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- PDB-9d9o: Crystal structure of CVB3 replication-linked RNA stem-loop D in c... -

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Basic information

Entry
Database: PDB / ID: 9d9o
TitleCrystal structure of CVB3 replication-linked RNA stem-loop D in complex with 3C protein
Components
  • Protease 3C
  • RNA (36-MER)
KeywordsVIRAL PROTEIN/RNA / Cloverleaf RNA-3C protein complex / Viral replication / enterovirus / Coxsackievirus B3 / 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
RNA / RNA (> 10) / Genome polyprotein
Similarity search - Component
Biological speciesCoxsackievirus B3
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.41 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 stem-loop D 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
A: Protease 3C
B: Protease 3C
R: RNA (36-MER)


Theoretical massNumber of molelcules
Total (without water)54,4093
Polymers54,4093
Non-polymers00
Water45025
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3090 Å2
ΔGint-24 kcal/mol
Surface area21080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.300, 78.869, 106.508
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
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 2 through 4 or resid 6...
d_2ens_1(chain "B" and (resid 2 through 4 or resid 6...

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_11GLYGLYALAALAAA1 - 32 - 4
d_12GLUGLUARGARGAA5 - 396 - 40
d_13ALAALAASNASNAA41 - 8042 - 81
d_14LYSLYSTHRTHRAA82 - 14283 - 143
d_15ALAALAGLUGLUAA144 - 182145 - 183
d_21GLYGLYALAALABB1 - 32 - 4
d_22GLUGLUARGARGBB5 - 396 - 40
d_23ALAALAASNASNBB41 - 8042 - 81
d_24LYSLYSTHRTHRBB82 - 14283 - 143
d_25ALAALAGLUGLUBB144 - 182145 - 183

NCS oper: (Code: givenMatrix: (-0.887573758163, 0.100996449195, 0.449458052626), (0.00518176773539, -0.973420322555, 0.228967300983), (0.460636486944, 0.205554355065, 0.863458993821)Vector: 28. ...NCS oper: (Code: given
Matrix: (-0.887573758163, 0.100996449195, 0.449458052626), (0.00518176773539, -0.973420322555, 0.228967300983), (0.460636486944, 0.205554355065, 0.863458993821)
Vector: 28.9500660753, -58.390256738, -0.467364479846)

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Components

#1: 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
#2: RNA chain RNA (36-MER)


Mass: 11471.787 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Coxsackievirus B3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / Source method: isolated from a natural source / Formula: H2O
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: 2.02 Å3/Da / Density % sol: 39.07 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion / pH: 7 / Details: DL-Malic Acid, PEG 3350

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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-1 / Wavelength: 0.97934 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Aug 4, 2023 / Details: KB bimorph mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.41→78.87 Å / Num. obs: 32615 / % possible obs: 100 % / Redundancy: 6.7 % / Biso Wilson estimate: 55.8 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.091 / Net I/σ(I): 13.8
Reflection shellResolution: 2.41→2.45 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.681 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 5449 / CC1/2: 0.873 / % possible all: 96.5

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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: 2.41→44.13 Å / SU ML: 0.3856 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.9368
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2378 3255 9.98 %
Rwork0.1943 29345 -
obs0.1987 32600 99.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 67.15 Å2
Refinement stepCycle: LAST / Resolution: 2.41→44.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2844 760 0 25 3629
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00843748
X-RAY DIFFRACTIONf_angle_d1.11125229
X-RAY DIFFRACTIONf_chiral_restr0.0589608
X-RAY DIFFRACTIONf_plane_restr0.0108546
X-RAY DIFFRACTIONf_dihedral_angle_d12.68821
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 1.08724440787 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.41-2.450.3361370.32561212X-RAY DIFFRACTION94.4
2.45-2.490.35111410.34131238X-RAY DIFFRACTION97.11
2.49-2.530.28481410.33591268X-RAY DIFFRACTION97.44
2.53-2.570.39211360.31111253X-RAY DIFFRACTION99.21
2.57-2.620.35071470.30691284X-RAY DIFFRACTION99.65
2.62-2.670.37111410.3061264X-RAY DIFFRACTION99.79
2.67-2.720.38951420.27851292X-RAY DIFFRACTION99.51
2.72-2.780.31221480.26191292X-RAY DIFFRACTION100
2.78-2.850.28211420.24581271X-RAY DIFFRACTION100
2.85-2.920.32751380.26151300X-RAY DIFFRACTION100
2.92-2.990.31861390.2411240X-RAY DIFFRACTION100
3-3.080.30691460.22941315X-RAY DIFFRACTION100
3.08-3.180.25591330.24021281X-RAY DIFFRACTION100
3.18-3.30.28131450.22141300X-RAY DIFFRACTION99.86
3.3-3.430.23391430.19021267X-RAY DIFFRACTION100
3.43-3.580.23341450.18041301X-RAY DIFFRACTION99.93
3.58-3.770.21541420.17071258X-RAY DIFFRACTION99.93
3.77-4.010.22761430.17671296X-RAY DIFFRACTION99.86
4.01-4.320.17581380.15921296X-RAY DIFFRACTION99.93
4.32-4.750.20421410.14331292X-RAY DIFFRACTION99.58
4.75-5.440.19471300.14431263X-RAY DIFFRACTION100
5.44-6.850.27031490.18351283X-RAY DIFFRACTION100
6.85-44.130.15351480.15931279X-RAY DIFFRACTION99.51
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)
12.25851906414-2.166313482131.112300605365.851781458020.09580040342227.962557967450.113170570088-0.0786837129303-0.666558630972-0.197966139084-0.0455691547503-0.346836356415-0.116066522894-0.0421656201491-0.06486152160360.256604878412-0.000363905703468-0.04224218097340.444050432568-0.03678458397030.63659216903612.4201861779-40.307378695-8.8201589486
25.90327556403-0.613471421497-1.227705852644.406906048090.1582765009025.39618439106-0.196807792724-0.917535171153-0.4821927587070.525564367767-0.3149288699850.5448179196820.47166544981-0.4082052070020.3965641285420.334065636625-0.04765371596410.06130212864520.571339046857-0.02478859022530.8238058838461.33987397654-46.6233489237-4.64965940306
33.568523289440.534284254795-0.773395614995.71392517844-1.89214014055.435081880770.1429211311090.146761607263-0.749911285031-0.0888301938573-0.0542136715850.5661925014730.290500898274-0.06502882638320.06855414927880.311310275262-0.0592592054479-0.03436774367250.500246607252-0.0375427260480.8031369900256.38539790626-50.9032761163-11.966761715
48.75647034813-4.898259272853.14329652013.0325242055-2.605966788883.588105566880.7260574173230.548317315768-2.48951192354-0.5366343367910.284187017215-0.6648715741240.4817811893930.8330225999051.245574097080.5260527879230.04660652367790.4542368490690.67928433971-0.1747422731611.3784849622824.0756501156-53.3800007176-16.1869422149
54.967910471555.0059793703-1.457422203695.81428569522-2.339357461541.90444510780.0688659328652-0.163116720358-0.9832688717280.223984572995-0.251213053881-0.6870266703520.09083119641670.03468425965490.2305291738860.3539830857620.04148786319070.03315900385680.6618681695980.02315850468870.9288302075120.9580455058-49.6244942769-3.71570223122
64.94381077411-4.013903122012.010489361583.36638641428-2.119072635892.459621869610.6060508469410.4956202723060.6711345378361.38099696957-1.37940596191-1.03270724803-0.3372800731240.7619298779330.5199794530770.593791268432-0.214033629608-0.07802712509850.7806430173850.2266974565341.2178959039222.0190322248-45.11035942871.53639998713
72.850789259220.9693995817791.224984216516.38850328012-0.8876494839676.69693375114-0.2279963144950.146636564286-0.651223642390.107504069151-0.321577861068-0.7218619589660.01330028020610.667445857966-0.3180332981720.2854020710850.01942878253780.0673491972630.534893659473-0.09049910213340.89754876980519.7132499769-47.3566728323-10.2632080672
84.98209834829-1.69997187503-0.6355018711796.49141731042-0.5940450736198.292780029330.0944623310828-0.545315090597-1.81263883852-0.0454732788551-0.08444559010850.008504254322730.491703525509-0.8143330389420.3004046686190.391156631827-0.008076705306150.09376258211420.508961370811-0.02590761102070.94226151810915.2981390832-54.4374279773-9.80980399373
98.110092691052.201923458118.383288919046.95957389535.731426326522.000734669570.1984276525714.113792520241.62509606174-2.12056362022.31622711257-1.01419404356-0.773456695521.552129613561.167064899660.815007508206-0.0587879787604-1.048823470372.53452832818-0.7096841512222.1143407227-11.1949024528-20.8118161015-24.3173631555
102.679111411131.184613301970.6778517890941.178688988371.162710216651.94693449651-0.1169958849940.508483016597-0.0263496009416-0.246899421793-0.4038883157610.1090037931490.273302423654-0.3213896716650.2159629671560.394433306155-0.0349433389825-0.003640941839170.728643586389-0.1098066290390.7419862078670.482015748551-32.3550547351-21.3874633983
113.108823552633.851044395050.7463074534165.121896698890.8168352086273.94810988635-0.3056589622930.948896086092-0.4930135439-0.5115302490060.0538255429299-0.6042675661040.1740265985780.557003640488-0.08993498617780.468014783035-0.06167897942480.1390788818360.851592234222-0.1816444566290.53697459929915.3464594897-33.5409757812-29.9477215994
125.99098015860.0242960376984-0.3262327187153.537723518051.182791528933.71787088967-0.102736592808-0.4930383694951.049132372970.07978256873-0.1438281130781.30390054777-0.516518954825-1.357075069690.3659360081390.4688347475170.101381208495-0.05618439271360.846532641025-0.1536214670171.07688231628-9.32897289362-33.1375617196-20.9617615033
131.99943093586.351881967-1.823411791246.20777431809-4.018540885319.23013476162-2.04033911260.4253555443070.922895928202-1.68499053558-0.886266100819-0.437089619743-1.278263858321.162224228891.970531399691.51646321711-0.2315475039740.01142202466043.56749062563-1.137059769472.65444187679-14.1668516099-20.3332568585-18.5435094605
148.35734145516-0.836639744181.448594605597.91004028760.3093996021425.3833116561-0.0875556523492-0.3156287012850.3307549108710.06269430961770.0885550300477-0.581230187419-0.0315123655820.3851738261420.06802133045790.2648651496110.04451139361710.03939267885390.40314850343-0.05511393909660.40401904619716.5083434442-18.283557465-11.8187287289
153.773185622060.470179511103-1.525724498265.825162722390.8993179516834.08301811902-0.2437922817360.2608568328480.483254729315-0.3349944230360.281345630831-0.0302923442806-0.061703690174-0.08202753625020.005434009364590.2884831736750.00753658441839-0.1105569472230.456752497410.01848711920960.50940994749510.1247579607-13.2518626596-14.0417982878
164.381458160463.39171614463-4.167437255462.90621311366-3.083555752155.500411131540.420868682235-0.2220675199960.9195192150770.605431971448-0.219889673510.359012683222-0.881606879612-0.0604223354197-0.1579618138880.4219952813030.00570545614016-0.06721373276860.592342657042-0.0601244890270.8108655713673.86826813246-5.37958497467-5.06839005778
171.52941230375-1.62853428615-1.206845715095.510596058411.005946298218.447176368510.0671663097094-0.24985656880.302607607599-0.140306973111-0.0442529519724-0.4106145762810.1124894088530.3486963262890.1293829664090.215995149668-0.0184760487043-0.1080656555320.530179057140.01851390534030.6252716626066.40668948135-10.7613643985-9.13678964162
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'B' and (resid 1 through 32 )BB1 - 321 - 32
22chain 'B' and (resid 33 through 62 )BB33 - 6233 - 62
33chain 'B' and (resid 63 through 90 )BB63 - 9063 - 90
44chain 'B' and (resid 91 through 100 )BB91 - 10091 - 100
55chain 'B' and (resid 101 through 139 )BB101 - 139101 - 139
66chain 'B' and (resid 140 through 150 )BB140 - 150140 - 150
77chain 'B' and (resid 151 through 165 )BB151 - 165151 - 165
88chain 'B' and (resid 166 through 183 )BB166 - 183166 - 183
99chain 'R' and (resid 46 through 50 )RD46 - 50
1010chain 'R' and (resid 51 through 55 )RD51 - 55
1111chain 'R' and (resid 56 through 75 )RD56 - 75
1212chain 'R' and (resid 76 through 80 )RD76 - 80
1313chain 'R' and (resid 81 through 81 )RD81
1414chain 'A' and (resid 1 through 62 )AA1 - 621 - 62
1515chain 'A' and (resid 63 through 112 )AA63 - 11263 - 112
1616chain 'A' and (resid 113 through 140 )AA113 - 140113 - 140
1717chain 'A' and (resid 141 through 183 )AA141 - 183141 - 183

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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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