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- PDB-2vq0: Capsid structure of Sesbania mosaic virus coat protein deletion m... -

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Basic information

Entry
Database: PDB / ID: 2vq0
TitleCapsid structure of Sesbania mosaic virus coat protein deletion mutant rCP(delta 48 to 59)
ComponentsCOAT PROTEIN
KeywordsVIRAL PROTEIN / CAPSID PROTEIN / SESBANIA MOSAIC VIRUS / VIRION / BETA-ANNULUS / COAT PROTEIN / VIRUS ASSEMBLY
Function / homology
Function and homology information


T=3 icosahedral viral capsid / structural molecule activity / metal ion binding
Similarity search - Function
Plant viruses icosahedral capsid proteins 'S' region signature. / Icosahedral viral capsid protein, S domain / Viral coat protein (S domain) / Jelly Rolls - #20 / Viral coat protein subunit / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesSESBANIA MOSAIC VIRUS
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.6 Å
AuthorsAnju, P. / Subashchandrabose, C. / Satheshkumar, P.S. / Savithri, H.S. / Murthy, M.R.N.
CitationJournal: Virology / Year: 2008
Title: Structure of Recombinant Capsids Formed by the Beta-Annulus Deletion Mutant-Rcp (Delta 48-59) of Sesbania Mosaic Virus
Authors: Anju, P. / Subashchandrabose, C. / Satheshkumar, P.S. / Savithri, H.S. / Murthy, M.R.N.
History
DepositionMar 10, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 13, 2008Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2012Group: Other / Refinement description / Version format compliance
Revision 1.2Jan 30, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: COAT PROTEIN
B: COAT PROTEIN
C: COAT PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,8676
Polymers82,7473
Non-polymers1203
Water00
1
A: COAT PROTEIN
B: COAT PROTEIN
C: COAT PROTEIN
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)4,972,043360
Polymers4,964,829180
Non-polymers7,214180
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: COAT PROTEIN
B: COAT PROTEIN
C: COAT PROTEIN
hetero molecules
x 5


  • icosahedral pentamer
  • 414 kDa, 15 polymers
Theoretical massNumber of molelcules
Total (without water)414,33730
Polymers413,73615
Non-polymers60115
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: COAT PROTEIN
B: COAT PROTEIN
C: COAT PROTEIN
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 497 kDa, 18 polymers
Theoretical massNumber of molelcules
Total (without water)497,20436
Polymers496,48318
Non-polymers72118
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
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)288.793, 288.793, 288.793
Angle α, β, γ (deg.)61.70, 61.70, 61.70
Int Tables number146
Space group name H-MR3
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrix
1given(1), (1), (1)
2generate(0.639553, 0.565756, 0.520566), (0.080019, 0.624429, -0.77697), (-0.764529, 0.538564, 0.354051)
3generate(0.639493, 0.080311, -0.764594), (0.565789, 0.624294, 0.538672), (0.520568, -0.777079, 0.353731)
4generate(0.056313, 0.995464, 0.077662), (0.695158, 0.016735, -0.718594), (-0.716544, 0.094437, -0.691083)
5generate(0.056297, 0.695281, -0.716634), (0.995316, 0.016731, 0.094453), (0.077641, -0.718611, -0.691062)
6generate(0.474088, 0.880477), (0.283174, -0.152474, 0.946871), (0.833698, -0.4489, -0.321615)
7generate(0.80134, 0.587751, 0.111804), (0.587731, -0.80824, 0.036291), (0.111739, 0.036629, -0.993016)
8generate(0.373659, 0.818014, -0.43731), (-0.555006, 0.574949, 0.601119), (0.743157, 0.018153, 0.668909)
9generate(0.903043, 0.344356, -0.256584), (-0.062302, -0.486097, -0.87168), (-0.424833, 0.80326, -0.417601)
10generate(0.638768, 0.486673, -0.595887), (-0.768521, 0.368758, -0.522808), (-0.034658, 0.792032, 0.609586)
11generate(0.474088, 0.283174, 0.833698), (0.880477, -0.152474, -0.4489), (0.946871, -0.321615)
12generate(0.89739, -0.432991, 0.084958), (0.243108, 0.324354, -0.914131), (0.368306, 0.841046, 0.396288)
13generate(-0.311523, 0.89404, 0.321948), (0.894108, 0.161165, 0.41788), (0.321651, 0.418044, -0.849558)
14generate(0.373267, -0.264742, -0.889138), (-0.137044, 0.932213, -0.335164), (0.917465, 0.246958, 0.31169)
15generate(-0.373833, 0.555408, -0.742823), (0.265246, 0.831539, 0.488174), (0.888676, -0.014526, -0.458153)
16generate(0.897407, 0.243167, 0.368276), (-0.433, 0.324028, 0.841139), (0.085225, -0.914201, 0.396083)
17generate(0.903181, -0.0623, -0.424893), (0.344301, -0.486117, 0.80315), (-0.256555, -0.871672, -0.417511)
18generate(0.311721, 0.857784, 0.408582), (-0.893904, 0.410559, -0.179926), (-0.322099, -0.309071, 0.89489)
19generate(0.321125, 0.364465, -0.874132), (0.364585, -0.899423, -0.24102), (-0.874059, -0.241284, -0.421621)
20generate(-0.044491, 0.932361, -0.358594), (-0.400584, -0.345446, -0.848666), (-0.915228, 0.105958, 0.388879)
21generate(0.373887, -0.555129, 0.742998), (0.81791, 0.575082, 0.018205), (-0.437405, 0.600833, 0.669064)
22generate(-0.373881, 0.265253, 0.888822), (0.55535, 0.831402, -0.014535), (-0.74282, 0.488148, -0.458176)
23generate(0.311795, -0.893903, -0.322083), (0.857901, 0.41056, -0.309147), (0.40852, -0.179948, 0.894757)
24generate(-0.897552, 0.432537, -0.086118), (0.432751, 0.82603, -0.360902), (-0.084951, -0.36117, -0.928646)
25generate(-0.473219, -0.283063, -0.834171), (0.619519, 0.566354, -0.543639), (0.626325, -0.774037, -0.092615)
26generate(0.373334, -0.137063, 0.917599), (-0.264785, 0.932096, 0.246956), (-0.889117, -0.335073, 0.311682)
27generate(0.638869, -0.76863, -0.034697), (0.486599, 0.368731, 0.791905), (-0.595912, -0.522791, 0.60957)
28generate(-0.473314, 0.61957, 0.626235), (-0.282786, 0.566341, -0.774121), (-0.834212, -0.543534, -0.092866)
29generate(-0.04468, -0.401657, -0.914757), (0.932463, -0.345131, 0.10605), (-0.358277, -0.848294, 0.389972)
30generate(-0.731907, 0.456365, -0.506058), (0.456299, -0.223261, -0.861317), (-0.506018, -0.861373, -0.044832)
31generate(0.044203, 0.400582, 0.915199), (0.400841, -0.846177, 0.351074), (0.915131, 0.351292, -0.197942)
32generate(0.731337, -0.457551, 0.505719), (-0.039663, -0.768882, -0.638107), (0.680935, 0.446621, -0.580489)
33generate(-0.639279, 0.768153, 0.035284), (-0.080418, -0.112347, 0.990479), (0.764746, 0.630235, 0.133593)
34generate(0.47325, -0.619133, -0.626628), (-0.792276, 0.011881, -0.610003), (0.385169, 0.785205, -0.484969)
35generate(-0.373798, 0.137864, -0.917236), (-0.818123, 0.417021, 0.396072), (0.437081, 0.898301, -0.043061)
36generate(-0.056144, 0.755709, 0.652462), (-0.695787, -0.498204, 0.517309), (0.716063, -0.424923, 0.553901)
37generate(-0.473379, 0.792381, -0.384705), (-0.880804, -0.425562, 0.207435), (0.000636, 0.437112, 0.899461)
38generate(0.73132, -0.039739, 0.680805), (-0.457534, -0.768894, 0.446614), (0.505844, -0.638192, -0.58046)
39generate(0.054772, 0.019781, -0.998286), (-0.755964, -0.652336, -0.054425), (-0.65228, 0.757723, -0.020836)
40generate(0.79983, -0.494301, -0.340301), (-0.49407, -0.86434, 0.094048), (-0.340605, 0.092892, -0.935658)
41generate(-0.639242, -0.080384, 0.764803), (0.76821, -0.112387, 0.630357), (0.035236, 0.990339, 0.133594)
42generate(-0.999951, 0.000961, 0.000257), (0.000853, 0.703158, 0.711106), (0.000533, 0.71106, -0.703125)
43generate(-0.056138, -0.695833, 0.715995), (0.755821, -0.498302, -0.424931), (0.6524, 0.517278, 0.553785)
44generate(-0.639643, -0.56499, -0.521195), (-0.486849, 0.822531, -0.294119), (0.594799, 0.065631, -0.801137)
45generate(-0.055828, -0.995374, -0.078526), (-0.020685, 0.079773, -0.996651), (0.998149, -0.053971, -0.025005)
46generate(0.054831, -0.756012, -0.652296), (0.01975, -0.652303, 0.75765), (-0.998316, -0.054404, -0.020777)
47generate(0.473145, -0.792327, 0.385246), (-0.619076, 0.012164, 0.785221), (-0.626827, -0.609942, -0.484789)
48generate(-0.73215, 0.039155, -0.679954), (0.038643, -0.994361, -0.09893), (-0.680012, -0.098776, 0.726554)
49generate(-0.05603, -0.020362, 0.998155), (-0.995264, 0.080932, -0.05415), (-0.079688, -0.996561, -0.02474)
50generate(-0.800701, 0.49334, 0.339794), (-0.588492, -0.541714, -0.600174), (-0.112041, -0.680497, 0.724167)
51generate(-0.800707, -0.588488, -0.11202), (0.49341, -0.54177, -0.680527), (0.339774, -0.60015, 0.724079)
52generate(-0.903086, -0.345364, 0.255354), (-0.345276, 0.23043, -0.90975), (0.255292, -0.909763, -0.327344)
53generate(-0.473579, -0.880696, 0.000827), (0.792369, -0.425678, 0.437097), (-0.384588, 0.207684, 0.899418)
54generate(-0.639657, -0.486842, 0.594875), (-0.564974, 0.822447, 0.065613), (-0.521192, -0.294075, -0.80119)
55generate(-0.374832, -0.817567, 0.437254), (0.13819, 0.417088, 0.898215), (-0.916758, 0.397141, -0.043316)
56generate(0.043384, -0.932754, 0.357848), (-0.932761, -0.166138, -0.319908), (0.35792, -0.31997, -0.877245)
57generate(-0.32077, -0.364923, 0.87401), (-0.365149, -0.803758, -0.469666), (0.87396, -0.469856, 0.124608)
58generate(-0.313079, -0.856949, -0.409464), (-0.857102, 0.069173, 0.510491), (-0.409037, 0.51078, -0.756137)
59generate(-0.902871, 0.061606, 0.425536), (0.060431, -0.961721, 0.267483), (0.425691, 0.267202, 0.864425)
60generate(-0.897757, -0.24308, -0.367347), (-0.243097, -0.422044, 0.873424), (-0.367334, 0.87333, 0.319801)

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Components

#1: Protein COAT PROTEIN


Mass: 27582.383 Da / Num. of mol.: 3 / Fragment: RESIDUES 1-47,60-268
Source method: isolated from a genetically manipulated source
Details: THE RESIDUES 48 TO 59 OF THE COAT PROTEIN WHICH ARE INVOLVED IN THE FORMATION OF A MOTIF CALLED THE BETA-ANNULUS IS DELETED IN THE MUTANT RCP(DELTA 48-59)
Source: (gene. exp.) SESBANIA MOSAIC VIRUS / Plasmid: PSBET A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9EB06
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
Has protein modificationY
Sequence detailsTHE RESIDUES 48 TO 59 OF THE COAT PROTEIN WHICH ARE INVOLVED IN THE FORMATION OF A MOTIF CALLED THE ...THE RESIDUES 48 TO 59 OF THE COAT PROTEIN WHICH ARE INVOLVED IN THE FORMATION OF A MOTIF CALLED THE BETA-ANNULUS IS DELETED IN THE MUTANT RCP(DELTA 48-59)

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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

CrystalDescription: NONE
Crystal growMethod: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M LI2SO4 MONOHYDRATE, 0.1 M BISTRIS (PH7.5), 25 % PEG 3350 VAPOUR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Details: OSMIC MIRRORS
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.6→50 Å / Num. obs: 262266 / % possible obs: 99.3 % / Observed criterion σ(I): 0 / Redundancy: 2.89 % / Rmerge(I) obs: 0.17 / Net I/σ(I): 5.7
Reflection shellResolution: 3.6→3.73 Å / Redundancy: 2.36 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 1.8 / % possible all: 99

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
GLRFphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1X33

1x33


Resolution: 3.6→20 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.2584 10868 4.1 %RANDOM
Rwork0.2567 ---
obs0.2567 218390 83 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 10 Å2 / ksol: 0.204 e/Å3
Displacement parametersBiso mean: 24.9 Å2
Baniso -1Baniso -2Baniso -3
1-0.24 Å2-2.97 Å2-3.96 Å2
2--0.24 Å2-3.19 Å2
3----0.48 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.49 Å0.49 Å
Luzzati d res low-5 Å
Luzzati sigma a0.77 Å0.77 Å
Refinement stepCycle: LAST / Resolution: 3.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4451 0 3 0 4454
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.00948
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.45693
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.01
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 3.6→3.82 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.334 1609 4.9 %
Rwork0.337 30939 -
obs--74.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP

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