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- PDB-9bcy: Crystal structure of Mayaro virus capsid C-terminal domain -

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Basic information

Entry
Database: PDB / ID: 9bcy
TitleCrystal structure of Mayaro virus capsid C-terminal domain
ComponentsStructural polyprotein
KeywordsVIRAL PROTEIN / Mayaro virus / arbovirus / alphavirus / capsid / C protein
Function / homology
Function and homology information


T=4 icosahedral viral capsid / host cell cytoplasm / symbiont entry into host cell / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / membrane
Similarity search - Function
Alphavirus E2 glycoprotein, domain B / Peptidase S3, togavirin / Alphavirus E2 glycoprotein / Alphavirus E3 spike glycoprotein / Alphavirus E1 glycoprotein / Alphavirus E2 glycoprotein, domain A / Alphavirus E2 glycoprotein, domain C / Alphavirus E2 glycoprotein / Alphavirus core protein / Alphavirus E3 glycoprotein ...Alphavirus E2 glycoprotein, domain B / Peptidase S3, togavirin / Alphavirus E2 glycoprotein / Alphavirus E3 spike glycoprotein / Alphavirus E1 glycoprotein / Alphavirus E2 glycoprotein, domain A / Alphavirus E2 glycoprotein, domain C / Alphavirus E2 glycoprotein / Alphavirus core protein / Alphavirus E3 glycoprotein / Alphavirus E1 glycoprotein / Alphavirus core protein (CP) domain profile. / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Flavivirus glycoprotein, central and dimerisation domain superfamily / Flaviviral glycoprotein E, dimerisation domain / Immunoglobulin E-set / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
Structural polyprotein
Similarity search - Component
Biological speciesMayaro virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.18 Å
AuthorsBezerra, E.H.S. / Scorsato, V. / Tonoli, C.C. / Benedetti, C.E. / Marques, R.E.
Funding support Brazil, 1items
OrganizationGrant numberCountry
Other government Brazil
CitationJournal: To Be Published
Title: Crystal structure of Mayaro virus capsid C-terminal domain
Authors: Bezerra, E.H.S. / Scorsato, V. / Tonoli, C.C. / Benedetti, C.E. / Marques, R.E.
History
DepositionApr 10, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 19, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Structural polyprotein
BBB: Structural polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,92810
Polymers34,4312
Non-polymers4978
Water8,809489
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.160, 40.112, 56.511
Angle α, β, γ (deg.)93.585, 94.403, 111.925
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Structural polyprotein / p130


Mass: 17215.588 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mayaro virus / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A515HFP9
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 489 / 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: 2.39 Å3/Da / Density % sol: 48.49 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.2 / Details: 22% PEG 3350, 100mM Bis-Tris pH 7.2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS SIRIUS / Beamline: MANACA / Wavelength: 0.9772 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 1, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9772 Å / Relative weight: 1
ReflectionResolution: 1.18→37.057 Å / Num. obs: 96920 / % possible obs: 93.08 % / Redundancy: 3.6 % / Biso Wilson estimate: 9.59 Å2 / CC1/2: 0.994 / CC star: 0.999 / Rmerge(I) obs: 0.05812 / Rpim(I) all: 0.03665 / Rrim(I) all: 0.06895 / Net I/σ(I): 16.96
Reflection shellResolution: 1.18→1.222 Å / Rmerge(I) obs: 0.09189 / Mean I/σ(I) obs: 10.72 / Num. unique obs: 8699 / CC1/2: 0.988 / CC star: 0.997 / Rpim(I) all: 0.05683 / Rrim(I) all: 0.1084

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Processing

Software
NameVersionClassification
MxCuBEdata collection
XDSdata reduction
SCALAdata scaling
BALBESphasing
REFMAC5.8.0258refinement
PDB-REDOrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.18→37.057 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.963 / SU B: 0.451 / SU ML: 0.022 / Cross valid method: FREE R-VALUE / ESU R: 0.039 / ESU R Free: 0.04
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1806 4894 5.05 %
Rwork0.1648 92026 -
all0.166 --
obs-96920 93.087 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 13.381 Å2
Baniso -1Baniso -2Baniso -3
1-0.459 Å2-0.115 Å20.046 Å2
2---0.15 Å2-0.048 Å2
3----0.156 Å2
Refinement stepCycle: LAST / Resolution: 1.18→37.057 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2286 0 32 489 2807
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0132526
X-RAY DIFFRACTIONr_bond_other_d0.0180.0172345
X-RAY DIFFRACTIONr_angle_refined_deg1.7861.6553444
X-RAY DIFFRACTIONr_angle_other_deg1.7471.5865483
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4595341
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.19522.727110
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.24815422
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8881511
X-RAY DIFFRACTIONr_chiral_restr0.1060.2325
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.022908
X-RAY DIFFRACTIONr_gen_planes_other0.0320.02513
X-RAY DIFFRACTIONr_nbd_refined0.2240.2457
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2110.22163
X-RAY DIFFRACTIONr_nbtor_refined0.1790.21168
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0820.21220
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1280.2319
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1560.216
X-RAY DIFFRACTIONr_nbd_other0.190.250
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1180.235
X-RAY DIFFRACTIONr_mcbond_it7.4021.0351278
X-RAY DIFFRACTIONr_mcbond_other7.41.0341277
X-RAY DIFFRACTIONr_mcangle_it11.6131.5371622
X-RAY DIFFRACTIONr_mcangle_other11.6111.5371623
X-RAY DIFFRACTIONr_scbond_it9.0021.3981248
X-RAY DIFFRACTIONr_scbond_other8.9991.3991249
X-RAY DIFFRACTIONr_scangle_it11.8551.9171813
X-RAY DIFFRACTIONr_scangle_other11.8511.9181814
X-RAY DIFFRACTIONr_lrange_it16.09615.0262937
X-RAY DIFFRACTIONr_lrange_other16.36413.5842774
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.18-1.2110.1963430.1886007X-RAY DIFFRACTION82.7146
1.211-1.2440.1913440.1896184X-RAY DIFFRACTION87.4715
1.244-1.280.1973550.1836334X-RAY DIFFRACTION91.3548
1.28-1.3190.2063280.1816259X-RAY DIFFRACTION92.3713
1.319-1.3620.1983470.1825980X-RAY DIFFRACTION92.5
1.362-1.410.1852900.1775907X-RAY DIFFRACTION93.104
1.41-1.4630.1783380.175659X-RAY DIFFRACTION93.5132
1.463-1.5230.1722710.1665568X-RAY DIFFRACTION94.1774
1.523-1.5910.1722970.1575294X-RAY DIFFRACTION94.6664
1.591-1.6680.1692530.1615131X-RAY DIFFRACTION94.9057
1.668-1.7590.1612220.1534865X-RAY DIFFRACTION95.0486
1.759-1.8650.1732630.1544605X-RAY DIFFRACTION94.9668
1.865-1.9940.1752190.1574296X-RAY DIFFRACTION94.8928
1.994-2.1530.1761990.1584102X-RAY DIFFRACTION96.8694
2.153-2.3580.1762130.1523814X-RAY DIFFRACTION97.4589
2.358-2.6360.1681920.1633411X-RAY DIFFRACTION97.3521
2.636-3.0430.181380.1633005X-RAY DIFFRACTION96.8866
3.043-3.7240.1831210.1622526X-RAY DIFFRACTION95.4562
3.724-5.2550.1761190.1541947X-RAY DIFFRACTION97.4988
5.255-37.0570.288420.2141132X-RAY DIFFRACTION98.4899

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