PDB-3s6p: Crystal Structure of Helicoverpa Armigera Stunt Virus

ID or keywords:

Entry

Database: PDB / ID: 3s6p

Title

Crystal Structure of Helicoverpa Armigera Stunt Virus

Components

(Capsid protein) x 2

Keywords

VIRUS / capsid / coat protein / beta barrel / Ig-like domain / icosahedral virus

Function / homology

Function and homology information

T=4 icosahedral viral capsid
Similarity search - Function

Biological species

Helicoverpa armigera stunt virus

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.5 Å

Authors

Speir, J.A. / Chen, Z. / Taylor, D.J. / Johnson, J.E.

Citation

Journal: To be Published
Title: Crystal Structure of Helicoverpa armigera stunt virus
Authors: Speir, J.A. / Natarajan, P. / Taylor, D.J. / Chen, Z. / Johnson, J.E.

History

Deposition	May 25, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 30, 2012	Provider: repository / Type: Initial release
Revision 1.1	Sep 13, 2023	Group: 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_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_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type / _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.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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3s6p.cif.gz	481.9 KB	Display	PDBx/mmCIF format
PDB format	pdb3s6p.ent.gz	394.7 KB	Display	PDB format
PDBx/mmJSON format	3s6p.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3s6p_validation.pdf.gz	494.9 KB	Display	wwPDB validaton report
Full document	3s6p_full_validation.pdf.gz	561.6 KB	Display
Data in XML	3s6p_validation.xml.gz	102.6 KB	Display
Data in CIF	3s6p_validation.cif.gz	145 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/s6/3s6p ftp://data.pdbj.org/pub/pdb/validation_reports/s6/3s6p	HTTPS FTP

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Related structure data

Related structure data	1ohfS S: Starting model for refinement
Similar structure data	1ohf-1 2qqp-1 9739 9296 1933 1935 2e0z-1 5131 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#200 - Aug 2016 Quasisymmetry in Icosahedral Viruses similarity (3)

Deposited unit

A: Capsid protein

E: Capsid protein

B: Capsid protein

F: Capsid protein

C: Capsid protein

G: Capsid protein

D: Capsid protein

H: Capsid protein

hetero molecules

283 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Capsid protein

E: Capsid protein

B: Capsid protein

F: Capsid protein

C: Capsid protein

G: Capsid protein

D: Capsid protein

H: Capsid protein

hetero molecules

x 60

complete icosahedral assembly
480-MERIC
17 MDa, 480 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

Idetical with deposited unit
icosahedral asymmetric unit

3

A: Capsid protein

E: Capsid protein

B: Capsid protein

F: Capsid protein

C: Capsid protein

G: Capsid protein

D: Capsid protein

H: Capsid protein

hetero molecules

x 5

icosahedral pentamer
1.42 MDa, 40 polymers

4

A: Capsid protein

E: Capsid protein

B: Capsid protein

F: Capsid protein

C: Capsid protein

G: Capsid protein

D: Capsid protein

H: Capsid protein

hetero molecules

x 6

icosahedral 23 hexamer
1.7 MDa, 48 polymers

5

Idetical with deposited unit in distinct coordinate
icosahedral asymmetric unit, std point frame

6

A: Capsid protein

E: Capsid protein

B: Capsid protein

F: Capsid protein

C: Capsid protein

G: Capsid protein

D: Capsid protein

H: Capsid protein

hetero molecules

x 60

crystal asymmetric unit, crystal frame
17 MDa, 480 polymers

Unit cell

Length a, b, c (Å)	404.120, 405.570, 406.040
Angle α, β, γ (deg.)	119.20, 114.44, 94.79
Int Tables number	1
Space group name H-M	P1

Symmetry

Point symmetry: (Schoenflies symbol: I (icosahedral))

Noncrystallographic symmetry (NCS)

NCS oper:

ID	Code	Matrix
1	given	(1), (1), (1)
2	generate	(0.752261, 0.176658, 0.634744), (0.464573, 0.540928, -0.701124), (-0.467209, 0.822312, 0.324851)
3	generate	(0.351403, 0.750407, 0.559834), (0.928346, -0.20187, -0.312131), (-0.121217, 0.629401, -0.767573)
4	generate	(0.351402, 0.928348, -0.121216), (0.750407, -0.20187, 0.6294), (0.559834, -0.312132, -0.767573)
5	generate	(0.75226, 0.464573, -0.467208), (0.176658, 0.540928, 0.822311), (0.634745, -0.701125, 0.324851)
6	generate	(0.880399, 0.128626, 0.456458), (0.128626, -0.991201, 0.031223), (0.456457, 0.031223, -0.889197)
7	generate	(0.974746, 0.158553, -0.157278), (-0.058524, -0.498304, -0.865028), (-0.215522, 0.852386, -0.476442)
8	generate	(0.806769, -0.036691, 0.589732), (-0.510468, 0.459383, 0.726908), (-0.297582, -0.887484, 0.351889)
9	generate	(0.974746, -0.058524, -0.215522), (0.158554, -0.498304, 0.852385), (-0.157278, -0.86503, -0.476442)
10	generate	(0.586122, 0.572289, -0.573545), (0.572289, -0.793516, -0.206943), (-0.573546, -0.206944, -0.792606)
11	generate	(0.327834, -0.509771, 0.795404), (0.307314, 0.853684, 0.420463), (-0.893358, 0.106602, 0.436522)
12	generate	(0.661437, -0.681125, -0.313972), (0.648875, 0.309758, 0.694994), (-0.376126, -0.663421, 0.646845)
13	generate	(0.373454, -0.878765, 0.297172), (0.921985, 0.316268, -0.223434), (0.102364, 0.357429, 0.928318)
14	generate	(0.314326, -0.510202, -0.800561), (0.607615, 0.75606, -0.243277), (0.729391, -0.409968, 0.547654)
15	generate	(-0.154315, 0.521148, 0.839403), (0.521147, -0.678848, 0.517278), (0.839403, 0.517279, -0.166837)
16	generate	(0.508785, -0.378313, 0.773321), (0.600457, -0.487771, -0.63367), (0.616926, 0.786744, -0.021014)
17	generate	(0.806768, -0.510469, -0.297582), (-0.036691, 0.459383, -0.887483), (0.589732, 0.726909, 0.351889)
18	generate	(0.508785, 0.600458, 0.616926), (-0.378312, -0.48777, 0.786743), (0.773321, -0.633672, -0.021014)
19	generate	(0.327833, 0.307315, -0.893358), (-0.509771, 0.853684, 0.106601), (0.795404, 0.420463, 0.436523)
20	generate	(-0.079627, -0.290337, 0.953609), (-0.290336, -0.908414, -0.300823), (0.953609, -0.300824, -0.011958)
21	generate	(0.494105, -0.862643, 0.108232), (-0.569831, -0.415357, -0.709067), (0.656628, 0.288679, -0.696788)
22	generate	(0.373454, 0.921987, 0.102364), (-0.878764, 0.316268, 0.357428), (0.297172, -0.223435, 0.928318)
23	generate	(0.661437, 0.648875, -0.376126), (-0.681125, 0.309758, -0.66342), (-0.313972, 0.694995, 0.646845)
24	generate	(0.494105, -0.569832, 0.656628), (-0.862641, -0.415357, 0.288678), (0.108231, -0.709068, -0.696788)
25	generate	(0.687824, -0.539065, -0.486123), (-0.539064, -0.827834, 0.155263), (-0.486124, 0.155263, -0.85999)
26	generate	(0.314327, 0.607616, 0.729391), (-0.510202, 0.75606, -0.409967), (-0.800561, -0.243277, 0.547654)
27	generate	(0.177956, 0.983984, 0.010443), (0.158975, -0.018275, -0.987112), (-0.971112, 0.177323, -0.159682)
28	generate	(0.177956, 0.158976, -0.971112), (0.983982, -0.018275, 0.177323), (0.010443, -0.987114, -0.159681)
29	generate	(-0.26615, -0.165009, 0.949703), (0.944887, 0.150216, 0.290901), (-0.190662, 0.974787, 0.115934)
30	generate	(-0.266151, 0.944888, -0.190662), (-0.165008, 0.150217, 0.974785), (0.949703, 0.290901, 0.115934)
31	generate	(0.288005, -0.312965, -0.905045), (-0.952109, 0.007741, -0.305659), (0.102666, 0.949734, -0.295746)
32	generate	(-0.199811, 0.318997, 0.926454), (-0.97676, -0.139683, -0.162565), (0.077553, -0.937407, 0.339494)
33	generate	(-0.289897, -0.948674, -0.12643), (-0.948672, 0.267392, 0.168902), (-0.12643, 0.168903, -0.977494)
34	generate	(-0.413105, 0.599058, -0.685918), (-0.908882, -0.223832, 0.351905), (0.057286, 0.768789, 0.636937)
35	generate	(-0.64032, 0.61304, 0.462797), (-0.499883, -0.790045, 0.354899), (0.583195, -0.004101, 0.812325)
36	generate	(-0.759766, -0.012522, -0.65008), (-0.517514, 0.616931, 0.592942), (0.393629, 0.786922, -0.475206)
37	generate	(-0.599735, -0.66834, 0.440056), (-0.668339, 0.115944, -0.734768), (0.440056, -0.734769, -0.516209)
38	generate	(-0.273636, -0.675558, -0.684655), (-0.37972, 0.729877, -0.568418), (0.883708, 0.104442, -0.456241)
39	generate	(-0.361831, 0.431333, -0.826462), (0.436227, 0.861819, 0.258805), (0.823887, -0.266886, -0.499988)
40	generate	(-0.199811, -0.976761, 0.077552), (0.318997, -0.139683, -0.937405), (0.926454, -0.162565, 0.339494)
41	generate	(-0.454454, 0.849539, -0.267882), (0.849538, 0.322921, -0.417149), (-0.267882, -0.41715, -0.868467)
42	generate	(-0.434959, -0.723721, -0.535768), (0.899089, -0.38179, -0.214199), (-0.049525, -0.574868, 0.816749)
43	generate	(-0.795127, -0.217913, -0.565944), (0.472941, 0.361349, -0.803591), (0.379615, -0.906614, -0.184262)
44	generate	(-0.640319, -0.499883, 0.583195), (0.613039, -0.790045, -0.0041), (0.462798, 0.3549, 0.812325)
45	generate	(-0.720583, 0.644677, 0.255266), (0.644676, 0.487389, 0.588941), (0.255266, 0.588941, -0.766807)
46	generate	(-0.759765, -0.517515, 0.393629), (-0.012522, 0.616931, 0.78692), (-0.65008, 0.592944, -0.475206)
47	generate	(-0.795127, 0.472942, 0.379614), (-0.217913, 0.361349, -0.906613), (-0.565944, -0.803592, -0.184262)
48	generate	(-0.884535, -0.038158, -0.464911), (-0.038158, -0.98739, 0.153641), (-0.46491, 0.153641, 0.871925)
49	generate	(-0.967241, -0.105612, 0.230857), (-0.105612, -0.659556, -0.744203), (0.230858, -0.744204, 0.626797)
50	generate	(-0.986388, 0.096051, 0.133489), (0.096051, -0.322428, 0.941711), (0.13349, 0.941713, 0.308816)
51	generate	(-0.995863, -0.090468, 0.008453), (-0.090468, 0.978591, -0.184864), (0.008453, -0.184865, -0.982728)
52	generate	(-0.434959, 0.899091, -0.049526), (-0.72372, -0.381789, -0.574867), (-0.535768, -0.214199, 0.816749)
53	generate	(-0.465918, -0.559202, -0.685727), (-0.559201, -0.414507, 0.717972), (-0.685727, 0.717974, -0.119575)
54	generate	(-0.273636, -0.37972, 0.883708), (-0.675557, 0.729877, 0.104442), (-0.684656, -0.568419, -0.456241)
55	generate	(0.288006, -0.95211, 0.102667), (-0.312964, 0.007741, 0.949733), (-0.905045, -0.305659, -0.295747)
56	generate	(0.113625, 0.368775, -0.92255), (-0.453205, -0.807088, -0.378444), (-0.884138, 0.461108, 0.075424)
57	generate	(-0.555788, 0.427526, -0.712973), (0.427525, -0.588543, -0.68618), (-0.712973, -0.686181, 0.144331)
58	generate	(-0.413105, -0.908883, 0.057286), (0.599057, -0.223832, 0.768788), (-0.685917, 0.351906, 0.636936)
59	generate	(-0.36183, 0.436227, 0.823887), (0.431332, 0.861819, -0.266885), (-0.826462, 0.258805, -0.499988)
60	generate	(0.113625, -0.453206, -0.884138), (0.368775, -0.807089, 0.461107), (-0.92255, -0.378444, 0.075424)

#1: Protein	Capsid protein / CP / Coat protein / 64 kDa capsid protein / 7 kDa capsid protein Mass: 63434.230 Da / Num. of mol.: 4 / Fragment: UNP Residues 1-575 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Helicoverpa armigera stunt virus / Gene: capsid protein / Plasmid: pVL941 / Cell line (production host): SF21 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q82462
#2: Protein	Capsid protein / CP / Coat protein / 64 kDa capsid protein / 7 kDa capsid protein Mass: 7321.584 Da / Num. of mol.: 4 / Fragment: UNP Residues 576-647 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Helicoverpa armigera stunt virus / Gene: capsid protein / Plasmid: pVL941 / Cell line (production host): SF21 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q82462
#3: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1309 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 62

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Sample preparation

Crystal	Density Matthews: 2.54 Å³/Da / Density % sol: 52 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 2 ul of 8mg/ml virus solution (50mM NaAce pH 5.0) added to 2 ul of 100mM bicine pH 8.0, 1.0% PEG8000, 150mM CaAce, 350-400mM NaCl. Trapezoid crystals appear in 2 days and grow for 3 weeks, ...Details: 2 ul of 8mg/ml virus solution (50mM NaAce pH 5.0) added to 2 ul of 100mM bicine pH 8.0, 1.0% PEG8000, 150mM CaAce, 350-400mM NaCl. Trapezoid crystals appear in 2 days and grow for 3 weeks, VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal

Density Matthews: 2.54 Å³/Da / Density % sol: 52 %

Crystal grow

Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 2 ul of 8mg/ml virus solution (50mM NaAce pH 5.0) added to 2 ul of 100mM bicine pH 8.0, 1.0% PEG8000, 150mM CaAce, 350-400mM NaCl. Trapezoid crystals appear in 2 days and grow for 3 weeks, ...

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Data collection

Diffraction

ID	Mean temperature (K)	Crystal-ID
1	298	1
2	298	1

Diffraction source

Source	Site	Beamline	ID	Wavelength (Å)
SYNCHROTRON	SSRL	BL11-1	1	0.979
SYNCHROTRON	APS	14-BM-C	2	0.9

Detector

Type	ID	Detector
ADSC QUANTUM 315	1	CCD
ADSC QUANTUM 4	2	CCD

Radiation

ID	Protocol	Monochromatic (M) / Laue (L)	Scattering type	Wavelength-ID
1	SINGLE WAVELENGTH	M	x-ray	1
2	SINGLE WAVELENGTH	M	x-ray	1

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.979	1
2	0.9	1

Reflection

Resolution: 2.5→40 Å / Num. all: 1807513 / Num. obs: 1807513 / % possible obs: 27.3 % / Observed criterion σ(I): -0.5 / Redundancy: 1.2 % / B_iso Wilson estimate: 35.9 Å² / R_merge(I) obs: 0.148 / Χ²: 2.378 / Net I/σ(I): 6.5

Reflection shell

Diffraction-ID: 1,2

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique all	Χ²	% possible all
2.5-2.59	1.1	0.332	2.1	80387	1.471	12.1
2.59-2.69	1.1	0.288		88124	1.548	13.3
2.69-2.82	1.1	0.276		101039	1.752	15.3
2.82-2.96	1.1	0.285		127688	1.85	19.3
2.96-3.15	1.2	0.27		170605	2.029	25.8
3.15-3.39	1.2	0.224		191506	2.131	28.9
3.39-3.73	1.2	0.192		217873	2.333	32.9
3.73-4.27	1.2	0.168		249978	2.495	37.8
4.27-5.38	1.2	0.134		278295	2.572	42.1
5.38-40	1.2	0.092		302018	2.731	45.7

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Processing

Software

Name	Version	Classification
SCALEPACK		data scaling
CNS		refinement
PDB_EXTRACT	3.1	data extraction
DENZO		data reduction
GLRF		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OHF

1ohf

Resolution: 2.5→40 Å / Occupancy max: 1 / Occupancy min: 0 / Cross valid method: NOT USED / σ(F): 0 / Stereochemistry target values: Engh & Huber

	R_factor	Num. reflection	% reflection
R_work	0.237	-	-
all	0.24	1807472	-
obs	0.24	1807472	27.3 %

Solvent computation

Solvent model: CNS / B_sol: 77.2284 Å² / k_sol: 0.35 e/Å³

Displacement parameters

B_iso max: 140.48 Å² / B_iso mean: 40.5781 Å² / B_iso min: 13.92 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.921 Å²	-0.487 Å²	3.506 Å²
2-	-	-2.112 Å²	-1.564 Å²
3-	-	-	0.191 Å²

Refinement step

Cycle: LAST / Resolution: 2.5→40 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	17902	0	4	1309	19215

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target
X-RAY DIFFRACTION	c_bond_d	0.011
X-RAY DIFFRACTION	c_angle_deg	1.619
X-RAY DIFFRACTION	c_mcbond_it	1.394	1.5
X-RAY DIFFRACTION	c_scbond_it	1.901	2
X-RAY DIFFRACTION	c_mcangle_it	2.491	2
X-RAY DIFFRACTION	c_scangle_it	3.038	2.5

Refine LS restraints NCS

NCS model details: 60-FOLD ICOSAHEDRAL CONSTRAINTS

LS refinement shell

Resolution: 2.5→2.61 Å /

	R_factor	Num. reflection
R_work	0.3356	-
obs	-	101707

Xplor file

Refine-ID	Serial no	Param file	Topol file
X-RAY DIFFRACTION	1	CNS_TOPPAR:protein_rep.param	CNS_TOPPAR:protein.top
X-RAY DIFFRACTION	2	CNS_TOPPAR:dna-rna_rep.param	CNS_TOPPAR:dna-rna.top
X-RAY DIFFRACTION	3	CNS_TOPPAR:water_rep.param	CNS_TOPPAR:water.top
X-RAY DIFFRACTION	4	CNS_TOPPAR:ion.param	CNS_TOPPAR:ion.top

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About Yorodumi

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Yorodumi