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- PDB-4fte: Crystal structure of the D75N mutant capsid of Flock House virus -

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Basic information

Entry
Database: PDB / ID: 4fte
TitleCrystal structure of the D75N mutant capsid of Flock House virus
Components
  • Capsid protein alpha
  • Random cellular RNAs
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: 2Q25
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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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 alpha
B: Capsid protein alpha
C: Capsid protein alpha
R: Random cellular RNAs
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,81713
Polymers135,8104
Non-polymers1,0079
Water4,612256
1
A: Capsid protein alpha
B: Capsid protein alpha
C: Capsid protein alpha
R: Random cellular RNAs
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)8,208,995780
Polymers8,148,590240
Non-polymers60,405540
Water4,324240
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 alpha
B: Capsid protein alpha
C: Capsid protein alpha
R: Random cellular RNAs
hetero molecules
x 5


  • icosahedral pentamer
  • 684 kDa, 20 polymers
Theoretical massNumber of molelcules
Total (without water)684,08365
Polymers679,04920
Non-polymers5,03445
Water36020
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Capsid protein alpha
B: Capsid protein alpha
C: Capsid protein alpha
R: Random cellular RNAs
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 821 kDa, 24 polymers
Theoretical massNumber of molelcules
Total (without water)820,89978
Polymers814,85924
Non-polymers6,04054
Water43224
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 alpha
B: Capsid protein alpha
C: Capsid protein alpha
R: Random cellular RNAs
hetero molecules
x 20


  • crystal asymmetric unit, crystal frame
  • 2.74 MDa, 80 polymers
Theoretical massNumber of molelcules
Total (without water)2,736,332260
Polymers2,716,19780
Non-polymers20,135180
Water1,44180
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation19
Unit cell
Length a, b, c (Å)325.600, 325.600, 770.660
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 oper:
IDCodeMatrix
1given(1), (1), (1)
2generate(0.3456727, -0.66638253, 0.66063961), (0.84515774, 0.5269951, 0.08935639), (-0.40769938, 0.5274566, 0.74536618)
3generate(-0.7130511, -0.23307186, 0.66123797), (0.7011114, -0.2383429, 0.67203829), (0.00096816, 0.94279911, 0.33336001)
4generate(-0.71305109, 0.7011114, 0.00096816), (-0.23307186, -0.2383429, 0.94279912), (0.66123796, 0.67203829, 0.33336)
5generate(0.34567271, 0.84515773, -0.40769938), (-0.66638254, 0.5269951, 0.52745662), (0.66063961, 0.0893564, 0.74536618)
6generate(-0.96408935, -0.2655781), (-0.26557809, 0.96408935, -4.0E-8), (-4.0E-8, -1)
7generate(-0.55771476, 0.50249395, -0.66064671), (0.72300449, 0.68504695, -0.08930389), (0.40769934, -0.52745663, -0.74536618)
8generate(0.50124514, 0.28800075, -0.81597113), (0.86530479, -0.16788511, 0.47229463), (-0.00096819, -0.9427991, -0.33336003)
9generate(0.74934375, -0.61263538, -0.25132019), (-0.03533138, -0.41598371, 0.90868546), (-0.66123795, -0.67203827, -0.33336004)
10generate(-0.15628277, -0.95476592, 0.25297771), (-0.73425544, 0.28361498, 0.6167913), (-0.66063958, -0.08935641, -0.7453662)
11generate(0.15589824, 0.3778736, 0.91263754), (0.95526336, 0.17741229, -0.23663645), (-0.25133178, 0.9087004, -0.33331053)
12generate(0.00117081, 0.57662637, 0.81700714), (0.57662637, -0.66789087, 0.47055693), (0.81700714, 0.47055693, -0.33327994)
13generate(0.15465165, 0.73403488, 0.66126822), (-0.55699491, -0.4880306, 0.67199912), (0.81598992, -0.47224879, 0.33337895)
14generate(0.40423547, 0.63256592, 0.66064669), (-0.8789744, 0.46843231, 0.08930387), (-0.25297767, -0.6167913, 0.74536621)
15generate(0.4050059, 0.41244614, 0.81600147), (0.05565261, 0.87969864, -0.4722638), (-0.91261876, 0.23668223, 0.33332945)
16generate(-0.40399686, -0.41142073, -0.81701868), (0.87955608, 0.07068631, -0.47051521), (0.25133174, -0.9087004, 0.33331055)
17generate(-0.15426809, -0.37854215, -0.91263749), (0.55560837, -0.79704582, 0.23667974), (-0.81700716, -0.4705569, 0.33327993)
18generate(-0.00117236, -0.57806497, -0.8159899), (-0.57806498, -0.66544867, 0.47224883), (-0.81598989, 0.47224882, -0.33337897)
19generate(-0.15628276, -0.73425543, -0.66063958), (-0.95476593, 0.28361498, -0.08935641), (0.25297771, 0.61679129, -0.74536621)
20generate(-0.405242, -0.63126362, -0.6612754), (-0.05390657, 0.73857142, -0.67201663), (0.91261876, -0.23668227, -0.33332942)
Detailsbiological unit is an icosahedral virus generated by applying the provided matrices

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Components

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Protein / RNA chain , 2 types, 4 molecules ABCR

#1: Protein Capsid protein alpha /


Mass: 43747.406 Da / Num. of mol.: 3 / Mutation: D75N
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: RNA chain Random cellular RNAs


Mass: 4567.617 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SPODOPTERA FRUGIPERDA (fall armyworm) / Cell line: SF21

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Non-polymers , 5 types, 265 molecules

#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#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.: 256 / 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: 363960 / % possible obs: 94.8 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.169 / Net I/σ(I): 5
Reflection shellResolution: 3.5→3.56 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 1.4 / Num. unique all: 15290 / % possible all: 80.2

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Phasing

PhasingMethod: molecular replacement

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Processing

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

Resolution: 3.5→40 Å / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: NONE / σ(F): 0
Details: Cross-validation not used due to 20-fold non-crystallographic symmetry
RfactorNum. reflection% reflection
Rwork0.239 --
Rfree-0 -
obs-363831 94.8 %
Solvent computationBsol: 54.4278 Å2
Displacement parametersBiso max: 365.52 Å2 / Biso mean: 82.1228 Å2 / Biso min: 1 Å2
Baniso -1Baniso -2Baniso -3
1-1.987 Å20 Å20 Å2
2--1.987 Å20 Å2
3----3.974 Å2
Refinement stepCycle: LAST / Resolution: 3.5→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7383 302 55 256 7996
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_d1.465
LS refinement shell
Resolution (Å)Rfactor RworkNum. reflection RworkRefine-IDTotal num. of bins used% reflection obs (%)
3.5-3.630.337531073X-RAY DIFFRACTION1081.2
3.63-3.770.317432714X-RAY DIFFRACTION1085.4
3.77-3.940.308734597X-RAY DIFFRACTION1090
3.94-4.150.27636258X-RAY DIFFRACTION1094.4
4.15-4.410.246737553X-RAY DIFFRACTION1097.8
4.41-4.750.223538163X-RAY DIFFRACTION1099.5
4.75-5.230.217438405X-RAY DIFFRACTION10100
5.23-5.980.210438343X-RAY DIFFRACTION10100
5.98-7.530.204938343X-RAY DIFFRACTION10100
7.53-400.189738382X-RAY DIFFRACTION1099.9
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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