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- PDB-4llf: Crystal structure of Cucumber Necrosis Virus -

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Basic information

Entry
Database: PDB / ID: 4llf
TitleCrystal structure of Cucumber Necrosis Virus
ComponentsCapsid protein
KeywordsVIRUS / Beta Barrel / Tombusvirus / Viral Beta barrel / Virus Capsid / Extracellular
Function / homology
Function and homology information


T=3 icosahedral viral capsid / structural molecule activity / RNA binding
Similarity search - Function
Immunoglobulin-like - #4030 / 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 / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesCucumber necrosis virus
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8891 Å
AuthorsSmith, T.
CitationJournal: J.Virol. / Year: 2013
Title: Atomic structure of cucumber necrosis virus and the role of the capsid in vector transmission.
Authors: Li, M. / Kakani, K. / Katpally, U. / Johnson, S. / Rochon, D. / Smith, T.J.
History
DepositionJul 9, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 30, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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_auth_seq_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.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Capsid protein
B: Capsid protein
D: Capsid protein
E: Capsid protein
F: Capsid protein
G: Capsid protein
H: Capsid protein
I: Capsid protein
J: Capsid protein
K: Capsid protein
L: Capsid protein
M: Capsid protein
N: Capsid protein
O: Capsid protein
P: Capsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)614,63935
Polymers613,71115
Non-polymers92820
Water1,09961
1
A: Capsid protein
B: Capsid protein
D: Capsid protein
E: Capsid protein
F: Capsid protein
G: Capsid protein
H: Capsid protein
I: Capsid protein
J: Capsid protein
K: Capsid protein
L: Capsid protein
M: Capsid protein
N: Capsid protein
O: Capsid protein
P: Capsid protein
hetero molecules
x 12


Theoretical massNumber of molelcules
Total (without water)7,375,666420
Polymers7,364,528180
Non-polymers11,139240
Water3,243180
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation11
2


  • Idetical with deposited unit
  • point asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit in distinct coordinate
  • point asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
4
A: Capsid protein
B: Capsid protein
D: Capsid protein
E: Capsid protein
F: Capsid protein
G: Capsid protein
H: Capsid protein
I: Capsid protein
J: Capsid protein
K: Capsid protein
L: Capsid protein
M: Capsid protein
N: Capsid protein
O: Capsid protein
P: Capsid protein
hetero molecules


  • crystal asymmetric unit, crystal frame
  • 615 kDa, 15 polymers
Theoretical massNumber of molelcules
Total (without water)614,63935
Polymers613,71115
Non-polymers92820
Water27015
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
Unit cell
Length a, b, c (Å)384.000, 384.000, 384.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))
Components on special symmetry positions
IDModelComponents
11G-401-

ZN

21M-401-

ZN

31G-503-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51
12
22
32
42
52
13
23
33
43
53

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111Chain A
211Chain E
311chain H
411chain K
511chain N
112Chain B
212chain F
312chain I
412chain L
512Chain O
113chain D
213chain G
313chain J
413chain M
513chain P

NCS ensembles :
ID
1
2
3

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Components

#1: Protein
Capsid protein / Coat protein / p41


Mass: 40914.043 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Source: (natural) Cucumber necrosis virus / Strain: Nicotiana benthamiana / References: UniProt: P15183
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 61 / 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: 4

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Sample preparation

CrystalDensity Matthews: 3.84 Å3/Da / Density % sol: 68 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6
Details: Virus concentration was adjusted to 10 mg/ml in 20 mM sodium acetate buffer at pH 5.0. The reservoir contained 0.16 M PIPES buffer and 3.2 M sodium formate, pH 6.0. Drop composed of 10 ...Details: Virus concentration was adjusted to 10 mg/ml in 20 mM sodium acetate buffer at pH 5.0. The reservoir contained 0.16 M PIPES buffer and 3.2 M sodium formate, pH 6.0. Drop composed of 10 microliters reservoir and virus solutions., VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418 Å
DetectorType: BRUKER SMART 6000 / Detector: CCD / Date: Jan 15, 2013
RadiationMonochromator: Montel mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.889→75.309 Å / Num. all: 140952 / Num. obs: 134159 / % possible obs: 64 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
PROTEUM PLUSPLUSdata collection
PHENIX(phenix.refine: 1.8.2_1309)model building
PHENIX(phenix.refine: 1.8.2_1309)refinement
SAINTdata reduction
SHELXdata scaling
PHENIX1.8.2_1309phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2TBV

2tbv


Resolution: 2.8891→75.309 Å / SU ML: 0.43 / σ(F): 0 / Phase error: 23.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2418 6793 5.06 %RANDOM
Rwork0.2127 ---
all0.2142 140952 --
obs0.2142 134159 64.36 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8891→75.309 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms34345 0 20 61 34426
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01135350
X-RAY DIFFRACTIONf_angle_d1.49148390
X-RAY DIFFRACTIONf_dihedral_angle_d16.25612395
X-RAY DIFFRACTIONf_chiral_restr0.15590
X-RAY DIFFRACTIONf_plane_restr0.0086320
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2212X-RAY DIFFRACTIONPOSITIONAL
12E2212X-RAY DIFFRACTIONPOSITIONAL0.112
13H2212X-RAY DIFFRACTIONPOSITIONAL0.083
14K2212X-RAY DIFFRACTIONPOSITIONAL0.053
15N2212X-RAY DIFFRACTIONPOSITIONAL0.051
21B2226X-RAY DIFFRACTIONPOSITIONAL
22F2226X-RAY DIFFRACTIONPOSITIONAL0.15
23I2226X-RAY DIFFRACTIONPOSITIONAL0.173
24L2226X-RAY DIFFRACTIONPOSITIONAL0.111
25O2226X-RAY DIFFRACTIONPOSITIONAL0.124
31D2462X-RAY DIFFRACTIONPOSITIONAL
32G2462X-RAY DIFFRACTIONPOSITIONAL0.145
33J2462X-RAY DIFFRACTIONPOSITIONAL0.119
34M2462X-RAY DIFFRACTIONPOSITIONAL0.113
35P2462X-RAY DIFFRACTIONPOSITIONAL0.142
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8891-2.92190.4917960.48461876X-RAY DIFFRACTION28
2.9219-2.95630.47511210.45472274X-RAY DIFFRACTION35
2.9563-2.99240.45791180.43632455X-RAY DIFFRACTION37
2.9924-3.03020.49061230.43112562X-RAY DIFFRACTION39
3.0302-3.07010.42231380.40312547X-RAY DIFFRACTION39
3.0701-3.11220.46481320.38942601X-RAY DIFFRACTION40
3.1122-3.15660.39871370.35762698X-RAY DIFFRACTION41
3.1566-3.20370.38361380.36022712X-RAY DIFFRACTION41
3.2037-3.25380.4071540.33612772X-RAY DIFFRACTION42
3.2538-3.30720.38371710.32523057X-RAY DIFFRACTION47
3.3072-3.36420.32191670.29513296X-RAY DIFFRACTION50
3.3642-3.42540.31661860.28973550X-RAY DIFFRACTION54
3.4254-3.49120.32762020.26613652X-RAY DIFFRACTION55
3.4912-3.56250.29922290.26234000X-RAY DIFFRACTION61
3.5625-3.640.24772080.2454285X-RAY DIFFRACTION65
3.64-3.72460.26022430.22964423X-RAY DIFFRACTION67
3.7246-3.81780.27442490.20784664X-RAY DIFFRACTION71
3.8178-3.9210.23772570.2124729X-RAY DIFFRACTION72
3.921-4.03640.23532740.2044978X-RAY DIFFRACTION76
4.0364-4.16660.2442870.18735146X-RAY DIFFRACTION78
4.1666-4.31550.20322960.16465255X-RAY DIFFRACTION80
4.3155-4.48830.1862960.14455501X-RAY DIFFRACTION84
4.4883-4.69260.17842990.14135589X-RAY DIFFRACTION85
4.6926-4.93990.15693250.13735724X-RAY DIFFRACTION87
4.9399-5.24930.1683320.1465787X-RAY DIFFRACTION88
5.2493-5.65450.1763370.15185951X-RAY DIFFRACTION90
5.6545-6.22330.19463060.16446084X-RAY DIFFRACTION92
6.2233-7.12320.20223390.18386242X-RAY DIFFRACTION94
7.1232-8.97220.1893070.17896489X-RAY DIFFRACTION96
8.9722-75.33420.18933260.18246467X-RAY DIFFRACTION94

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