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- PDB-5cfc: Crystal Structure of Human Cardiovirus SAFV-3 -

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Basic information

Entry
Database: PDB / ID: 5cfc
TitleCrystal Structure of Human Cardiovirus SAFV-3
Components
  • VP1
  • VP2
  • VP3
  • VP4
KeywordsVIRUS / Virion / capsid / saffold virus / pathogen
Function / homology
Function and homology information


icosahedral viral capsid / RNA-protein covalent cross-linking / : / host cell nucleolus / symbiont-mediated suppression of host mRNA export from nucleus / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / : ...icosahedral viral capsid / RNA-protein covalent cross-linking / : / host cell nucleolus / symbiont-mediated suppression of host mRNA export from nucleus / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / : / protein complex oligomerization / monoatomic ion channel activity / host cell cytoplasm / RNA helicase activity / RNA helicase / RNA-directed RNA polymerase / symbiont entry into host cell / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / structural molecule activity / virion attachment to host cell / ATP hydrolysis activity / proteolysis / RNA binding / ATP binding / membrane / metal ion binding / cytoplasm
Similarity search - Function
Capsid protein VP4, Picornavirus / Viral protein VP4 subunit / Capsid protein VP4 superfamily, Picornavirus / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / Jelly Rolls - #20 / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirus capsid ...Capsid protein VP4, Picornavirus / Viral protein VP4 subunit / Capsid protein VP4 superfamily, Picornavirus / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / Jelly Rolls - #20 / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / 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 / Jelly Rolls / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / Peptidase S1, PA clan, chymotrypsin-like fold / DNA/RNA polymerase superfamily / Peptidase S1, PA clan / Sandwich / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Genome polyprotein / Genome polyprotein / Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesSaffold virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsMullapudi, E. / Plevka, P.
CitationJournal: J Virol / Year: 2016
Title: Structure and Genome Release Mechanism of the Human Cardiovirus Saffold Virus 3.
Authors: Edukondalu Mullapudi / Jiří Nováček / Lenka Pálková / Pavel Kulich / A Michael Lindberg / Frank J M van Kuppeveld / Pavel Plevka /
Abstract: In order to initiate an infection, viruses need to deliver their genomes into cells. This involves uncoating the genome and transporting it to the cytoplasm. The process of genome delivery is not ...In order to initiate an infection, viruses need to deliver their genomes into cells. This involves uncoating the genome and transporting it to the cytoplasm. The process of genome delivery is not well understood for nonenveloped viruses. We address this gap in our current knowledge by studying the uncoating of the nonenveloped human cardiovirus Saffold virus 3 (SAFV-3) of the family Picornaviridae SAFVs cause diseases ranging from gastrointestinal disorders to meningitis. We present a structure of a native SAFV-3 virion determined to 2.5 Å by X-ray crystallography and an 11-Å-resolution cryo-electron microscopy reconstruction of an "altered" particle that is primed for genome release. The altered particles are expanded relative to the native virus and contain pores in the capsid that might serve as channels for the release of VP4 subunits, N termini of VP1, and the RNA genome. Unlike in the related enteroviruses, pores in SAFV-3 are located roughly between the icosahedral 3- and 5-fold axes at an interface formed by two VP1 and one VP3 subunit. Furthermore, in native conditions many cardioviruses contain a disulfide bond formed by cysteines that are separated by just one residue. The disulfide bond is located in a surface loop of VP3. We determined the structure of the SAFV-3 virion in which the disulfide bonds are reduced. Disruption of the bond had minimal effect on the structure of the loop, but it increased the stability and decreased the infectivity of the virus. Therefore, compounds specifically disrupting or binding to the disulfide bond might limit SAFV infection.
IMPORTANCE: A capsid assembled from viral proteins protects the virus genome during transmission from one cell to another. However, when a virus enters a cell the virus genome has to be released from ...IMPORTANCE: A capsid assembled from viral proteins protects the virus genome during transmission from one cell to another. However, when a virus enters a cell the virus genome has to be released from the capsid in order to initiate infection. This process is not well understood for nonenveloped viruses. We address this gap in our current knowledge by studying the genome release of Human Saffold virus 3 Saffold viruses cause diseases ranging from gastrointestinal disorders to meningitis. We show that before the genome is released, the Saffold virus 3 particle expands, and holes form in the previously compact capsid. These holes serve as channels for the release of the genome and small capsid proteins VP4 that in related enteroviruses facilitate subsequent transport of the virus genome into the cell cytoplasm.
History
DepositionJul 8, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 15, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 22, 2016Group: Database references
Revision 1.2Aug 24, 2016Group: Database references
Revision 1.3Apr 11, 2018Group: Data collection / Source and taxonomy / Structure summary
Category: diffrn_source / entity / entity_src_nat
Item: _diffrn_source.pdbx_wavelength_list / _entity.pdbx_description ..._diffrn_source.pdbx_wavelength_list / _entity.pdbx_description / _entity_src_nat.pdbx_cell_line / _entity_src_nat.pdbx_ncbi_taxonomy_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: VP1
B: VP3
C: VP2
D: VP4


Theoretical massNumber of molelcules
Total (without water)85,3044
Polymers85,3044
Non-polymers00
Water6,125340
1
A: VP1
B: VP3
C: VP2
D: VP4
x 60


Theoretical massNumber of molelcules
Total (without water)5,118,218240
Polymers5,118,218240
Non-polymers00
Water4,324240
TypeNameSymmetry operationNumber
point symmetry operation60
2


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
point symmetry operation1
3
A: VP1
B: VP3
C: VP2
D: VP4
x 5


  • icosahedral pentamer
  • 427 kDa, 20 polymers
Theoretical massNumber of molelcules
Total (without water)426,51820
Polymers426,51820
Non-polymers00
Water36020
TypeNameSymmetry operationNumber
point symmetry operation5
4
A: VP1
B: VP3
C: VP2
D: VP4
x 6


  • icosahedral 23 hexamer
  • 512 kDa, 24 polymers
Theoretical massNumber of molelcules
Total (without water)511,82224
Polymers511,82224
Non-polymers00
Water43224
TypeNameSymmetry operationNumber
point symmetry operation6
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
Unit cell
Length a, b, c (Å)300.502, 300.502, 722.103
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(0.309, -0.940069, -0.144052), (0.940069, 0.324881, -0.103454), (0.144052, -0.103454, 0.984119)89.91245, -86.28468, -13.21844
3generate(0.309, -0.291551, -0.905251), (0.291551, 0.935035, -0.201622), (0.905251, -0.201622, 0.373965)181.52313, -6.35625, -19.73492
4generate(0.809, -0.580992, -0.089049), (0.180207, 0.38933, -0.903287), (0.55947, 0.714713, 0.41967)30.77779, 89.78393, 11.0819
5generate(0.809, -0.180207, -0.55947), (0.580992, 0.38933, 0.714713), (0.089049, -0.903287, 0.41967)87.39317, -147.03757, 60.49024
6generate(0.5, -0.289441, 0.816202), (0.759862, 0.598712, -0.253174), (-0.415418, 0.746826, 0.519288)-45.71533, -49.33865, 101.48526
7generate(0.5, -0.759862, 0.415418), (0.289441, 0.598712, 0.746826), (-0.816202, -0.253174, 0.519288)2.51925, -120.28084, 143.57965
8generate(0.5, 0.759862, -0.415418), (-0.289441, 0.598712, 0.746826), (0.816202, -0.253174, 0.519288)102.51073, -59.48089, -27.87179
9generate(0.5, 0.289441, -0.816202), (-0.759862, 0.598712, -0.253174), (0.415418, 0.746826, 0.519288)150.74535, 110.27793, 14.22259
10generate(0.809, 0.580992, 0.089049), (-0.180207, 0.38933, -0.903287), (-0.55947, 0.714713, 0.41967)9.34367, 127.63828, 128.60411
11generate(0.809, 0.180207, 0.55947), (-0.580992, 0.38933, 0.714713), (-0.089049, -0.903287, 0.41967)-47.27173, -24.99445, 79.1958
12generate(0.309, 0.291551, 0.905251), (-0.291551, 0.935035, -0.201622), (-0.905251, -0.201622, 0.373965)-36.37167, 54.88693, 170.42209
13generate(0.309, 0.940069, 0.144052), (-0.940069, 0.324881, -0.103454), (-0.144052, -0.103454, 0.984119)55.23902, 111.18625, 17.04111
14generate(-0.309, -0.940069, -0.144052), (0.291551, 0.050534, -0.95519), (0.905251, -0.33719, 0.258466)154.821, 84.33598, -5.8345
15generate(-0.309, -0.291551, -0.905251), (0.940069, 0.050534, -0.33719), (0.144052, -0.95519, 0.258466)246.43167, -58.15451, 74.11424
16generate(-0.648518, 0.761199), (0.761199, -0.493652, -0.420576), (0.648518, 0.579424, 0.493652)13.41933, -29.33218, -7.17461
17generate(-0.761199, -0.648518), (0.648518, -0.493652, 0.579424), (-0.761199, -0.420576, 0.493652)183.0795, -137.84785, 140.88803
18generate(0.648518, -0.761199), (0.761199, 0.493651, 0.420576), (0.648518, -0.579424, -0.493652)196.64066, -130.56529, 111.64783
19generate(-0.761199, -0.648518), (-0.648518, 0.493652, -0.579424), (0.761199, 0.420576, -0.493652)183.07953, 137.84784, 99.81297
20generate(-0.5, -0.759862, 0.415418), (0.759862, -0.154856, 0.631326), (-0.415418, 0.631326, 0.654856)107.54926, -155.78873, 85.16963
21generate(-0.5, 0.289441, -0.816202), (-0.289441, 0.832448, 0.472479), (0.816202, 0.472478, -0.332447)255.77533, -26.46306, 74.63499
22generate(0.809, 0.180207, 0.55947), (0.580992, -0.38933, -0.714713), (0.089049, 0.903287, -0.41967)-47.27173, 24.99447, 161.50519
23generate(0.809, -0.580992, -0.089049), (-0.180207, -0.38933, 0.903287), (-0.55947, -0.714713, -0.41967)30.77778, -89.78391, 229.61911
24generate(0.809, 0.580992, 0.089049), (0.180207, -0.38933, 0.903287), (0.55947, -0.714713, -0.41967)9.34365, -127.63826, 112.09689
25generate(0.809, -0.180207, -0.55947), (-0.580992, -0.38933, -0.714713), (-0.089049, 0.903287, -0.41967)87.39318, 147.03757, 180.21077
26generate(-0.5, -0.289441, 0.816202), (0.289441, 0.832448, 0.472479), (-0.816202, 0.472479, -0.332447)59.31466, -87.26301, 246.08643
27generate(-0.5, 0.759862, -0.415418), (-0.759862, -0.154856, 0.631326), (0.415418, 0.631326, 0.654856)207.54074, 3.82785, -2.09304
28generate(0.761199, 0.648518), (0.648518, 0.493651, -0.579424), (-0.761199, 0.420576, -0.493652)26.98048, 1.62007, 259.71045
29generate(-0.648518, 0.761199), (-0.761199, 0.493652, 0.420576), (-0.648518, -0.579424, -0.493652)13.41932, 29.3322, 247.87561
30generate(0.761199, 0.648518), (-0.648518, -0.493652, 0.579424), (0.761199, -0.420576, 0.493652)26.98049, -1.62006, -19.00944
31generate(0.648518, -0.761199), (-0.761199, -0.493652, -0.420576), (-0.648518, 0.579424, 0.493652)196.64069, 130.56528, 129.05319
32generate(-0.309, 0.940069, 0.144052), (-0.291551, 0.050534, -0.95519), (-0.905251, -0.33719, 0.258466)120.14755, 145.57916, 184.32251
33generate(-0.309, 0.291551, 0.905251), (-0.940069, 0.050534, -0.33719), (-0.144052, -0.95519, 0.258466)28.53688, 139.31647, 104.37378
34generate(-0.809, -0.580992, -0.089049), (0.580992, -0.767482, -0.270856), (0.089049, -0.270856, 0.958482)200.71634, -28.42389, -4.35609
35generate(-0.809, -0.180207, -0.55947), (0.180208, 0.829974, -0.527872), (0.55947, -0.527872, -0.638974)257.33173, 44.60246, 138.49028
36generate(0.5, -0.759862, 0.415418), (-0.289441, -0.598712, -0.746826), (0.816202, 0.253174, -0.519288)2.51926, 120.28085, 97.12135
37generate(0.5, 0.289441, -0.816202), (0.759862, -0.598712, 0.253174), (-0.415418, -0.746826, -0.519288)150.74532, -110.27793, 226.47842
38generate(-0.309, 0.291551, 0.905251), (0.940069, -0.050534, 0.33719), (0.144052, 0.95519, -0.258466)28.53687, -139.31644, 136.32722
39generate(-0.309, -0.940069, -0.144052), (-0.291551, -0.050534, 0.95519), (-0.905251, 0.33719, -0.258466)154.82098, -84.33598, 246.53549
40generate(-0.309, 0.940069, 0.144052), (0.291551, -0.050534, 0.95519), (0.905251, 0.33719, -0.258466)120.14754, -145.57916, 56.3785
41generate(-0.309, -0.291551, -0.905251), (-0.940069, -0.050534, 0.33719), (-0.144052, 0.95519, -0.258466)246.43167, 58.15449, 166.58676
42generate(0.5, 0.759862, -0.415418), (0.289441, -0.598712, -0.746826), (-0.816202, 0.253174, -0.519288)102.51073, 59.48089, 268.57278
43generate(0.5, -0.289441, 0.816202), (-0.759862, -0.598712, 0.253174), (0.415418, -0.746826, -0.519288)-45.71533, 49.33867, 139.21574
44generate(-0.809, 0.180208, 0.55947), (-0.180207, 0.829974, -0.527872), (-0.55947, -0.527872, -0.638974)122.66682, 82.45682, 256.01248
45generate(-0.809, 0.580992, 0.089049), (-0.580992, -0.767482, -0.270856), (-0.089049, -0.270856, 0.958482)179.28223, 93.61924, 14.34948
46generate(-1), (-0.158848, -0.987303), (-0.987303, 0.158848)210.06001, 118.82241, 101.23309
47generate(-0.5, -0.289441, 0.816202), (-0.289441, -0.832448, -0.472479), (0.816202, -0.472479, 0.332447)59.31468, 87.26301, -5.38543
48generate(-0.5, 0.289441, -0.816202), (0.289441, -0.832448, -0.472478), (-0.816202, -0.472478, 0.332447)255.77533, 26.46304, 166.06601
49generate(-0.5, 0.759862, -0.415418), (0.759862, 0.154856, -0.631326), (-0.415418, -0.631326, -0.654856)207.54074, -3.82787, 242.79404
50generate(-0.5, -0.759862, 0.415418), (-0.759862, 0.154856, -0.631326), (0.415418, -0.631326, -0.654856)107.54927, 155.78873, 155.53137
51generate(-0.809, 0.180207, 0.55947), (0.180207, -0.829974, 0.527872), (0.55947, 0.527872, 0.638974)122.66682, -82.45682, -15.31147
52generate(-0.809, -0.180207, -0.55947), (-0.180207, -0.829974, 0.527872), (-0.55947, 0.527872, 0.638974)257.33173, -44.60249, 102.21073
53generate(-0.809, 0.580992, 0.089049), (0.580992, 0.767482, 0.270856), (0.089049, 0.270856, -0.958482)179.2822, -93.61926, 226.35153
54generate(-0.809, -0.580992, -0.089049), (-0.580992, 0.767482, 0.270856), (-0.089049, 0.270856, -0.958482)200.71634, 28.42387, 245.0571
55generate(0.309, 0.291551, 0.905251), (0.291551, -0.935035, 0.201622), (0.905251, 0.201622, -0.373965)-36.37167, -54.88691, 70.27892
56generate(0.309, -0.291551, -0.905251), (-0.291551, -0.935035, 0.201622), (-0.905251, 0.201622, -0.373965)181.52312, 6.35624, 260.43591
57generate(0.309, 0.940069, 0.144052), (0.940069, -0.324882, 0.103454), (0.144052, 0.103454, -0.984119)55.23899, -111.18625, 223.65988
58generate(0.309, -0.940069, -0.144052), (-0.940069, -0.324881, 0.103454), (-0.144052, 0.103454, -0.984119)89.91245, 86.28469, 253.91943
59generate(1), (-1), (-1)-2.0E-5, 2.0E-5, 240.701
60generate(-1), (0.158848, 0.987303), (0.987303, -0.158848)210.06, -118.82243, 139.46791

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Components

#1: Protein VP1


Mass: 28302.705 Da / Num. of mol.: 1 / Fragment: residues 647-898 / Source method: isolated from a natural source / Source: (natural) Saffold virus / References: UniProt: C0MHL9
#2: Protein VP3


Mass: 25611.986 Da / Num. of mol.: 1 / Fragment: residues 415-646 / Source method: isolated from a natural source / Source: (natural) Saffold virus / References: UniProt: E3TMG8
#3: Protein VP2


Mass: 28698.160 Da / Num. of mol.: 1 / Fragment: residues 154-411 / Source method: isolated from a natural source / Source: (natural) Saffold virus / References: UniProt: C0MHL9
#4: Protein/peptide VP4


Mass: 2690.789 Da / Num. of mol.: 1 / Fragment: residues 98-121 / Source method: isolated from a natural source / Source: (natural) Saffold virus / References: UniProt: C5J497, UniProt: C3U5A3*PLUS
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 340 / Source method: isolated from a natural source / Formula: H2O

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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

Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7 / Details: 2.8 M Na acetate pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.00001 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 23, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00001 Å / Relative weight: 1
ReflectionResolution: 2.5→70 Å / Num. obs: 794529 / % possible obs: 61.9 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.114 / Net I/σ(I): 6.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
PHASERphasing
CNSrefinement
PDB_EXTRACT3.15data extraction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→70 Å / Cross valid method: NONE / σ(F): 0
RfactorNum. reflection% reflection
Rwork0.22 802320 -
Rfree-0 0 %
obs-802320 62.4 %
Solvent computationBsol: 9.5639 Å2
Displacement parametersBiso max: 163.97 Å2 / Biso mean: 32.786 Å2 / Biso min: 17.11 Å2
Baniso -1Baniso -2Baniso -3
1--12.623 Å20 Å20 Å2
2---12.623 Å2-0 Å2
3---25.247 Å2
Refinement stepCycle: final / Resolution: 2.5→70 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6012 0 0 340 6352
Biso mean---37.62 -
Num. residues----766
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.0651.5
X-RAY DIFFRACTIONc_scbond_it1.7692
X-RAY DIFFRACTIONc_mcangle_it1.812
X-RAY DIFFRACTIONc_scangle_it2.6412.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.param
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION4CNS_TOPPAR:ion.param
X-RAY DIFFRACTION5CNS_TOPPAR:carbohydrate.param

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Jul 12, 2017. Major update of PDB

Major update of PDB

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External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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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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