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- PDB-3kz4: Crystal Structure of the Rotavirus Double Layered Particle -

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Basic information

Entry
Database: PDB / ID: 3kz4
TitleCrystal Structure of the Rotavirus Double Layered Particle
Components
  • Inner capsid protein VP2
  • Intermediate capsid protein VP6
KeywordsVIRUS / icosahedral virus / capsid / Core protein / RNA-binding / dsRNA virus / Metal-binding / Virion / Zinc / Rotavirus
Function / homology
Function and homology information


viral intermediate capsid / T=13 icosahedral viral capsid / T=2 icosahedral viral capsid / viral inner capsid / host cell surface receptor binding / viral nucleocapsid / fusion of virus membrane with host plasma membrane / viral envelope / structural molecule activity / RNA binding / metal ion binding
Similarity search - Function
Viral capsid alpha domain / Viral capsid alpha domain / Jelly Rolls - #170 / Rotavirus major capsid protein VP6 / Rotavirus A/C, major capsid protein VP6 / Rotavirus VP2 protein / Rotavirus VP2 / Virus capsid protein, alpha-helical / Viral capsid/haemagglutinin protein / Jelly Rolls ...Viral capsid alpha domain / Viral capsid alpha domain / Jelly Rolls - #170 / Rotavirus major capsid protein VP6 / Rotavirus A/C, major capsid protein VP6 / Rotavirus VP2 protein / Rotavirus VP2 / Virus capsid protein, alpha-helical / Viral capsid/haemagglutinin protein / Jelly Rolls / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Intermediate capsid protein VP6 / Inner capsid protein VP2 / Intermediate capsid protein VP6
Similarity search - Component
Biological speciesBovine Rotavirus
Bovine rotavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / Molecular Replacement from EM model / Resolution: 3.8 Å
AuthorsMcclain, B. / Settembre, E.C. / Bellamy, A.R. / Harrison, S.C.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: X-ray crystal structure of the rotavirus inner capsid particle at 3.8 A resolution.
Authors: McClain, B. / Settembre, E. / Temple, B.R. / Bellamy, A.R. / Harrison, S.C.
History
DepositionDec 7, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Inner capsid protein VP2
B: Inner capsid protein VP2
C: Intermediate capsid protein VP6
D: Intermediate capsid protein VP6
E: Intermediate capsid protein VP6
F: Intermediate capsid protein VP6
G: Intermediate capsid protein VP6
H: Intermediate capsid protein VP6
I: Intermediate capsid protein VP6
J: Intermediate capsid protein VP6
K: Intermediate capsid protein VP6
L: Intermediate capsid protein VP6
M: Intermediate capsid protein VP6
N: Intermediate capsid protein VP6
O: Intermediate capsid protein VP6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)789,51220
Polymers789,18415
Non-polymers3275
Water0
1
A: Inner capsid protein VP2
B: Inner capsid protein VP2
C: Intermediate capsid protein VP6
D: Intermediate capsid protein VP6
E: Intermediate capsid protein VP6
F: Intermediate capsid protein VP6
G: Intermediate capsid protein VP6
H: Intermediate capsid protein VP6
I: Intermediate capsid protein VP6
J: Intermediate capsid protein VP6
K: Intermediate capsid protein VP6
L: Intermediate capsid protein VP6
M: Intermediate capsid protein VP6
N: Intermediate capsid protein VP6
O: Intermediate capsid protein VP6
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)47,370,6901200
Polymers47,351,068900
Non-polymers19,623300
Water0
TypeNameSymmetry operationNumber
point symmetry operation60
2


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
point symmetry operation1
3
A: Inner capsid protein VP2
B: Inner capsid protein VP2
C: Intermediate capsid protein VP6
D: Intermediate capsid protein VP6
E: Intermediate capsid protein VP6
F: Intermediate capsid protein VP6
G: Intermediate capsid protein VP6
H: Intermediate capsid protein VP6
I: Intermediate capsid protein VP6
J: Intermediate capsid protein VP6
K: Intermediate capsid protein VP6
L: Intermediate capsid protein VP6
M: Intermediate capsid protein VP6
N: Intermediate capsid protein VP6
O: Intermediate capsid protein VP6
hetero molecules
x 5


  • icosahedral pentamer
  • 3.95 MDa, 75 polymers
Theoretical massNumber of molelcules
Total (without water)3,947,558100
Polymers3,945,92275
Non-polymers1,63525
Water0
TypeNameSymmetry operationNumber
point symmetry operation5
4
A: Inner capsid protein VP2
B: Inner capsid protein VP2
C: Intermediate capsid protein VP6
D: Intermediate capsid protein VP6
E: Intermediate capsid protein VP6
F: Intermediate capsid protein VP6
G: Intermediate capsid protein VP6
H: Intermediate capsid protein VP6
I: Intermediate capsid protein VP6
J: Intermediate capsid protein VP6
K: Intermediate capsid protein VP6
L: Intermediate capsid protein VP6
M: Intermediate capsid protein VP6
N: Intermediate capsid protein VP6
O: Intermediate capsid protein VP6
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 4.74 MDa, 90 polymers
Theoretical massNumber of molelcules
Total (without water)4,737,069120
Polymers4,735,10790
Non-polymers1,96230
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
6
A: Inner capsid protein VP2
B: Inner capsid protein VP2
C: Intermediate capsid protein VP6
D: Intermediate capsid protein VP6
E: Intermediate capsid protein VP6
F: Intermediate capsid protein VP6
G: Intermediate capsid protein VP6
H: Intermediate capsid protein VP6
I: Intermediate capsid protein VP6
J: Intermediate capsid protein VP6
K: Intermediate capsid protein VP6
L: Intermediate capsid protein VP6
M: Intermediate capsid protein VP6
N: Intermediate capsid protein VP6
O: Intermediate capsid protein VP6
hetero molecules
x 60


  • crystal asymmetric unit, crystal frame
  • 47.4 MDa, 900 polymers
Theoretical massNumber of molelcules
Total (without water)47,370,6901200
Polymers47,351,068900
Non-polymers19,623300
Water0
TypeNameSymmetry operationNumber
transform to crystal frame1
point symmetry operation60
Unit cell
γ
α
β
Length a, b, c (Å)740.750, 1198.070, 1345.410
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(0.49847398, -0.7834082, 0.37120788), (0.83204272, 0.31213817, -0.45855717), (0.24336929, 0.53743963, 0.80742184)69.78713, -140.57822, -31.9022
3generate(-0.31301218, -0.43553837, 0.84399626), (0.5628652, -0.80084565, -0.20452145), (0.76498767, 0.41103842, 0.49582384)202.86198, -111.76319, -116.22899
4generate(-0.31301219, 0.5628652, 0.76498767), (-0.43553837, -0.80084564, 0.41103842), (0.84399627, -0.20452145, 0.49582384)215.31963, 46.6237, -136.44362
5generate(0.49847397, 0.83204272, 0.24336929), (-0.7834082, 0.31213818, 0.53743963), (0.37120789, -0.45855717, 0.80742184)89.94403, 115.69714, -64.61015
6generate(-0.82789086, 0.32708838, 0.45564231), (0.32708838, -0.37837811, 0.86593487), (0.45564231, 0.86593487, 0.20626897)415.37271, -249.24588, 22.02604
7generate(-0.0296412, 0.99555349, -0.08941278), (0.05896025, 0.09103775, 0.9941005), (0.99782017, 0.02419452, -0.06139655)297.07909, -200.85283, -74.48801
8generate(0.79180734, 0.28591743, -0.53971506), (0.34707098, 0.51649542, 0.78279896), (0.50257623, -0.80714541, 0.30973122)157.90984, -241.25008, -6.29554
9generate(0.5012408, -0.82112689, -0.27296209), (0.79326134, 0.31002687, 0.52404178), (-0.34567922, -0.47920139, 0.80676632)190.19214, -314.61001, 132.36377
10generate(-0.49978774, -0.79568184, 0.3422026), (0.78091141, -0.24303539, 0.5754226), (-0.37468598, 0.55481909, 0.74282313)349.31294, -319.55168, 149.86746
11generate(-0.4563976, -0.80727459, 0.37417771), (-0.8072746, 0.19883994, -0.55567113), (0.37417772, -0.55567114, -0.74244234)331.41933, 327.97478, 226.1101
12generate(-0.80812591, 0.30666234, 0.50288242), (-0.37219535, 0.39585138, -0.83950718), (-0.45651193, -0.865598, -0.20575946)401.11678, 261.41197, 354.02369
13generate(-0.02528743, 0.99908242, -0.03456667), (-0.0604747, -0.03604322, -0.99751877), (-0.99784937, -0.02313427, 0.06133065)285.56689, 206.57157, 450.41344
14generate(0.81026166, 0.31308464, -0.49543318), (-0.3029, -0.49998021, -0.81133925), (-0.50172465, 0.80746381, -0.31028146)144.45568, 239.24114, 382.07199
15generate(0.54382093, -0.80330539, -0.24281526), (-0.76444772, -0.35481443, -0.53826239), (0.34623472, 0.47833793, -0.80704048)172.79405, 314.27246, 243.4449
16generate(0.28428846, 0.48018621, -0.82982002), (0.48018622, -0.82046183, -0.31026374), (-0.82982003, -0.31026373, -0.46382663)351.29574, -69.14432, 503.679
17generate(0.33929313, -0.51880763, -0.78467752), (-0.51880762, -0.7990273, 0.30396384), (-0.78467753, 0.30396385, -0.54026583)330.10478, 89.60365, 504.18165
18generate(-0.45350773, -0.84946148, -0.26971453), (-0.84946149, 0.32039344, 0.41924126), (-0.26971453, 0.41924126, -0.86688571)451.74907, 156.02627, 423.92623
19generate(-0.99849028, -0.05482295, 0.0034076), (-0.05482297, 0.99079898, -0.12374096), (0.0034076, -0.12374096, -0.9923087)548.12033, 38.32974, 373.823
20generate(-0.54250716, 0.76694451, -0.34275663), (0.76694451, 0.28571164, -0.57459984), (-0.34275663, -0.57459984, -0.74320449)486.03676, -100.83335, 423.11292
21generate(-0.49991079, -0.83007131, -0.24712511), (0.82317458, -0.3667002, -0.43349115), (0.26920775, -0.42013402, 0.86661099)460.19549, -141.22838, -47.82576
22generate(-0.99998997, -0.00027756, -0.00446989), (-0.00027756, -0.99231817, 0.12371167), (-0.00446989, 0.12371167, 0.99230814)549.88193, -18.402, 2.37637
23generate(-0.49978775, 0.78091141, -0.37468597), (-0.79568184, -0.24303538, 0.55481908), (0.3422026, 0.57542261, 0.74282313)480.27712, 117.13027, -46.98355
24generate(0.3094334, 0.43391899, -0.84614731), (-0.46381659, 0.84566482, 0.26405529), (0.83013562, 0.31074963, 0.46293577)347.57254, 78.06745, -127.69179
25generate(0.30935736, -0.56172309, -0.76731036), (0.5366917, 0.76923576, -0.34675403), (0.78502232, -0.3045382, 0.53944087)335.16141, -81.60697, -128.2123
26generate(0.02976424, -0.06342845, -0.99754244), (-0.99895899, 0.03262706, -0.03188109), (0.03456904, 0.99745291, -0.0623913)453.99487, 282.5463, 187.80046
27generate(-0.28070968, -0.57923483, -0.76530326), (-0.47856683, 0.77564265, -0.41152432), (0.83197108, 0.25072989, -0.49493298)496.81249, 209.26224, 51.98321
28generate(-0.8081259, -0.37219534, -0.45651194), (0.30666233, 0.39585138, -0.865598), (0.50288243, -0.83950719, -0.20575946)583.06522, 79.95451, 90.58637
29generate(-0.82361314, 0.27156848, -0.49790757), (0.27156848, -0.58188813, -0.76658774), (-0.49790757, -0.76658774, 0.40550127)593.55472, 73.32199, 250.26169
30generate(-0.30576856, 0.46239691, -0.83228281), (-0.53534988, -0.8063731, -0.25132236), (-0.78734116, 0.36871604, 0.49410767)513.78486, 198.5306, 310.34331
31generate(0.80578485, 0.37583424, 0.45766733), (-0.24186988, -0.49656405, 0.83362048), (0.54056427, -0.78241471, -0.30922081)-33.60454, -86.69755, 99.55103
32generate(0.8257551, -0.26797769, 0.49630281), (-0.33085071, 0.48250694, 0.81100238), (-0.45680009, -0.83389149, 0.30977195)-44.80583, -60.3652, 257.13074
33generate(0.30943341, -0.46381658, 0.83013562), (0.43391899, 0.84566481, 0.31074963), (-0.84614732, 0.26405529, 0.46293577)34.65992, -177.15704, 332.59655
34generate(-0.02964119, 0.05896025, 0.99782016), (0.99555349, 0.09103774, 0.02419453), (-0.08941279, 0.99410051, -0.06139655)94.97375, -275.67073, 221.65726
35generate(0.27712087, 0.577893, 0.76762211), (0.57789301, -0.73850531, 0.34734648), (0.76762211, 0.34734648, -0.53861556)52.78399, -219.76369, 77.62721
36generate(-0.3356383, 0.51766552, 0.78700021), (0.41765429, 0.83063718, -0.36824824), (-0.84434106, 0.20509581, -0.49499888)217.50196, -45.0358, 512.28941
37generate(0.45494455, 0.84749007, 0.27347035), (0.8096951, -0.26583142, -0.52318973), (-0.3707011, 0.45944992, -0.80714711)96.19919, -120.91047, 440.32482
38generate(0.99848025, 0.05510051, 0.00106229), (0.05510052, -0.99848081, 2.929E-5), (0.00106229, 2.929E-5, -0.99999944)0.08552, -10.34316, 375.61577
39generate(0.54382093, -0.76444772, 0.34623472), (-0.80330539, -0.35481443, 0.47833793), (-0.24281526, -0.53826239, -0.80704049)61.98677, 133.86586, 407.58797
40generate(-0.28070968, -0.47856682, 0.83197107), (-0.57923483, 0.77564266, 0.2507299), (-0.76530327, -0.41152432, -0.49493298)196.35752, 112.42463, 492.05692
41generate(-0.4999108, 0.82317458, 0.26920774), (-0.83007131, -0.36670019, -0.42013401), (-0.24712511, -0.43349115, 0.86661099)359.18737, 310.11338, 93.95094
42generate(0.50124079, 0.79326133, -0.34567922), (-0.82112689, 0.31002688, -0.47920139), (-0.27296209, 0.52404179, 0.80676633)199.9913, 317.13834, 109.99741
43generate(0.8257551, -0.33085072, -0.45680009), (-0.26797768, 0.48250693, -0.83389149), (0.49630281, 0.81100238, 0.30977195)134.48412, 231.5388, -8.45832
44generate(0.02516439, -0.99567692, 0.0894104), (0.0649429, -0.08762159, -0.99403464), (0.99757164, 0.03082084, 0.0624572)253.19453, 171.61042, -97.71444
45generate(-0.7941422, -0.28245007, 0.53810791), (-0.28245007, -0.61246045, -0.73831846), (0.53810792, -0.73831847, 0.40660265)392.06878, 220.17218, -34.42204
46generate(0.80578486, -0.24186988, 0.54056426), (0.37583425, -0.49656405, -0.7824147), (0.45766733, 0.83362048, -0.30922081)-47.70523, 47.46904, 118.43581
47generate(0.33197345, -0.41623463, 0.84648825), (-0.41623462, -0.86992889, -0.26452308), (0.84648826, -0.26452308, -0.46204456)25.28464, 168.46427, 43.05104
48generate(0.02516438, 0.0649429, 0.99757163), (-0.99567692, -0.08762158, 0.03082084), (0.08941041, -0.99403465, 0.0624572)79.96079, 270.14837, 154.05145
49generate(0.30935735, 0.53669171, 0.78502231), (-0.56172309, 0.76923577, -0.30453819), (-0.76731037, -0.34675402, 0.53944087)40.76266, 211.99737, 298.03824
50generate(0.79180734, 0.34707098, 0.50257622), (0.28591743, 0.51649542, -0.8071454), (-0.53971507, 0.78279897, 0.30973123)-38.13928, 74.37397, 276.02656
51generate(-0.3356383, 0.4176543, -0.84434105), (0.51766551, 0.83063718, 0.2050958), (0.78700022, -0.36824825, -0.49499888)524.35836, -180.25326, 65.82424
52generate(-0.02528743, -0.0604747, -0.99784936), (0.99908243, -0.03604322, -0.02313428), (-0.03456666, -0.99751877, 0.06133065)469.15837, -267.43937, 188.30596
53generate(-0.30576855, -0.53534988, -0.78734115), (0.46239692, -0.80637311, 0.36871603), (-0.83228282, -0.25132235, 0.49410767)507.72865, -191.91135, 324.16648
54generate(-0.78946629, -0.35070988, -0.50373162), (-0.35070988, -0.41578275, 0.83912292), (-0.50373163, 0.83912293, 0.20524905)586.76638, -58.04635, 285.65118
55generate(-0.80792682, 0.23827909, -0.53895949), (-0.31655201, 0.59594524, 0.73800006), (0.49704033, 0.76685875, -0.40605242)597.04411, -50.84126, 125.98689
56generate(0.02976424, -0.99895899, 0.03456905), (-0.06342845, 0.03262706, 0.99745291), (-0.99754244, -0.03188108, -0.0623913)262.24727, -167.74458, 473.60415
57generate(-0.80792681, -0.316552, 0.49704033), (0.23827908, 0.59594524, 0.76685875), (-0.5389595, 0.73800007, -0.40605242)403.65348, -208.57867, 410.46073
58generate(-0.54515093, 0.8012577, 0.24656961), (0.80125769, 0.41148775, 0.43435462), (0.24656961, 0.43435462, -0.86633682)375.91422, -300.19125, 282.05553
59generate(0.45494455, 0.80969509, -0.37070109), (0.84749008, -0.26583142, 0.45944992), (0.27347035, -0.52318974, -0.80714712)217.36421, -315.97686, 265.84016
60generate(0.81026167, -0.30290001, -0.50172464), (0.31308465, -0.49998021, 0.8074638), (-0.49543318, -0.81133925, -0.31028146)147.11417, -234.12032, 384.22372
Detailsbiological unit is the same as asymmetric unit. The icosahedral asymmetry unit is reported. To generate the full double layer particle apply the following MTRIX records in the PDB file above coordinates.

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Components

#1: Protein Inner capsid protein VP2


Mass: 102595.039 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bovine Rotavirus / Strain: UK/G6 / Cell line (production host): Kidney Cells / Organ (production host): Kidney / Production host: Chlorocebus sabaeus (green monkey) / References: UniProt: P17462*PLUS
#2: Protein
Intermediate capsid protein VP6


Mass: 44922.645 Da / Num. of mol.: 13
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bovine rotavirus / Strain: UK/G6 / Cell line (production host): Kidney Cells / Organ (production host): Kidney / Production host: Chlorocebus sabaeus (green monkey) / References: UniProt: A7J3A1, UniProt: P18610*PLUS
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn

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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

Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 50 mM NaCl, 375 mM Sodium Sulfate, 1.6% PEG 10,000, 0.02% Sodium Azide, 20 mM HEPES pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 3.8→223 Å / Num. obs: 1823596 / % possible obs: 20.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.1 % / Rmerge(I) obs: 0.182 / Net I/σ(I): 3.4

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT3.005data extraction
ADSCQuantumdata collection
SCALAdata scaling
CCP4phasing
RefinementMethod to determine structure: Molecular Replacement from EM model
Resolution: 3.8→30 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.339 36830 0.3 %
Rwork0.328 --
obs-1823596 15.9 %
Solvent computationBsol: 16.832 Å2
Displacement parametersBiso max: 208.66 Å2 / Biso mean: 155.027 Å2 / Biso min: 9.66 Å2
Baniso -1Baniso -2Baniso -3
1--13.123 Å20 Å20 Å2
2--4.882 Å20 Å2
3---8.241 Å2
Refinement stepCycle: LAST / Resolution: 3.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms54104 0 5 0 54109
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_d1.667
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep_eth2.param
X-RAY DIFFRACTION2CNS_TOPPAR:ion.param

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