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- PDB-1za7: The crystal structure of salt stable cowpea cholorotic mottle vir... -

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Basic information

Entry
Database: PDB / ID: 1za7
TitleThe crystal structure of salt stable cowpea cholorotic mottle virus at 2.7 angstroms resolution.
ComponentsCoat protein
KeywordsVIRUS / mutant virus capsid structure / icosahedral particle / stablizing mutation / stable mutant / beta hexamer / beta barrel / bromovirus / point mutation / Icosahedral virus
Function / homology
Function and homology information


T=3 icosahedral viral capsid / viral nucleocapsid / ribonucleoprotein complex / structural molecule activity / RNA binding
Similarity search - Function
Satellite virus coat domain / Bromovirus coat protein / Bromovirus coat protein / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesCowpea chlorotic mottle virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsBothner, B. / Speir, J.A. / Qu, C. / Willits, D.A. / Young, M.J. / Johnson, J.E.
Citation
Journal: J.Virol. / Year: 2006
Title: Enhanced local symmetry interactions globally stabilize a mutant virus capsid that maintains infectivity and capsid dynamics.
Authors: Speir, J.A. / Bothner, B. / Qu, C. / Willits, D.A. / Young, M.J. / Johnson, J.E.
#1: Journal: J.Gen.Virol. / Year: 1973
Title: A salt stable mutant of cowpea chlorotic mottle virus.
Authors: Bancroft, J.B. / Rees, M.W. / Johnson, M.W. / Dawson, J.R.O.
#2: Journal: Virology / Year: 1996
Title: Analysis of a salt stable mutant of cowpea chlorotic mottle virus.
Authors: Fox, J.M. / Zhao, X. / Speir, J.A. / Young, M.J.
#3: Journal: Structure / Year: 1995
Title: Structures of the native and swollen forms of cowpea chlorotic mottle virus determined by x-ray crystallography and cryo-electron microscopy.
Authors: Speir, J.A. / Munshi, S. / Wang, G. / Baker, T.S. / Johnson, J.E.
History
DepositionApr 5, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 21, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Aug 23, 2023Group: Data collection / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Coat protein
B: Coat protein
C: Coat protein


Theoretical massNumber of molelcules
Total (without water)52,8033
Polymers52,8033
Non-polymers00
Water2,270126
1
A: Coat protein
B: Coat protein
C: Coat protein
x 60


Theoretical massNumber of molelcules
Total (without water)3,168,184180
Polymers3,168,184180
Non-polymers00
Water3,243180
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
x 5


  • icosahedral pentamer
  • 264 kDa, 15 polymers
Theoretical massNumber of molelcules
Total (without water)264,01515
Polymers264,01515
Non-polymers00
Water27015
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Coat protein
B: Coat protein
C: Coat protein
x 6


  • icosahedral 23 hexamer
  • 317 kDa, 18 polymers
Theoretical massNumber of molelcules
Total (without water)316,81818
Polymers316,81818
Non-polymers00
Water32418
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
6
A: Coat protein
B: Coat protein
C: Coat protein
x 60


  • crystal asymmetric unit, crystal frame
  • 3.17 MDa, 180 polymers
Theoretical massNumber of molelcules
Total (without water)3,168,184180
Polymers3,168,184180
Non-polymers00
Water3,243180
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation59
Unit cell
Length a, b, c (Å)365.480, 374.860, 402.490
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
SymmetryPoint symmetry: (Hermann–Mauguin notation: 532 / Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(0.40791186, -0.6688262, 0.62151381), (0.8925282, 0.43552149, -0.11710867), (-0.19235728, 0.60248862, 0.77460063)52.56537, -18.94549, -14.35082
3generate(-0.55010687, -0.18965533, 0.81327319), (0.77531476, -0.47782392, 0.41300282), (0.3102732, 0.8577384, 0.4098968)77.75942, 21.40002, -46.99274
4generate(-0.55010687, 0.77531476, 0.3102732), (-0.18965533, -0.47782392, 0.8577384), (0.81327319, 0.41300282, 0.4098968)40.76483, 65.28041, -52.81575
5generate(0.40791186, 0.8925282, -0.19235728), (-0.6688262, 0.43552149, 0.60248862), (0.62151381, -0.11710866, 0.77460063)-7.29314, 52.05447, -23.77263
6generate(-0.99913357, -0.00406396, -0.04141971), (-0.00406396, -0.98093812, 0.19427784), (-0.04141971, 0.19427784, 0.98007169)188.15351, 160.6699, -11.82853
7generate(-0.40321825, 0.64152187, -0.65258312), (-0.91454343, -0.30745136, 0.26283829), (-0.03202106, 0.7027968, 0.71066962)136.30509, 176.25258, -31.75129
8generate(0.53362797, 0.15590559, -0.83122478), (-0.69802099, 0.63612601, -0.32880145), (0.47750172, 0.75566999, 0.44828001)112.32092, 130.23214, -56.94801
9generate(0.51671545, -0.7898076, -0.33046798), (0.34627672, 0.54580214, -0.76301537), (0.78300547, 0.27982846, 0.55551639)149.34632, 86.20726, -52.59768
10generate(-0.43058327, -0.88867422, 0.1576584), (0.77516575, -0.45359845, -0.43973458), (0.46229439, -0.06713097, 0.88418173)196.21344, 105.01883, -24.71231
11generate(0.13484565, 0.98815794, -0.07321564), (0.98815794, -0.13956923, -0.06375195), (-0.07321564, -0.06375195, -0.99527642)-2.88285, 19.11352, 213.28217
12generate(0.95104753, 0.29606413, -0.08862631), (0.29077503, -0.76010115, 0.58111628), (0.10468273, -0.57843952, -0.80898038)-13.46507, 74.61551, 224.9244
13generate(0.66923707, -0.56053956, 0.48776751), (-0.67158307, -0.1754024, 0.71986816), (-0.31795899, -0.80933886, -0.49383467)32.18988, 95.96121, 252.99544
14generate(-0.32113326, -0.39785594, 0.85940915), (-0.56897017, 0.80649322, 0.16075332), (-0.75706431, -0.43735493, -0.48535996)70.98841, 53.65158, 258.70206
15generate(-0.65140532, 0.55929176, 0.51270249), (0.45680619, 0.82863934, -0.32355054), (-0.6058046, 0.02344312, -0.79526801)49.31227, 6.1571, 234.15791
16generate(-0.13571208, -0.98409398, 0.11463535), (-0.98409398, 0.12050735, -0.1305259), (0.11463535, -0.1305259, -0.98479527)182.1221, 183.36843, 201.03603
17generate(-0.95574114, -0.26875979, 0.11969561), (-0.26875979, 0.63203102, -0.7268459), (0.11969561, -0.7268459, -0.67628987)191.98738, 131.22925, 223.66737
18generate(-0.65275817, 0.5942893, -0.46981592), (0.5942893, 0.0171003, -0.80406953), (-0.46981592, -0.80406953, -0.36434213)145.12255, 115.55848, 253.43498
19generate(0.35452467, 0.41234878, -0.83921436), (0.41234878, -0.87447145, -0.25547635), (-0.83921436, -0.25547635, -0.48005322)106.29321, 158.0126, 249.20103
20generate(0.67407673, -0.56314573, -0.4780036), (-0.56314573, -0.81056238, 0.16079651), (-0.4780036, 0.16079651, -0.86351435)129.16019, 199.92145, 216.8167
21generate(0.46582414, -0.51330141, 0.72078397), (0.52029734, -0.49998733, -0.69231737), (0.71575034, 0.69752013, 0.03416319)23.13765, 158.05507, -31.88197
22generate(-0.40676884, -0.10084505, 0.9079479), (-0.10084505, -0.98285706, -0.15434464), (0.9079479, -0.15434464, 0.3896259)47.00478, 204.81252, -7.96342
23generate(-0.43058327, 0.77516575, 0.46229439), (-0.88867422, -0.45359845, -0.06713097), (0.1576584, -0.43973458, 0.88418173)14.50359, 220.34724, 37.09588
24generate(0.42729157, 0.90411383, -0.00029855), (-0.75443704, 0.35637109, -0.55120269), (-0.49824358, 0.2357495, 0.83437133)-29.45038, 183.19078, 41.02551
25generate(0.98130182, 0.10779733, 0.1594568), (0.11635528, 0.32770119, -0.93758913), (-0.15332379, 0.93861156, 0.30903098)-24.11423, 144.6921, -1.60515
26generate(-0.49318916, 0.64165619, 0.58740258), (-0.48913903, 0.35384024, -0.79720768), (-0.71937991, -0.68049571, 0.13934892)19.7862, 183.80703, 214.45535
27generate(0.25852737, 0.96321626, 0.07333503), (0.26963548, 0.00094548, -0.962962), (-0.92761, 0.26872576, -0.25947285)-26.72467, 162.83216, 187.53344
28generate(0.95104753, 0.29077503, 0.10468273), (0.29606413, -0.76010115, -0.57843952), (-0.08862631, 0.58111628, -0.80898038)-32.43611, 190.80702, 137.40578
29generate(0.627332, -0.44637659, 0.63812421), (-0.44637659, -0.87755906, -0.17503724), (0.63812421, -0.17503724, -0.74977294)10.5449, 229.07131, 133.3471
30generate(-0.26525537, -0.2295201, 0.93646149), (-0.93165883, -0.18910542, -0.3102434), (0.24829704, -0.95475634, -0.1636732)42.82006, 224.74508, 180.96636
31generate(-0.49718117, 0.48599752, -0.71876094), (-0.37321816, 0.62805538, 0.68282842), (0.78327459, 0.60774407, -0.13087421)165.71412, -0.66034, -13.32691
32generate(0.3692193, 0.11114487, -0.92267217), (0.27697001, 0.93454605, 0.22340836), (0.88711032, -0.33803919, 0.31426864)140.68695, -41.97665, 18.21036
33generate(0.42729157, -0.75443704, -0.49824358), (0.90411383, 0.35637109, 0.2357495), (-0.00029855, -0.55120269, 0.83437133)171.23051, -48.32915, 66.73595
34generate(-0.40321825, -0.91454343, -0.03202106), (0.64152187, -0.30745136, 0.7027968), (-0.65258312, 0.26283829, 0.71066962)215.13463, -10.93889, 65.18915
35generate(-0.97457383, -0.14791271, -0.16830829), (-0.14791271, -0.13954124, 0.97910677), (-0.16830829, 0.97910677, 0.11411507)211.72532, 18.52205, 15.70758
36generate(0.52454619, -0.6143523, -0.58942561), (0.34205985, -0.48190829, 0.80669664), (-0.77964502, -0.62476848, -0.0426379)158.75479, 21.95009, 233.24319
37generate(-0.22097783, -0.97351609, -0.05861077), (-0.44576044, 0.04736554, 0.89389828), (-0.86744823, 0.22365807, -0.44442169)206.4257, 37.48383, 204.70929
38generate(-0.94775584, -0.31150374, -0.06873354), (-0.31150374, 0.85732851, 0.40982099), (-0.06873354, 0.40982099, -0.90957268)214.09478, 0.32673, 161.25206
39generate(-0.65140532, 0.45680619, -0.6058046), (0.55929176, 0.82863934, 0.02344312), (0.51270249, -0.32355054, -0.79526801)171.16361, -38.17135, 162.9279
40generate(0.25852737, 0.26963548, -0.92761), (0.96321626, 0.00094548, 0.26872576), (0.07333503, -0.962962, -0.25947285)136.96162, -24.80738, 207.42087
41generate(0.46582414, 0.52029734, 0.71575034), (-0.51330141, -0.49998733, 0.69752013), (0.72078397, -0.69231737, 0.03416319)-70.19418, 113.14044, 93.83621
42generate(0.51671545, 0.34627672, 0.78300547), (-0.7898076, 0.54580214, 0.27982846), (-0.33046799, -0.76301537, 0.55551639)-65.83685, 85.62108, 144.35051
43generate(0.3692193, 0.27697001, 0.88711032), (0.11114487, 0.93454605, -0.33803919), (-0.92267217, 0.22340836, 0.31426864)-56.47266, 29.7483, 133.46293
44generate(0.22717034, 0.40815672, 0.88419552), (0.94447032, 0.12901352, -0.30221074), (-0.23742252, 0.90374974, -0.35618386)-55.0426, 22.73637, 76.21973
45generate(0.28687542, 0.55854129, 0.77828923), (0.55854129, -0.75757687, 0.33780012), (0.77828923, 0.33780012, -0.52929855)-63.52296, 74.27555, 51.72907
46generate(-0.49718117, -0.37321816, 0.78327459), (0.48599752, 0.62805538, 0.60774407), (-0.71876094, 0.68282842, -0.13087421)92.58212, -72.02258, 117.81559
47generate(-0.6865824, 0.64189729, 0.34142711), (0.64189729, 0.31464262, 0.69926239), (0.34142711, 0.69926239, -0.62806022)62.27777, -67.09638, 68.97528
48generate(0.22717034, 0.94447032, -0.23742252), (0.40815672, 0.12901352, 0.90374974), (0.88419552, -0.30221074, -0.35618386)9.1265, -49.35085, 82.68783
49generate(0.98130182, 0.11635528, -0.15332379), (0.10779733, 0.32770119, 0.93861156), (0.1594568, -0.93758913, 0.30903098)6.58155, -43.30971, 140.00296
50generate(0.53362797, -0.69802099, 0.47750172), (0.15590559, 0.63612601, 0.75566999), (-0.83122478, -0.32880145, 0.44828001)58.15995, -57.32161, 161.71311
51generate(0.52454619, 0.34205985, -0.77964502), (-0.6143523, -0.48190829, -0.62476848), (-0.58942561, 0.80669664, -0.0426379)91.06442, 253.8323, 85.81208
52generate(0.66923707, -0.67158307, -0.31795899), (-0.56053956, -0.1754024, -0.80933886), (0.48776751, 0.71986816, -0.49383467)123.34544, 239.63457, 40.15733
53generate(-0.26525537, -0.93165883, 0.24829704), (-0.2295201, -0.18910542, -0.95475634), (0.93646149, -0.3102434, -0.1636732)175.81058, 225.10735, 59.24568
54generate(-0.98749433, -0.07875156, 0.13657649), (-0.07875156, -0.50408025, -0.86005889), (0.13657649, -0.86005889, 0.49157458)175.9548, 230.32677, 116.69769
55generate(-0.49937012, 0.70844987, -0.49872664), (-0.31659094, -0.68504237, -0.65611518), (-0.80647359, -0.16975198, 0.5663785)123.57879, 248.07976, 133.11662
56generate(-0.49318916, -0.48913903, -0.71937991), (0.64165619, 0.35384024, -0.68049571), (0.58740258, -0.79720768, 0.13934892)253.9404, 68.20169, 105.02579
57generate(-0.49937012, -0.31659094, -0.80647359), (0.70844987, -0.68504237, -0.16975198), (-0.49872664, -0.65611518, 0.5663785)247.6064, 104.99258, 149.00654
58generate(-0.33113427, -0.2897815, -0.89798484), (-0.2897815, -0.87445415, 0.38904578), (-0.89798484, 0.38904578, 0.20558842)238.92835, 157.64705, 127.09322
59generate(-0.22097783, -0.44576044, -0.86744823), (-0.97351609, 0.04736554, 0.22365807), (-0.05861077, 0.89389828, -0.44442169)239.89902, 153.39842, 69.56929
60generate(-0.32113326, -0.56897017, -0.75706431), (-0.39785594, 0.80649322, -0.43735493), (0.85940915, 0.16075332, -0.48535996)249.17698, 98.11814, 55.93087

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Components

#1: Protein Coat protein / Capsid protein / CP


Mass: 17601.021 Da / Num. of mol.: 3 / Mutation: K42R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cowpea chlorotic mottle virus / Genus: Bromovirus / Gene: RNA4 / Plasmid details: Mixture of RNAs 1, 2, and 3 (1:1:2) / Production host: Vigna unguiculata (cowpea) / Strain (production host): California blackeye / References: UniProt: P03601
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 126 / 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

CrystalDensity Matthews: 3.83 Å3/Da / Density % sol: 68 %
Crystal growTemperature: 298 K / pH: 3.3
Details: 0.3M succinate, 4% PEG 8000, pH 3.3, VAPOR DIFFUSION, SITTING DROP, temperature 298K, pH 3.30

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Data collection

DiffractionMean temperature: 130 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 28, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 1258085 / % possible obs: 84.6 % / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Biso Wilson estimate: 36.1 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 12.1
Reflection shellResolution: 2.7→2.75 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.406 / Mean I/σ(I) obs: 1.9 / % possible all: 55.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT1.6data extraction
GLRFphasing
RAVEphasing
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CWP

1cwp


Resolution: 2.7→20 Å / Data cutoff high absF: 166463.9 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
Details: STANDARD PROCEDURES WITH THE EXCEPTION OF EXCLUDING USE OF R-FREE, WHICH IS NOT MEANINGFUL WITH HIGH LEVELS OF NON-CRYSTALLOGRAPHIC SYMMETRY (60-FOLD IN THIS CASE).
RfactorNum. reflection% reflectionSelection details
Rwork0.245 ---
obs0.245 1201758 80.9 %-
Rfree-0 -NOT USED DUE TO HIGH LEVEL (60-FOLD) OF NON- CRYSTALLOGRAPHIC SYMMETRY
all-1201758 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 19.4349 Å2 / ksol: 0.331228 e/Å3
Displacement parametersBiso mean: 35.05 Å2
Baniso -1Baniso -2Baniso -3
1--0.129 Å20 Å20 Å2
2---0.35 Å20 Å2
3---0.479 Å2
Refine analyzeLuzzati coordinate error obs: 0.41 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.55 Å
Refinement stepCycle: LAST / Resolution: 2.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3615 0 0 126 3741
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
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_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.8
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.31.5
X-RAY DIFFRACTIONc_mcangle_it2.312
X-RAY DIFFRACTIONc_scbond_it2.352
X-RAY DIFFRACTIONc_scangle_it3.732.5
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 2.7→2.87 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rwork0.361 119246 -
obs--51 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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