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- PDB-9d9p: Crystal structure of CVB3 replication-linked RNA in complex with ... -

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Basic information

Entry
Database: PDB / ID: 9d9p
TitleCrystal structure of CVB3 replication-linked RNA in complex with 3C protein
Components
  • Protease 3C
  • RNA (90-MER)
KeywordsVIRAL PROTEIN/RNA / Cloverleaf RNA-3C protein complex / Viral replication / enterovirus / Coxsackievirus / Viral RNA / 3C proteinase / RNA / VIRAL PROTEIN-RNA complex
Function / homology
Function and homology information


symbiont-mediated perturbation of host transcription / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane ...symbiont-mediated perturbation of host transcription / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport / symbiont-mediated suppression of host NF-kappaB cascade / DNA replication / RNA helicase activity / endocytosis involved in viral entry into host cell / symbiont-mediated activation of host autophagy / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / DNA-templated transcription / virion attachment to host cell / host cell nucleus / structural molecule activity / ATP hydrolysis activity / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane
Similarity search - Function
Picornavirus coat protein VP4 superfamily / Picornavirus coat protein / Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Peptidase C3, picornavirus core protein 2A / Picornavirus core protein 2A / Picornavirus coat protein VP4 ...Picornavirus coat protein VP4 superfamily / Picornavirus coat protein / Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Peptidase C3, picornavirus core protein 2A / Picornavirus core protein 2A / Picornavirus coat protein VP4 / Picornavirus coat protein (VP4) / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Picornavirus capsid / picornavirus capsid protein / Helicase, superfamily 3, single-stranded RNA virus / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA helicase / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / Reverse transcriptase/Diguanylate cyclase domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
PHOSPHATE ION / RNA / RNA (> 10) / Genome polyprotein
Similarity search - Component
Biological speciesCoxsackievirus B3
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.69 Å
AuthorsDas, N.K. / Koirala, D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB-2236996 United States
CitationJournal: To Be Published
Title: Crystal structure of CVB3 replication-linked RNA in complex with 3C protein
Authors: Das, N.K. / Koirala, D.
History
DepositionAug 21, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 1, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
R: RNA (90-MER)
A: Protease 3C
B: Protease 3C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,2018
Polymers71,7263
Non-polymers4755
Water1,76598
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4250 Å2
ΔGint-56 kcal/mol
Surface area29370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.406, 95.251, 113.637
Angle α, β, γ (deg.)90.000, 98.630, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 1 through 4 or resid 7...
d_2ens_1(chain "B" and (resid 1 through 4 or resid 7...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11METMETALAALAAB0 - 31 - 4
d_12PHEPHETHRTHRAB6 - 207 - 21
d_13TYRTYRASPASPAB22 - 3223 - 33
d_14TRPTRPPROPROAB34 - 3835 - 39
d_15HISHISALAALAAB40 - 5941 - 60
d_16GLUGLUALAALAAB61 - 9162 - 92
d_17GLUGLUSERSERAB93 - 10794 - 108
d_18PHEPHEASNASNAB109 - 139110 - 140
d_19PROPROGLYGLYAB141 - 166142 - 167
d_110GLNGLNASNASNAB168 - 180169 - 181
d_21METMETALAALABC0 - 31 - 4
d_22PHEPHETHRTHRBC6 - 207 - 21
d_23TYRTYRASPASPBC22 - 3223 - 33
d_24TRPTRPPROPROBC34 - 3835 - 39
d_25HISHISALAALABC40 - 5941 - 60
d_26GLUGLUALAALABC61 - 9162 - 92
d_27GLUGLUSERSERBC93 - 10794 - 108
d_28PHEPHEASNASNBC109 - 139110 - 140
d_29PROPROGLYGLYBC141 - 166142 - 167
d_210GLNGLNASNASNBC168 - 180169 - 181

NCS oper: (Code: givenMatrix: (-0.397738039858, -0.668119017018, -0.628825437421), (-0.663414702273, -0.264013454116, 0.700127009087), (-0.633786544869, 0.695639184595, -0.338231785022)Vector: 21. ...NCS oper: (Code: given
Matrix: (-0.397738039858, -0.668119017018, -0.628825437421), (-0.663414702273, -0.264013454116, 0.700127009087), (-0.633786544869, 0.695639184595, -0.338231785022)
Vector: 21.7497447233, -19.1810008852, 41.4770575386)

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Components

#1: RNA chain RNA (90-MER)


Mass: 28789.004 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Coxsackievirus B3
#2: Protein Protease 3C / Picornain 3C / P3C


Mass: 21468.578 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Coxsackievirus B3 / Production host: Escherichia coli (E. coli) / References: UniProt: P03313, picornain 3C
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 4.11 Å3/Da / Density % sol: 70.05 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion / pH: 7 / Details: Glycerol, Bis-Tris, Ammonium Sulfate

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Liquid Nitrogen Jet / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.97934 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Oct 25, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.69→37.45 Å / Num. obs: 59666 / % possible obs: 99.8 % / Redundancy: 3.4 % / Biso Wilson estimate: 61.25 Å2 / CC1/2: 0.997 / Net I/σ(I): 19.2
Reflection shellResolution: 2.69→2.74 Å / Num. unique obs: 5248 / CC1/2: 0.93

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487phasing
DIALSdata reduction
xia2data scaling
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.69→37.45 Å / SU ML: 0.3489 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 28.297
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2316 3800 6.39 %
Rwork0.1982 55699 -
obs0.2003 59499 97.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 103.38 Å2
Refinement stepCycle: LAST / Resolution: 2.69→37.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2844 1904 25 98 4871
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00795045
X-RAY DIFFRACTIONf_angle_d1.14887248
X-RAY DIFFRACTIONf_chiral_restr0.0528878
X-RAY DIFFRACTIONf_plane_restr0.0095600
X-RAY DIFFRACTIONf_dihedral_angle_d20.11871469
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.677567932351 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.69-2.720.37261390.38532028X-RAY DIFFRACTION94.01
2.72-2.760.40021430.36772057X-RAY DIFFRACTION95.94
2.76-2.80.31171280.33511959X-RAY DIFFRACTION94.65
2.8-2.840.29591400.31692054X-RAY DIFFRACTION95.47
2.84-2.880.37711380.29582084X-RAY DIFFRACTION96.61
2.88-2.930.31411350.29521976X-RAY DIFFRACTION95.65
2.93-2.970.32561410.2762075X-RAY DIFFRACTION94.54
2.97-3.020.2911330.26571967X-RAY DIFFRACTION94.89
3.02-3.080.25421460.24822110X-RAY DIFFRACTION98.26
3.08-3.140.26491390.25462079X-RAY DIFFRACTION98.4
3.14-3.20.30291440.26422077X-RAY DIFFRACTION98.14
3.2-3.270.26771450.26892096X-RAY DIFFRACTION98.51
3.27-3.350.30811380.22222070X-RAY DIFFRACTION98.31
3.35-3.430.24321470.19622113X-RAY DIFFRACTION98.39
3.43-3.520.24631370.1922062X-RAY DIFFRACTION98.04
3.53-3.630.25741410.18782101X-RAY DIFFRACTION98.51
3.63-3.750.18561390.19012078X-RAY DIFFRACTION97.62
3.75-3.880.22481390.17492018X-RAY DIFFRACTION97.43
3.88-4.030.22631400.1892054X-RAY DIFFRACTION95.31
4.03-4.220.19221450.16312079X-RAY DIFFRACTION96.61
4.22-4.440.19351420.14792020X-RAY DIFFRACTION96.52
4.44-4.720.19181420.14712075X-RAY DIFFRACTION97.97
4.72-5.080.16171430.15632113X-RAY DIFFRACTION98.9
5.08-5.590.1921420.17392091X-RAY DIFFRACTION98.94
5.59-6.40.23031460.20772106X-RAY DIFFRACTION98.86
6.4-8.040.21691430.19092051X-RAY DIFFRACTION97.38
8.05-37.450.21951450.16372106X-RAY DIFFRACTION98.95
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)
12.872636195752.21054052848-3.256878017385.442241186680.7276068611396.53653123325-0.5221920263220.506138824896-0.5855519454510.2851873259430.0558880672218-1.684172064480.3810886037121.500478551380.4571965220630.600800872014-0.0634687961914-0.2466679168381.06913557915-0.04156178232251.411440860536.7826324294-12.66554910818.14198401178
22.674983335762.33175535946-2.900004653434.052505319660.1182516183556.648368674290.253692981014-0.3685567774540.08990102611060.255371647136-0.210765647798-0.08105410903530.1410370396580.283418403032-0.05366378520830.463877043063-0.175023108208-0.2137022160110.6663335896930.0192283350140.82729326191431.4558631012-4.4864199617816.1548996916
32.006272864442.96720649086-0.6200836128266.148399386142.41975013216.1570148009-0.0354274515005-0.332595515810.641173597246-0.3928376314660.12595505673-0.368455109901-0.5458777557620.686057997428-0.1156893458310.473189332141-0.249946574943-0.1665380226450.610971428056-0.0155818353570.7350236766331.90552015452.3920039956311.7745910341
44.754831385021.106035494060.6286762278683.4199723297-0.3858803247621.797689127470.509223213325-0.497902636761-0.4298198174020.467391124106-0.501374066823-0.4449573441620.2156329959540.322887336117-0.01898430781070.420285538125-0.169513315983-0.161692250140.8134736286140.04648918180110.71545445819512.7047731179-27.386262737521.4863462278
51.57493962906-0.0752115354640.5213383700863.97089518165-0.5444624822653.365797538380.40006345475-0.209816033672-0.3555505071710.165985396939-0.3673518792610.1085590897090.1180488980180.0878664334077-0.07156031885620.294573410533-0.103799739677-0.1151245613040.766775299020.02232800919030.829251660973.40357187805-30.670054172117.3088477728
63.90570978347-0.141955395003-0.867943917363.445412564140.7163142220992.318013968330.343339849762-0.238709773088-0.5379839595960.050759523515-0.3098294778080.2360705175920.3462622572970.0720536058767-0.1242185243860.3553265943-0.0644334239542-0.1967993153170.6468540268790.04130364779630.8886687666772.05293788596-32.402453127913.9131150766
75.13285789581-1.624843230485.699502955278.8580152589-3.491986929376.657159127340.815947012709-0.646786818345-0.4379580430651.24262698872-0.952049863013-0.7140040999040.5158321221941.740968545880.1867695713631.41444256567-0.0428437543906-0.2628218304582.52882683090.2404760497681.4086134215330.3653562498-11.138177719450.1702540837
84.0457788079-2.863509696454.476644359122.05266014128-3.219112758025.0749533978-1.74614976424-1.685649192762.042553288472.133567796840.334252850266-1.30973855735-1.269429127230.7417660240021.370663616552.46138769523-0.0840138542029-0.7082647489783.01429687231-0.5700462212232.1278709231130.765709174110.209431952358.1797286724
94.68356618729-0.4951653634351.477455956852.37022503534-0.07532406425323.85090678764-0.0516857241759-0.9489300484730.4940353973970.7027875704790.07169466857250.130419299003-0.676573477202-0.3185762277730.0495785060290.64630808119-0.128608922492-0.002616641279680.831277326029-0.1851269268180.808417676748.40794768301-0.55834963515931.8001950272
102.10962723731-0.9233777475632.894254894320.432120114165-1.335054430344.18977806479-0.92523362065-0.9469309879790.1415853934871.48423620190.0110384410297-1.14650010771-0.7129458747770.3180090888980.9134839313121.44158615138-0.156047466803-0.3563957462691.776940841010.08351065387591.1321192322832.3642145958-10.862734413852.7679867048
113.053209230180.906122863816-3.553605084192.275180135890.949502629346.50789732075-0.0951419826617-0.119909960532-0.121716813880.50024281646-0.380243222419-0.04990913808680.763512466966-0.01389696392540.3660053501090.511769895594-0.121522451696-0.1620207732340.5213841863670.06943759936360.73325863027722.9069965357-11.068924034216.5384021461
126.781596347530.497382269054-2.462937389552.912545216731.597017903013.42256409236-0.1816182867410.9768560308880.271408594642-0.487303077537-0.4009971011360.221215327129-0.136839337332-0.420992469040.4767769711050.388268610623-0.0721706307211-0.1105376730260.6202909636180.0388392615860.71685497557124.0802517844-5.326933320394.05026323698
136.907724702041.24630444387-1.229634124163.855053972050.9408092054064.093186004570.003173786683650.354114414931-0.135433476012-0.218511713419-0.08628177416580.0968154466052-0.1445308461010.4880163883830.188791475650.377953820154-0.106096510747-0.1977726988890.7143095872130.013179442950.8617056105321.2797625297-3.130795464531.82890911161
144.423316068290.876085457158-1.992313658567.55776829174-0.457955774156.662885846520.03456852526740.7420883590411.14698074049-0.565086988482-0.3157493665770.298915200151-0.600290995304-0.3591675659640.3048181038730.428949839412-0.0859286068599-0.164684037920.703335462860.006961725761240.79202158465617.76818360160.0956815805867-0.393120508456
152.532651729193.66853460633-0.7117888419365.68096974359-0.4468033985893.10248551292-0.156355380825-0.2483438245250.797406656525-0.1714579321540.1773609977390.0294856954006-0.3932758706030.254561649461-0.04333830801740.400083813704-0.0632189466313-0.1177163810670.6693749614030.1208580928970.74719911878829.44976261827.171598091294.52706083181
161.25270661878-0.123881053624-1.38866566092.03085440276-1.485964408542.93194854157-0.078417197394-0.05389660143580.7224152161030.0825645562676-0.1292665212450.832154658781-0.242281402119-0.09655063180150.1172708619280.358802739208-0.166927189806-0.03712302952840.727354637367-0.08938278551630.98213920367414.8547100648-0.92818518754513.5826700421
176.08839409747-5.063375944461.048757208396.67350596237-2.295148101712.81260369064-0.266129241676-0.6098066922720.752029845611.646805228050.10261298077-0.689913226206-0.6766004295190.5620989032470.05879221939230.7297545476-0.350608181553-0.2030632148670.879799145621-0.03248845861881.0210922802134.87434278522.0870454567921.8826382212
182.469223090782.4038428128-1.650954686164.189230509591.821874501857.58462857628-0.1341288795450.179920103891-0.05979765347910.314094658722-0.3992385149220.6196125355190.739440198419-0.3677567954150.4901152459490.463908883043-0.0900034211589-0.1798382478230.606626666282-0.1090068387810.9463474033829.1304207639-15.399367349510.5422471987
193.644277315451.93692014012-1.030173370924.96975912387-0.9803921679291.895054518680.136544643719-0.343245558806-0.5150620748640.3401874566680.290966336299-0.7747648728010.1860476591140.5614674052-0.5062257800410.536285717399-0.0135579732947-0.3002802078260.739083032864-0.04226826665361.0873155283138.7010240178-5.696819199716.1186067325
204.14496880952.1073455037-2.401720634631.94140141391-1.181539535251.667407044260.199831689969-0.137748195536-0.114473737507-0.0347400674498-0.123038859689-0.4194500784060.2623503671850.1880424094830.03204697029310.415000731516-0.11018948705-0.2202149130630.67759588059-0.02270069512651.0050829822540.88690669581.266440435727.89389701384
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 141 through 150 )AB141 - 150141 - 150
22chain 'A' and (resid 151 through 165 )AB151 - 165151 - 165
33chain 'A' and (resid 166 through 183 )AB166 - 183166 - 183
44chain 'B' and (resid 1 through 62 )BC1 - 621 - 62
55chain 'B' and (resid 63 through 133 )BC63 - 13363 - 133
66chain 'B' and (resid 134 through 183 )BC134 - 183134 - 183
77chain 'R' and (resid 1 through 10 )RA1 - 10
88chain 'R' and (resid 11 through 30 )RA11 - 30
99chain 'R' and (resid 31 through 80 )RA31 - 80
1010chain 'R' and (resid 81 through 90 )RA81 - 90
1111chain 'A' and (resid 1 through 21 )AB1 - 211 - 21
1212chain 'A' and (resid 22 through 32 )AB22 - 3222 - 32
1313chain 'A' and (resid 33 through 52 )AB33 - 5233 - 52
1414chain 'A' and (resid 53 through 62 )AB53 - 6253 - 62
1515chain 'A' and (resid 63 through 78 )AB63 - 7863 - 78
1616chain 'A' and (resid 79 through 90 )AB79 - 9079 - 90
1717chain 'A' and (resid 91 through 100 )AB91 - 10091 - 100
1818chain 'A' and (resid 101 through 112 )AB101 - 112101 - 112
1919chain 'A' and (resid 113 through 125 )AB113 - 125113 - 125
2020chain 'A' and (resid 126 through 140 )AB126 - 140126 - 140

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