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- PDB-4fsj: Crystal structure of the virus like particle of Flock House virus -

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Basic information

Entry
Database: PDB / ID: 4fsj
TitleCrystal structure of the virus like particle of Flock House virus
Components
  • (Capsid protein ...Capsid) x 2
  • Random cellular RNA fragments
KeywordsVIRUS / FLOCK HOUSE VIRUS / Nodavirus / RNA / BETA-BARREL / JELLYROLL / ASPARTYL PROTEASE / CAPSID PROTEIN / HYDROLASE / autoproteolysis / VIRION / ICOSAHEDRAL VIRUS
Function / homology
Function and homology information


nodavirus endopeptidase / permeabilization of host organelle membrane involved in viral entry into host cell / symbiont entry into host cell via permeabilization of inner membrane / T=3 icosahedral viral capsid / aspartic-type endopeptidase activity / proteolysis / metal ion binding
Similarity search - Function
Peptidase A6, nodavirus coat protein / Peptidase A6 family / Jelly Rolls - #20 / Viral coat protein subunit / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
RNA / RNA (> 10) / Capsid protein alpha
Similarity search - Component
Biological speciesFlock house virus
Spodoptera frugiperda (fall armyworm)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.5 Å
AuthorsSpeir, J.A. / Chen, Z. / Reddy, V.S. / Johnson, J.E.
CitationJournal: to be published / Year: 2012
Title: Structural study of virus assembly intermediates reveals maturation event sequence and a staging position for externalized lytic peptides
Authors: Speir, J.A. / Chen, Z. / Reddy, V.S. / Johnson, J.E.
History
DepositionJun 27, 2012Deposition site: RCSB / Processing site: RCSB
SupersessionAug 1, 2012ID: 2Q26
Revision 1.0Aug 1, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2024Group: 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.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.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 beta
D: Capsid protein Gamma
B: Capsid protein beta
E: Capsid protein Gamma
C: Capsid protein beta
F: Capsid protein Gamma
R: Random cellular RNA fragments
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,47115
Polymers135,5617
Non-polymers9118
Water2,486138
1
A: Capsid protein beta
D: Capsid protein Gamma
B: Capsid protein beta
E: Capsid protein Gamma
C: Capsid protein beta
F: Capsid protein Gamma
R: Random cellular RNA fragments
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)8,188,282900
Polymers8,133,641420
Non-polymers54,641480
Water6,485360
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: Capsid protein beta
D: Capsid protein Gamma
B: Capsid protein beta
E: Capsid protein Gamma
C: Capsid protein beta
F: Capsid protein Gamma
R: Random cellular RNA fragments
hetero molecules
x 5


  • icosahedral pentamer
  • 682 kDa, 35 polymers
Theoretical massNumber of molelcules
Total (without water)682,35775
Polymers677,80335
Non-polymers4,55340
Water54030
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Capsid protein beta
D: Capsid protein Gamma
B: Capsid protein beta
E: Capsid protein Gamma
C: Capsid protein beta
F: Capsid protein Gamma
R: Random cellular RNA fragments
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 819 kDa, 42 polymers
Theoretical massNumber of molelcules
Total (without water)818,82890
Polymers813,36442
Non-polymers5,46448
Water64936
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: Capsid protein beta
D: Capsid protein Gamma
B: Capsid protein beta
E: Capsid protein Gamma
C: Capsid protein beta
F: Capsid protein Gamma
R: Random cellular RNA fragments
hetero molecules
x 20


  • crystal asymmetric unit, crystal frame
  • 2.73 MDa, 140 polymers
Theoretical massNumber of molelcules
Total (without water)2,729,427300
Polymers2,711,214140
Non-polymers18,214160
Water2,162120
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation19
Unit cell
Length a, b, c (Å)326.480, 326.480, 772.400
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS domain: (Details: chain AAAA,CCCC, using strict)
NCS oper:
IDCodeMatrix
1given(1), (1), (1)
2generate(0.34597919, -0.6660728, 0.66079152), (0.84546753, 0.52668859, 0.08822568), (-0.40679609, 0.52815354, 0.74536621)
3generate(-0.71224873, -0.23226089, 0.66238706), (0.70192241, -0.23914534, 0.67090568), (0.00258163, 0.94279605, 0.33336009)
4generate(-0.71224874, 0.70192241, 0.00258163), (-0.23226089, -0.23914534, 0.94279604), (0.66238706, 0.67090568, 0.33336009)
5generate(0.34597917, 0.84546754, -0.40679608), (-0.66607279, 0.5266886, 0.52815353), (0.66079153, 0.08822568, 0.74536621)
6generate(-0.96499285, -0.26227618, 2.0E-8), (-0.26227619, 0.96499285, -1.8E-7), (2.0E-8, -1.8E-7, -1)
7generate(-0.55561345, 0.50461763, -0.66079857), (0.72512809, 0.68294567, -0.08817287), (0.40679595, -0.52815365, -0.74536621)
8generate(0.5032174, 0.28685225, -0.81516135), (0.86415599, -0.16985721, 0.47369077), (-0.00258177, -0.94279602, -0.33336019)
9generate(0.74823146, -0.61462797, -0.2497642), (-0.03732432, -0.4148712, 0.90911428), (-0.66238704, -0.67090562, -0.33336026)
10generate(-0.15917238, -0.954008, 0.25403324), (-0.7334977, 0.28650471, 0.61635717), (-0.6607914, -0.08822575, -0.74536632)
11generate(0.15818002, 0.37790635, 0.91223126), (0.95529631, 0.1751304, -0.23819801), (-0.24977598, 0.90912933, -0.33331042)
12generate(0.00314244, 0.57547772, 0.81781141), (0.57547773, -0.66986282, 0.46915795), (0.81781142, 0.46915795, -0.33327961)
13generate(0.15495246, 0.73293445, 0.66241741), (-0.55809557, -0.48833173, 0.67086618), (0.81518039, -0.47364461, 0.33337927)
14generate(0.4038138, 0.63267669, 0.66079847), (-0.87886382, 0.46885388, 0.08817276), (-0.25403307, -0.61635725, 0.74536631)
15generate(0.40580854, 0.41325726, 0.81519192), (0.05646381, 0.87889602, -0.47365981), (-0.9122123, 0.23824404, 0.33332943)
16generate(-0.40319406, -0.41060944, -0.81782298), (0.8803673, 0.06988358, -0.46911586), (0.24977581, -0.90912935, 0.33331048)
17generate(-0.15396651, -0.37964281, -0.91223113), (0.55450756, -0.79734703, 0.23824166), (-0.81781152, -0.46915782, 0.33327955)
18generate(-0.00315282, -0.57919873, -0.81518028), (-0.57919873, -0.66346781, 0.47364469), (-0.81518029, 0.47364471, -0.33337937)
19generate(-0.15917239, -0.7334977, -0.66079139), (-0.954008, 0.28650471, -0.08822576), (0.25403323, 0.61635718, -0.74536631)
20generate(-0.40641147, -0.62930379, -0.66242468), (-0.05194659, 0.7397408, -0.67088382), (0.9122123, -0.23824419, -0.33332932)
Detailsbiological unit is an icosahedral virus generated by applying the 60 provided matrices

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Components

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Capsid protein ... , 2 types, 6 molecules ABCDEF

#1: Protein Capsid protein beta / / Coat protein beta


Mass: 39367.355 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Flock house virus / Gene: alpha, coat protein alpha / Plasmid: PBACPAK9 / Cell line (production host): SF21 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P12870, nodavirus endopeptidase
#2: Protein/peptide Capsid protein Gamma / / Peptide gamma / Coat protein gamma


Mass: 4399.056 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Flock house virus / Gene: alpha, coat protein alpha / Plasmid: pBacPak9 / Cell line (production host): SF21 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P12870

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RNA chain , 1 types, 1 molecules R

#3: RNA chain Random cellular RNA fragments


Mass: 4261.452 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: random cellular RNAs / Source: (natural) Spodoptera frugiperda (fall armyworm) / Cell line: SF21

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Non-polymers , 4 types, 146 molecules

#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#6: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 138 / 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: 1

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Sample preparation

CrystalDensity Matthews: 3.91 Å3/Da / Density % sol: 69 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 7
Details: 5-6% PEG 8K, 0.15M LITHIUM SULFATE, 0.1M HEPES AND 0.01M CALCIUM CHLORIDE, pH 7.0, VAPOR DIFFUSION, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 3.5→40 Å / Num. obs: 311408 / % possible obs: 80.6 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.117 / Net I/σ(I): 7.1
Reflection shellResolution: 3.5→3.56 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.588 / Mean I/σ(I) obs: 1.1 / Num. unique all: 13408 / % possible all: 69.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT3.11data extraction
DENZOdata reduction
GLRFphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Wild-type FHV coordinates

Resolution: 3.5→40 Å / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: NONE / σ(F): 0
Details: Cross-validation was not used due to 20-fold non-crystallographic symmetry.
RfactorNum. reflection% reflection
Rwork0.262 --
Rfree-0 -
obs-309103 79.9 %
Solvent computationBsol: 78.6943 Å2
Displacement parametersBiso max: 461.53 Å2 / Biso mean: 118.933 Å2 / Biso min: 9.75 Å2
Baniso -1Baniso -2Baniso -3
1-0.331 Å20 Å20 Å2
2--0.331 Å20 Å2
3----0.662 Å2
Refinement stepCycle: LAST / Resolution: 3.5→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7389 282 50 138 7859
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_d1.5
Refine LS restraints NCSRms: 0 / Type: strict / Weight: 300
LS refinement shell
Resolution (Å)Rfactor RworkNum. reflection RworkRefine-IDTotal num. of bins used% reflection obs (%)
3.5-3.630.372226570X-RAY DIFFRACTION1068.6
3.63-3.770.370627594X-RAY DIFFRACTION1071.4
3.77-3.940.365528464X-RAY DIFFRACTION1073.5
3.94-4.150.343329716X-RAY DIFFRACTION1076.9
4.15-4.410.312430738X-RAY DIFFRACTION1079.5
4.41-4.750.279631710X-RAY DIFFRACTION1081.9
4.75-5.230.255932852X-RAY DIFFRACTION1085.1
5.23-5.980.231433797X-RAY DIFFRACTION1087.4
5.98-7.530.207833725X-RAY DIFFRACTION1087.1
7.53-400.177933937X-RAY DIFFRACTION1087.7
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.paramCNS_TOPPAR:protein.top
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.paramCNS_TOPPAR:dna-rna.top
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.paramCNS_TOPPAR:water.top
X-RAY DIFFRACTION4CNS_TOPPAR:ion.paramCNS_TOPPAR:ion.top
X-RAY DIFFRACTION5CNS_TOPPAR:carbohydrate.paramCNS_TOPPAR:carbohydrate.top
X-RAY DIFFRACTION6EPE.paramEPE.top

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