04883457822650.08900509264550.0164764135695-0.1461519788890.1432703560930.0979128520243-0.489047281296-0.0006368253926180.266324037733-0.00157897068620.02513530634040.2699875780860.00821924964940.253359939956-15.96302413086.78406375114-0.425045824662
110.037376568753-0.0833636208221-0.08923034283980.1200491522340.1934680599230.3474213767140.1138617005850.4312828650250.0187573050367-0.7833101892740.1010587512590.1283752363030.0431429396177-0.2424361940370.0007143069316380.305376038828-0.000636481421468-0.01242547474120.3102202531610.006094788803160.263523075617-7.1478616405512.2318187757-32.6928833371
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1481 through 1512 )1481 - 15121 - 32
22chain 'A' and (resid 1513 through 1538 )1513 - 153833 - 58
33chain 'A' and (resid 1539 through 1553 )1539 - 155359 - 73
44chain 'A' and (resid 1554 through 1578 )1554 - 157874 - 98
55chain 'A' and (resid 1579 through 1594 )1579 - 159499 - 114
66chain 'A' and (resid 1595 through 1619 )1595 - 1619115 - 136
77chain 'A' and (resid 1620 through 1653 )1620 - 1653137 - 170
88chain 'A' and (resid 1654 through 1676 )1654 - 1676171 - 193
99chain 'A' and (resid 1677 through 1689 )1677 - 1689194 - 206
1010chain 'A' and (resid 1690 through 1727 )1690 - 1727207 - 244
1111chain 'A' and (resid 1728 through 1743 )1728 - 1743245 - 260

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