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- PDB-3zxa: Structure and Assembly of Turnip Crinkle Virus I. X-ray Crystallo... -

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Basic information

Entry
Database: PDB / ID: 3zxa
TitleStructure and Assembly of Turnip Crinkle Virus I. X-ray Crystallographic Structure Analysis at 3.2 A Resolution
ComponentsCAPSID PROTEINCapsid
KeywordsVIRUS / SSRNA VIRUS / ICOSAHEDRAL VIRUS
Function / homology
Function and homology information


T=3 icosahedral viral capsid / structural molecule activity / RNA binding
Similarity search - Function
Immunoglobulin-like - #3420 / 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 speciesTURNIP CRINKLE VIRUS
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsHogle, J.M. / Maeda, A. / Harrison, S.C.
CitationJournal: J Mol Biol / Year: 1986
Title: Structure and assembly of turnip crinkle virus. I. X-ray crystallographic structure analysis at 3.2 A resolution.
Abstract: The structure of turnip crinkle virus has been determined at 3.2 A resolution, using the electron density of tomato bushy stunt virus as a starting point for phase refinement by non-crystallographic ...The structure of turnip crinkle virus has been determined at 3.2 A resolution, using the electron density of tomato bushy stunt virus as a starting point for phase refinement by non-crystallographic symmetry. The structures are very closely related, especially in the subunit arm and S domain, where only small insertions and deletions and small co-ordinate shifts relate one chain to another. The P domains, although quite similar in fold, are oriented somewhat differently with respect to the S domains. Understanding of the structure of turnip crinkle virus has been important for analyzing its assembly, as described in an accompanying paper.
History
DepositionAug 8, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 8, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 4, 2015Group: Database references
Revision 1.2Feb 3, 2016Group: Derived calculations
Revision 1.3Jun 28, 2017Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_wavelength_list / _diffrn_source.type
Revision 1.4Nov 13, 2019Group: Data collection / Database references / Category: pdbx_database_related / Item: _pdbx_database_related.content_type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: CAPSID PROTEIN


Theoretical massNumber of molelcules
Total (without water)37,7561
Polymers37,7561
Non-polymers00
Water0
1
C: CAPSID PROTEIN
x 60


Theoretical massNumber of molelcules
Total (without water)2,265,33560
Polymers2,265,33560
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation60
2


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
point symmetry operation1
3
C: CAPSID PROTEIN
x 5


  • icosahedral pentamer
  • 189 kDa, 5 polymers
Theoretical massNumber of molelcules
Total (without water)188,7785
Polymers188,7785
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation5
4
C: CAPSID PROTEIN
x 6


  • icosahedral 23 hexamer
  • 227 kDa, 6 polymers
Theoretical massNumber of molelcules
Total (without water)226,5346
Polymers226,5346
Non-polymers00
Water0
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)348.800, 379.100, 397.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-1), (1), (-1)1.0E-5, 2.0E-5, 2.0E-5
2generate(0.309017, -0.809017, 0.5), (0.809017, 0.5, 0.309017), (-0.5, 0.309017, 0.809017)
3generate(-0.809017, -0.5, 0.309017), (0.5, -0.309017, 0.809017), (-0.309017, 0.809017, 0.5)
4generate(-0.809017, 0.5, -0.309017), (-0.5, -0.309017, 0.809017), (0.309017, 0.809017, 0.5)
5generate(0.309017, 0.809017, -0.5), (-0.809017, 0.5, 0.309017), (0.5, 0.309017, 0.809017)
6generate(-1), (-1), (1)
7generate(-0.309017, 0.809017, -0.5), (-0.809017, -0.5, -0.309017), (-0.5, 0.309017, 0.809017)
8generate(0.809017, 0.5, -0.309017), (-0.5, 0.309017, -0.809017), (-0.309017, 0.809017, 0.5)
9generate(0.809017, -0.5, 0.309017), (0.5, 0.309017, -0.809017), (0.309017, 0.809017, 0.5)
10generate(-0.309017, -0.809017, 0.5), (0.809017, -0.5, -0.309017), (0.5, 0.309017, 0.809017)
11generate(-1), (1), (-1)
12generate(-0.309017, 0.809017, -0.5), (0.809017, 0.5, 0.309017), (0.5, -0.309017, -0.809017)
13generate(0.809017, 0.5, -0.309017), (0.5, -0.309017, 0.809017), (0.309017, -0.809017, -0.5)
14generate(0.809017, -0.5, 0.309017), (-0.5, -0.309017, 0.809017), (-0.309017, -0.809017, -0.5)
15generate(-0.309017, -0.809017, 0.5), (-0.809017, 0.5, 0.309017), (-0.5, -0.309017, -0.809017)
16generate(1), (-1), (-1)
17generate(0.309017, -0.809017, 0.5), (-0.809017, -0.5, -0.309017), (0.5, -0.309017, -0.809017)
18generate(-0.809017, -0.5, 0.309017), (-0.5, 0.309017, -0.809017), (0.309017, -0.809017, -0.5)
19generate(-0.809017, 0.5, -0.309017), (0.5, 0.309017, -0.809017), (-0.309017, -0.809017, -0.5)
20generate(0.309017, 0.809017, -0.5), (0.809017, -0.5, -0.309017), (-0.5, -0.309017, -0.809017)
21generate(1), (1), (1)
22generate(-0.5, 0.309017, 0.809017), (0.309017, -0.809017, 0.5), (0.809017, 0.5, 0.309017)
23generate(-0.309017, 0.809017, 0.5), (-0.809017, -0.5, 0.309017), (0.5, -0.309017, 0.809017)
24generate(0.309017, 0.809017, 0.5), (-0.809017, 0.5, -0.309017), (-0.5, -0.309017, 0.809017)
25generate(0.5, 0.309017, 0.809017), (0.309017, 0.809017, -0.5), (-0.809017, 0.5, 0.309017)
26generate(1), (-1), (-1)
27generate(-0.5, 0.309017, 0.809017), (-0.309017, 0.809017, -0.5), (-0.809017, -0.5, -0.309017)
28generate(-0.309017, 0.809017, 0.5), (0.809017, 0.5, -0.309017), (-0.5, 0.309017, -0.809017)
29generate(0.309017, 0.809017, 0.5), (0.809017, -0.5, 0.309017), (0.5, 0.309017, -0.809017)
30generate(0.5, 0.309017, 0.809017), (-0.309017, -0.809017, 0.5), (0.809017, -0.5, -0.309017)
31generate(-1), (-1), (1)
32generate(0.5, -0.309017, -0.809017), (-0.309017, 0.809017, -0.5), (0.809017, 0.5, 0.309017)
33generate(0.309017, -0.809017, -0.5), (0.809017, 0.5, -0.309017), (0.5, -0.309017, 0.809017)
34generate(-0.309017, -0.809017, -0.5), (0.809017, -0.5, 0.309017), (-0.5, -0.309017, 0.809017)
35generate(-0.5, -0.309017, -0.809017), (-0.309017, -0.809017, 0.5), (-0.809017, 0.5, 0.309017)
36generate(-1), (1), (-1)
37generate(0.5, -0.309017, -0.809017), (0.309017, -0.809017, 0.5), (-0.809017, -0.5, -0.309017)
38generate(0.309017, -0.809017, -0.5), (-0.809017, -0.5, 0.309017), (-0.5, 0.309017, -0.809017)
39generate(-0.309017, -0.809017, -0.5), (-0.809017, 0.5, -0.309017), (0.5, 0.309017, -0.809017)
40generate(-0.5, -0.309017, -0.809017), (0.309017, 0.809017, -0.5), (0.809017, -0.5, -0.309017)
41generate(1), (1), (1)
42generate(0.809017, 0.5, 0.309017), (-0.5, 0.309017, 0.809017), (0.309017, -0.809017, 0.5)
43generate(0.5, -0.309017, 0.809017), (-0.309017, 0.809017, 0.5), (-0.809017, -0.5, 0.309017)
44generate(-0.5, -0.309017, 0.809017), (0.309017, 0.809017, 0.5), (-0.809017, 0.5, -0.309017)
45generate(-0.809017, 0.5, 0.309017), (0.5, 0.309017, 0.809017), (0.309017, 0.809017, -0.5)
46generate(-1), (1), (-1)
47generate(-0.809017, -0.5, -0.309017), (-0.5, 0.309017, 0.809017), (-0.309017, 0.809017, -0.5)
48generate(-0.5, 0.309017, -0.809017), (-0.309017, 0.809017, 0.5), (0.809017, 0.5, -0.309017)
49generate(0.5, 0.309017, -0.809017), (0.309017, 0.809017, 0.5), (0.809017, -0.5, 0.309017)
50generate(0.809017, -0.5, -0.309017), (0.5, 0.309017, 0.809017), (-0.309017, -0.809017, 0.5)
51generate(1), (-1), (-1)
52generate(0.809017, 0.5, 0.309017), (0.5, -0.309017, -0.809017), (-0.309017, 0.809017, -0.5)
53generate(0.5, -0.309017, 0.809017), (0.309017, -0.809017, -0.5), (0.809017, 0.5, -0.309017)
54generate(-0.5, -0.309017, 0.809017), (-0.309017, -0.809017, -0.5), (0.809017, -0.5, 0.309017)
55generate(-0.809017, 0.5, 0.309017), (-0.5, -0.309017, -0.809017), (-0.309017, -0.809017, 0.5)
56generate(-1), (-1), (1)
57generate(-0.809017, -0.5, -0.309017), (0.5, -0.309017, -0.809017), (0.309017, -0.809017, 0.5)
58generate(-0.5, 0.309017, -0.809017), (0.309017, -0.809017, -0.5), (-0.809017, -0.5, 0.309017)
59generate(0.5, 0.309017, -0.809017), (-0.309017, -0.809017, -0.5), (-0.809017, 0.5, -0.309017)
60generate(0.809017, -0.5, -0.309017), (-0.5, -0.309017, -0.809017), (0.309017, 0.809017, -0.5)

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Components

#1: Protein CAPSID PROTEIN / Capsid / COAT PROTEIN / P38


Mass: 37755.586 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) TURNIP CRINKLE VIRUS / References: UniProt: P06663
Sequence detailsSEQUENCE WAS PUBLISHED AFTER CRYSTAL STRUCTURE WAS SOLVED. NO SEQUENCE INFORMATION WAS AVAILABLE AT ...SEQUENCE WAS PUBLISHED AFTER CRYSTAL STRUCTURE WAS SOLVED. NO SEQUENCE INFORMATION WAS AVAILABLE AT THE TIME OF SOLVING THE CRYSTAL STRUCTURE. GB M22445.2

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 50

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Sample preparation

CrystalDescription: DATA COLLECTED ON KODAK FILM, WITH GX-6 ROTATING ANODE AND DOUBLE-MIRROR FRANKS CAMERA
Crystal growpH: 7
Details: THE METHYL MERCURY ADDUCT WAS OBTAINED BY BRINGING STOCK SOLUTION OF VIRUS (3.5% TCV (W/V) IN 0.01% SODIUM AZIDE,) TO 6 EQUIVALENT METHYL MERCURY/PROTEIN SUBUNIT BY ADDITION OF 15 MILLIMOLAR- ...Details: THE METHYL MERCURY ADDUCT WAS OBTAINED BY BRINGING STOCK SOLUTION OF VIRUS (3.5% TCV (W/V) IN 0.01% SODIUM AZIDE,) TO 6 EQUIVALENT METHYL MERCURY/PROTEIN SUBUNIT BY ADDITION OF 15 MILLIMOLAR-METHYL MERCURY NITRATE AND INCUBATING FOR 1 H. CRYSTALLIZATION WAS THEN INITIATED BY ADDITION OF AN APPROXIMATELY EQUAL VOLUME OF SATURATED SODIUM CITRATE (PH 7.0) AND ALLOWED TO PROCEED UNDISTURBED FOR 2 TO 4 MONTHS. THE OPTIMUM CONCENTRATION OF SODIUM CITRATE REQUIRED TO PRODUCE LARGE CRYSTALS VARIED FROM EXPERIMENT TO EXPERIMENT BUT WAS GENERALLY IN THE RANGE 42 TO 46% SATURATED.

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: ELLIOTT GX-6 / Wavelength: 1.5418 / Wavelength: 1.5418 Å
DetectorType: KODAK NO-SCREEN X-RAY FILM / Detector: FILM / Details: FRANKS MIRROR OPTICS
RadiationMonochromator: DOUBLE MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.2→100 Å / Num. obs: 310000 / % possible obs: 73 % / Observed criterion σ(I): 0 / Redundancy: 2.2 % / Rmerge(I) obs: 0.18
Reflection shellHighest resolution: 3.2 Å

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Processing

Software
NameVersionClassification
OPTRONICSP1000 ROTATING DRUM SCANNERdata reduction
DIGITALPDP11.34 COMPUTERdata reduction
SCAN12SOFTWAREdata reduction
HARVARDSOFTWAREdata scaling
COMBINEphasing
FFTphasing
BILDERrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: TBSV

Resolution: 3.2→100 Å / Num. reflection obs: 680000
Details: THIS STRUCTURE WAS DETERMINED IN THE EARLY 1980S WHEN NO REFINEMENT PROGRAM WAS AVAILABLE. THE AUTHORS USED BILDER SOFTWARE TO CHECK THE STEREOCHEMISTRY OF THE MODEL AND DID SOME LOCAL REAL ...Details: THIS STRUCTURE WAS DETERMINED IN THE EARLY 1980S WHEN NO REFINEMENT PROGRAM WAS AVAILABLE. THE AUTHORS USED BILDER SOFTWARE TO CHECK THE STEREOCHEMISTRY OF THE MODEL AND DID SOME LOCAL REAL SPACE REFINEMENT. THIS ENTRY LACKS THE COODRDINATES OF CHAINS A AND B, WHICH ARE REQUIRED TO GENERATE THE FULL CAPSID.AT THE TIME THIS STRUCTURE WAS DETERMINED ONLY THE C-SUBUNIT WAS BUILT. IN THE NEWLY DEPOSITED EM DATA (EMD-1863) THIS C-SUBUNIT HAS BEEN PLACED AND THE POSITIONS AND CONFORMATIONS OF THE A & B SUBUNITS HAVE BEEN GENERATED FROM IT. HENCE THE STRUCTURE OF THE FULL NATIVE TCV CAPSID, OBTAINED FROM A CRYO-EM RECONSTRUCTION OF THE TCV CAPSID AND THE ATOMIC COORDINATES HERE, CAN BE FOUND IN PDB 3ZX8.
Refinement stepCycle: LAST / Resolution: 3.2→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2237 0 0 0 2237

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