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- PDB-4f5x: Location of the dsRNA-dependent polymerase, VP1, in rotavirus par... -

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Basic information

Entry
Database: PDB / ID: 4f5x
TitleLocation of the dsRNA-dependent polymerase, VP1, in rotavirus particles
Components
  • Intermediate capsid protein VP6
  • RNA-directed RNA polymeraseRNA-dependent RNA polymerase
  • VP2 protein
KeywordsVIRUS / beta-jellyroll / polymerase / transcriptase
Function / homology
Function and homology information


viral intermediate capsid / T=2 icosahedral viral capsid / viral inner capsid / viral genome replication / virion component / viral nucleocapsid / host cell surface receptor binding / RNA-directed RNA polymerase / fusion of virus membrane with host plasma membrane / RNA-dependent RNA polymerase activity ...viral intermediate capsid / T=2 icosahedral viral capsid / viral inner capsid / viral genome replication / virion component / viral nucleocapsid / host cell surface receptor binding / RNA-directed RNA polymerase / fusion of virus membrane with host plasma membrane / RNA-dependent RNA polymerase activity / nucleotide binding / viral envelope / DNA-templated transcription / structural molecule activity / RNA binding / metal ion binding
Similarity search - Function
Rotavirus VP2 / Rotavirus VP2 protein / Rotavirus VP1 RNA-directed RNA polymerase, C-terminal / Viral RNA-directed RNA polymerase, 4-helical domain / Rotavirus VP1 C-terminal domain / Rotavirus A/C, major capsid protein VP6 / Rotavirus major capsid protein VP6 / RNA-directed RNA polymerase, luteovirus / Viral RNA-directed RNA-polymerase / Virus capsid protein, alpha-helical ...Rotavirus VP2 / Rotavirus VP2 protein / Rotavirus VP1 RNA-directed RNA polymerase, C-terminal / Viral RNA-directed RNA polymerase, 4-helical domain / Rotavirus VP1 C-terminal domain / Rotavirus A/C, major capsid protein VP6 / Rotavirus major capsid protein VP6 / RNA-directed RNA polymerase, luteovirus / Viral RNA-directed RNA-polymerase / Virus capsid protein, alpha-helical / RNA-directed RNA polymerase, reovirus / RdRp of Reoviridae dsRNA viruses catalytic domain profile. / Viral capsid/haemagglutinin protein / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
Intermediate capsid protein VP6 / Inner capsid protein VP2 / RNA-directed RNA polymerase
Similarity search - Component
Biological speciesBovine rotavirus A
Bovine rotavirus
Simian 11 rotavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 5 Å
AuthorsEstrozi, L.F. / Settembre, E.C. / Goret, G. / McClain, B. / Zhang, X. / Chen, J.Z. / Grigorieff, N. / Harrison, S.C.
CitationJournal: J Mol Biol / Year: 2013
Title: Location of the dsRNA-dependent polymerase, VP1, in rotavirus particles.
Authors: Leandro F Estrozi / Ethan C Settembre / Gaël Goret / Brian McClain / Xing Zhang / James Z Chen / Nikolaus Grigorieff / Stephen C Harrison /
Abstract: Double-stranded RNA (dsRNA) viruses transcribe and replicate RNA within an assembled, inner capsid particle; only plus-sense mRNA emerges into the intracellular milieu. During infectious entry of a ...Double-stranded RNA (dsRNA) viruses transcribe and replicate RNA within an assembled, inner capsid particle; only plus-sense mRNA emerges into the intracellular milieu. During infectious entry of a rotavirus particle, the outer layer of its three-layer structure dissociates, delivering the inner double-layered particle (DLP) into the cytosol. DLP structures determined by X-ray crystallography and electron cryomicroscopy (cryoEM) show that the RNA coils uniformly into the particle interior, avoiding a "fivefold hub" of more structured density projecting inward from the VP2 shell of the DLP along each of the twelve 5-fold axes. Analysis of the X-ray crystallographic electron density map suggested that principal contributors to the hub are the N-terminal arms of VP2, but reexamination of the cryoEM map has shown that many features come from a molecule of VP1, randomly occupying five equivalent and partly overlapping positions. We confirm here that the electron density in the X-ray map leads to the same conclusion, and we describe the functional implications of the orientation and position of the polymerase. The exit channel for the nascent transcript directs the nascent transcript toward an opening along the 5-fold axis. The template strand enters from within the particle, and the dsRNA product of the initial replication step exits in a direction tangential to the inner surface of the VP2 shell, allowing it to coil optimally within the DLP. The polymerases of reoviruses appear to have similar positions and functional orientations.
History
DepositionMay 13, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 24, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 7, 2012Group: Database references
Revision 1.2Jan 16, 2013Group: Database references
Revision 1.3Sep 13, 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_sheet / 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_label_asym_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_label_asym_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_sheet.number_strands / _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

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Assembly

Deposited unit
A: VP2 protein
B: VP2 protein
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
W: RNA-directed RNA polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)915,00721
Polymers914,68016
Non-polymers3275
Water0
1
A: VP2 protein
B: VP2 protein
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
W: RNA-directed RNA polymerase
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)54,900,4271260
Polymers54,880,804960
Non-polymers19,623300
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: VP2 protein
B: VP2 protein
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
W: RNA-directed RNA polymerase
hetero molecules
x 5


  • icosahedral pentamer
  • 4.58 MDa, 80 polymers
Theoretical massNumber of molelcules
Total (without water)4,575,036105
Polymers4,573,40080
Non-polymers1,63525
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: VP2 protein
B: VP2 protein
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
W: RNA-directed RNA polymerase
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 5.49 MDa, 96 polymers
Theoretical massNumber of molelcules
Total (without water)5,490,043126
Polymers5,488,08096
Non-polymers1,96230
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
6
A: VP2 protein
B: VP2 protein
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
W: RNA-directed RNA polymerase
hetero molecules
x 60


  • crystal asymmetric unit, crystal frame
  • 54.9 MDa, 960 polymers
Theoretical massNumber of molelcules
Total (without water)54,900,4271260
Polymers54,880,804960
Non-polymers19,623300
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation59
Unit cell
Length a, b, c (Å)740.750, 1198.070, 1345.410
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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(0.49847401, -0.78340814, 0.37120795), (0.83204271, 0.31213818, -0.45855718), (0.24336926, 0.53743971, 0.8074218)69.78711, -140.57816, -31.90219
3generate(-0.3130121, -0.4355383, 0.84399633), (0.56286524, -0.80084563, -0.20452139), (0.76498769, 0.41103852, 0.49582374)202.8619, -111.76313, -116.22896
4generate(-0.3130121, 0.56286523, 0.76498767), (-0.4355383, -0.80084563, 0.41103853), (0.84399635, -0.20452141, 0.49582374)215.31953, 46.62369, -136.44358
5generate(0.498474, 0.8320427, 0.24336925), (-0.78340815, 0.31213818, 0.5374397), (0.37120795, -0.45855719, 0.80742181)89.94398, 115.6971, -64.61013
6generate(-0.82789077, 0.3270885, 0.45564238), (0.3270885, -0.37837797, 0.86593488), (0.45564239, 0.86593488, 0.20626875)415.37259, -249.24589, 22.02606
7generate(-0.02964108, 0.99555349, -0.08941282), (0.05896042, 0.09103778, 0.99410049), (0.99782017, 0.02419439, -0.0613967)297.079, -200.85286, -74.48793
8generate(0.79180738, 0.28591732, -0.53971506), (0.34707106, 0.51649537, 0.78279896), (0.50257612, -0.80714548, 0.30973124)157.90983, -241.25009, -6.29546
9generate(0.50124076, -0.82112694, -0.27296195), (0.79326132, 0.31002687, 0.52404182), (-0.34567932, -0.47920128, 0.80676635)190.19214, -314.60997, 132.36379
10generate(-0.49978775, -0.79568176, 0.34220278), (0.78091142, -0.24303527, 0.57542265), (-0.37468596, 0.55481925, 0.74282302)349.31288, -319.55164, 149.86745
11generate(-0.45639767, -0.80727454, 0.37417775), (-0.80727455, 0.19883993, -0.55567122), (0.37417775, -0.55567121, -0.74244226)331.41931, 327.97479, 226.11014
12generate(-0.80812591, 0.30666242, 0.50288236), (-0.37219536, 0.39585121, -0.83950726), (-0.45651193, -0.86559805, -0.20575929)401.11671, 261.41201, 354.02369
13generate(-0.02528742, 0.99908241, -0.03456683), (-0.06047486, -0.03604338, -0.99751875), (-0.99784937, -0.02313425, 0.0613308)285.56686, 206.57165, 450.41339
14generate(0.81026162, 0.31308455, -0.49543332), (-0.30290018, -0.4999802, -0.81133918), (-0.50172463, 0.80746384, -0.31028141)144.45571, 239.24123, 382.07196
15generate(0.54382083, -0.80330545, -0.24281527), (-0.76444777, -0.35481433, -0.53826239), (0.34623476, 0.4783379, -0.80704049)172.79409, 314.27249, 243.44492
16generate(0.28428844, 0.48018604, -0.82982012), (0.48018604, -0.82046196, -0.31026367), (-0.82982014, -0.31026367, -0.46382648)351.29575, -69.14421, 503.67901
17generate(0.33929298, -0.51880776, -0.78467748), (-0.51880777, -0.79902717, 0.30396394), (-0.78467751, 0.30396395, -0.54026581)330.10482, 89.6037, 504.18164
18generate(-0.45350787, -0.84946143, -0.26971443), (-0.84946144, 0.32039364, 0.41924119), (-0.26971445, 0.4192412, -0.86688577)451.74907, 156.02626, 423.92623
19generate(-0.99849028, -0.05482283, 0.0034076), (-0.05482284, 0.99079896, -0.12374117), (0.0034076, -0.12374115, -0.99230868)548.12027, 38.32974, 373.82304
20generate(-0.54250709, 0.7669445, -0.34275676), (0.7669445, 0.28571143, -0.57459996), (-0.34275676, -0.57459996, -0.74320434)486.0367, -100.83326, 423.11296
21generate(-0.49991079, -0.83007134, -0.24712498), (0.8231746, -0.36670028, -0.43349104), (0.26920771, -0.42013387, 0.86661107)460.19545, -141.22833, -47.82575
22generate(-0.99998997, -0.00027755, -0.00446979), (-0.00027755, -0.99231814, 0.12371188), (-0.00446978, 0.12371187, 0.99230811)549.88185, -18.40199, 2.37634
23generate(-0.49978775, 0.78091141, -0.37468596), (-0.79568176, -0.24303527, 0.55481925), (0.34220278, 0.57542264, 0.74282302)480.27705, 117.13022, -46.98358
24generate(0.3094334, 0.43391895, -0.84614733), (-0.46381645, 0.84566488, 0.26405532), (0.8301357, 0.31074951, 0.46293571)347.57253, 78.06739, -127.69177
25generate(0.30935736, -0.56172314, -0.76731031), (0.5366918, 0.7692357, -0.34675402), (0.78502226, -0.30453825, 0.53944094)335.16142, -81.60697, -128.21226
26generate(0.02976412, -0.0634285, -0.99754243), (-0.998959, 0.03262723, -0.03188099), (0.03456921, 0.9974529, -0.06239135)453.99489, 282.54628, 187.80042
27generate(-0.28070975, -0.57923482, -0.76530323), (-0.4785667, 0.77564271, -0.41152438), (0.83197113, 0.25072975, -0.49493296)496.81249, 209.26221, 51.98324
28generate(-0.80812591, -0.37219534, -0.45651192), (0.30666242, 0.39585121, -0.86559804), (0.50288237, -0.83950726, -0.20575929)583.06518, 79.95453, 90.58642
29generate(-0.82361316, 0.27156841, -0.49790759), (0.2715684, -0.58188832, -0.76658762), (-0.49790759, -0.76658763, 0.40550148)593.55467, 73.32206, 250.26168
30generate(-0.30576864, 0.46239681, -0.83228284), (-0.53535001, -0.80637308, -0.25132214), (-0.78734105, 0.36871619, 0.49410773)513.78485, 198.53064, 310.34324
31generate(0.80578491, 0.37583417, 0.45766729), (-0.24186987, -0.49656406, 0.83362048), (0.54056419, -0.78241474, -0.30922086)-33.60457, -86.69754, 99.55112
32generate(0.82575507, -0.2679777, 0.49630286), (-0.33085075, 0.48250697, 0.81100234), (-0.45680014, -0.83389147, 0.30977196)-44.80584, -60.36519, 257.13078
33generate(0.30943341, -0.46381645, 0.83013569), (0.43391895, 0.84566488, 0.31074951), (-0.84614734, 0.26405533, 0.4629357)34.65989, -177.157, 332.59654
34generate(-0.02964108, 0.0589604, 0.99782015), (0.9955535, 0.09103778, 0.0241944), (-0.08941282, 0.9941005, -0.06139671)94.97367, -275.67065, 221.65729
35generate(0.27712102, 0.57789302, 0.76762203), (0.57789304, -0.73850532, 0.34734643), (0.76762204, 0.34734642, -0.53861571)52.78391, -219.76363, 77.6273
36generate(-0.33563824, 0.51766568, 0.78700013), (0.41765426, 0.8306371, -0.36824845), (-0.8443411, 0.2050957, -0.49499886)217.50188, -45.03573, 512.28941
37generate(0.45494466, 0.84749007, 0.27347017), (0.80969499, -0.26583154, -0.52318985), (-0.37070121, 0.45944985, -0.80714711)96.19915, -120.91035, 440.32486
38generate(0.99848025, 0.05510038, 0.00106219), (0.05510039, -0.99848082, 2.929E-5), (0.00106218, 2.929E-5, -0.99999944)0.08553, -10.34306, 375.61584
39generate(0.54382083, -0.76444776, 0.34623477), (-0.80330545, -0.35481434, 0.47833789), (-0.24281529, -0.53826238, -0.80704048)61.98678, 133.86589, 407.58802
40generate(-0.28070974, -0.47856669, 0.83197112), (-0.57923483, 0.77564271, 0.25072974), (-0.76530325, -0.41152437, -0.49493297)196.35748, 112.42465, 492.05693
41generate(-0.49991079, 0.82317459, 0.26920769), (-0.83007135, -0.36670028, -0.42013386), (-0.24712499, -0.43349106, 0.86661107)359.1873, 310.11338, 93.9509
42generate(0.50124076, 0.79326131, -0.34567932), (-0.82112696, 0.31002688, -0.47920128), (-0.27296196, 0.52404182, 0.80676635)199.99129, 317.13834, 109.99735
43generate(0.82575506, -0.33085074, -0.45680013), (-0.2679777, 0.48250698, -0.83389146), (0.49630286, 0.81100235, 0.30977195)134.48415, 231.53882, -8.45833
44generate(0.02516437, -0.99567691, 0.08941044), (0.06494295, -0.08762162, -0.99403464), (0.99757164, 0.03082084, 0.06245725)253.19452, 171.61046, -97.7144
45generate(-0.79414218, -0.28245003, 0.53810795), (-0.28245004, -0.61246057, -0.73831837), (0.53810797, -0.73831838, 0.40660275)392.06871, 220.1722, -34.42202
46generate(0.80578491, -0.24186987, 0.54056418), (0.37583417, -0.49656405, -0.78241473), (0.45766729, 0.83362048, -0.30922087)-47.70524, 47.46913, 118.43584
47generate(0.33197348, -0.41623463, 0.84648824), (-0.41623463, -0.86992889, -0.26452307), (0.84648825, -0.26452308, -0.46204459)25.28461, 168.46431, 43.05111
48generate(0.02516438, 0.06494294, 0.99757163), (-0.99567692, -0.08762163, 0.03082084), (0.08941044, -0.99403464, 0.06245725)79.96074, 270.14837, 154.05148
49generate(0.30935736, 0.5366918, 0.78502224), (-0.56172316, 0.7692357, -0.30453825), (-0.76731033, -0.34675403, 0.53944093)40.76262, 211.99739, 298.03821
50generate(0.79180739, 0.34707105, 0.50257611), (0.28591731, 0.51649538, -0.80714547), (-0.53971507, 0.78279896, 0.30973122)-38.1393, 74.37405, 276.02654
51generate(-0.33563825, 0.41765427, -0.84434109), (0.51766569, 0.8306371, 0.2050957), (0.78700014, -0.36824845, -0.49499885)524.35831, -180.25327, 65.82432
52generate(-0.02528742, -0.06047485, -0.99784935), (0.99908242, -0.03604339, -0.02313425), (-0.03456683, -0.99751876, 0.06133081)469.15835, -267.43931, 188.30602
53generate(-0.30576864, -0.53535, -0.78734103), (0.46239681, -0.80637309, 0.3687162), (-0.83228284, -0.25132214, 0.49410774)507.72863, -191.91129, 324.16646
54generate(-0.78946639, -0.35070987, -0.50373148), (-0.35070987, -0.41578253, 0.83912303), (-0.50373149, 0.83912304, 0.20524892)586.76634, -58.04636, 285.65114
55generate(-0.80792682, 0.23827916, -0.53895945), (-0.31655183, 0.5959454, 0.738), (0.49704044, 0.76685861, -0.40605257)597.04405, -50.84131, 125.98691
56generate(0.02976413, -0.99895899, 0.03456921), (-0.0634285, 0.03262723, 0.9974529), (-0.99754245, -0.03188098, -0.06239135)262.24727, -167.74456, 473.60415
57generate(-0.80792682, -0.31655183, 0.49704043), (0.23827916, 0.5959454, 0.7668586), (-0.53895946, 0.73800002, -0.40605257)403.6534, -208.57866, 410.46073
58generate(-0.5451508, 0.8012578, 0.24656953), (0.80125781, 0.41148774, 0.43435443), (0.24656954, 0.43435444, -0.86633694)375.91412, -300.19122, 282.05559
59generate(0.45494465, 0.80969499, -0.37070121), (0.84749008, -0.26583154, 0.45944985), (0.27347017, -0.52318985, -0.8071471)217.36417, -315.97679, 265.84027
60generate(0.81026162, -0.30290017, -0.50172461), (0.31308455, -0.49998022, 0.80746384), (-0.49543333, -0.81133919, -0.3102814)147.11419, -234.12026, 384.22378

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Components

#1: Protein VP2 protein


Mass: 102595.039 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bovine rotavirus A / References: UniProt: H9N1A6
#2: Protein
Intermediate capsid protein VP6


Mass: 44922.645 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Source: (natural) Bovine rotavirus / Strain: RV-A / References: UniProt: A7J3A1
#3: Protein RNA-directed RNA polymerase / RNA-dependent RNA polymerase / Protein VP1


Mass: 125495.602 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: 10922 / Source: (natural) Simian 11 rotavirus / Strain: SA11 / References: UniProt: O37061, RNA-directed RNA polymerase
#4: 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: 150

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 10, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.8→223 Å / Num. obs: 1823596 / % possible obs: 20.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
CNSrefinement
HKL-2000data reduction
SCALAdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3KZ4 AND 2R7S

3kz4

2r7s


Resolution: 5→30 Å / σ(F): 1
RfactorNum. reflection
Rfree0.2958 -
Rwork0.2931 -
obs-908231
Refinement stepCycle: LAST / Resolution: 5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms62009 0 5 0 62014

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