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- PDB-4ftb: Crystal structure of the authentic Flock House virus particle -

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Basic information

Entry
Database: PDB / ID: 4ftb
TitleCrystal structure of the authentic Flock House virus particle
Components
  • (Capsid protein ...) x 2
  • Flock House virus genomic RNA
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 / symbiont entry into host cell via permeabilization of host 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
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.7 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: 2Z2Q
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
Revision 1.2Nov 27, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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: Flock House virus genomic RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,77815
Polymers135,8677
Non-polymers9118
Water8,611478
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: Flock House virus genomic RNA
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)8,206,652900
Polymers8,152,011420
Non-polymers54,641480
Water7,566420
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: Flock House virus genomic RNA
hetero molecules
x 5


  • icosahedral pentamer
  • 684 kDa, 35 polymers
Theoretical massNumber of molelcules
Total (without water)683,88875
Polymers679,33435
Non-polymers4,55340
Water63135
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: Flock House virus genomic RNA
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 821 kDa, 42 polymers
Theoretical massNumber of molelcules
Total (without water)820,66590
Polymers815,20142
Non-polymers5,46448
Water75742
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: Flock House virus genomic RNA
hetero molecules
x 20


  • crystal asymmetric unit, crystal frame
  • 2.74 MDa, 140 polymers
Theoretical massNumber of molelcules
Total (without water)2,735,551300
Polymers2,717,337140
Non-polymers18,214160
Water2,522140
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation19
Unit cell
Length a, b, c (Å)327.660, 327.660, 774.490
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(0.34687152, -0.66518281, 0.66122007), (0.84635759, 0.52579621, 0.08495393), (-0.4041769, 0.53016052, 0.74536626)
3generate(-0.70991254, -0.2299308, 0.66569964), (0.70425255, -0.24148165, 0.66761888), (0.0072481, 0.94277168, 0.3333602)
4generate(-0.70991254, 0.70425255, 0.0072481), (-0.2299308, -0.24148165, 0.94277168), (0.66569964, 0.66761888, 0.3333602)
5generate(0.34687153, 0.84635759, -0.4041769), (-0.66518281, 0.52579621, 0.53016052), (0.66122006, 0.08495394, 0.74536625)
6generate(-0.96754162, -0.25271171, -4.0E-8), (-0.2527117, 0.96754162, 3.2E-7), (-4.0E-8, 3.0E-7, -1)
7generate(-0.5494971, 0.51071717, -0.66122682), (0.73122758, 0.67682937, -0.08490135), (0.40417714, -0.53016033, -0.74536626)
8generate(0.50889707, 0.28349282, -0.81280723), (0.86079686, -0.17553704, 0.47771907), (-0.00724786, -0.94277174, -0.33336002)
9generate(0.74497611, -0.62036844, -0.2452623), (-0.0430642, -0.4116162, 0.91033927), (-0.66569968, -0.66761898, -0.33335991)
10generate(-0.16751318, -0.95176106, 0.25708017), (-0.73125034, 0.29484527, 0.61509284), (-0.66122028, -0.08495381, -0.74536608)
11generate(0.16477876, 0.3779577, 0.91104114), (0.95534752, 0.16853173, -0.24271006), (-0.24527348, 0.91035434, -0.33331049)
12generate(0.00882265, 0.57211877, 0.82012334), (0.57211876, -0.67554269, 0.4651045), (0.82012332, 0.4651045, -0.33327996)
13generate(0.15580248, 0.72974622, 0.66572971), (-0.56128347, -0.48918131, 0.66757959), (0.81282621, -0.47767363, 0.33337882)
14generate(0.40259713, 0.63300427, 0.66122701), (-0.87853582, 0.47007078, 0.08490153), (-0.25708046, -0.61509272, 0.74536607)
15generate(0.40814478, 0.41558701, 0.8128378), (0.05879368, 0.8765598, -0.47768841), (-0.91102203, 0.24275575, 0.33332941)
16generate(-0.40085781, -0.40827978, -0.82013453), (0.88269689, 0.06754742, -0.46506295), (0.24527376, -0.9103543, 0.33331038)
17generate(-0.15311742, -0.38283119, -0.91104081), (0.55131939, -0.79819663, 0.24275309), (-0.82012315, -0.46510473, 0.33328007)
18generate(-0.00890251, -0.58243798, -0.8128264), (-0.58243797, -0.65771884, 0.47767346), (-0.81282639, 0.47767345, -0.33337865)
19generate(-0.16751318, -0.73125035, -0.66122029), (-0.95176106, 0.29484526, -0.0849538), (0.25708017, 0.61509283, -0.74536607)
20generate(-0.40975487, -0.62361467, -0.66573696), (-0.04625792, 0.74308447, -0.66759694), (0.91102203, -0.2427555, -0.33332959)
Detailsbiological unit is an icosahedral virus generated by applying the 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 / Cell line (production host): DL-1 / Production host: DROSOPHILA MELANOGASTER (fruit fly) / 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 / Cell line (production host): DL-1 / Production host: DROSOPHILA MELANOGASTER (fruit fly) / References: UniProt: P12870

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RNA chain , 1 types, 1 molecules R

#3: RNA chain Flock House virus genomic RNA


Mass: 4567.617 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Genomic RNA produced during virus replication in DL-1 cells.
Source: (natural) Flock house virus

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Non-polymers , 4 types, 486 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


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


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


Mass: 18.015 Da / Num. of mol.: 478 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 7.5
Details: 5-6% PEG 8K, 0.15M LITHIUM SULFATE, 0.1M HEPES AND 0.01M CALCIUM CHLORIDE, pH 7.5, 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: 2.7→40 Å / Num. obs: 709014 / % possible obs: 83.5 % / Redundancy: 2.3 % / Rmerge(I) obs: 0.105 / Net I/σ(I): 9
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.824 / Mean I/σ(I) obs: 1 / Num. unique all: 45803 / % possible all: 53.9

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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 coordinates (from 1992)

Resolution: 2.7→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
Rwork0.24 --
Rfree-0 -
obs-700018 82.2 %
Solvent computationBsol: 53.3466 Å2
Displacement parametersBiso max: 251.13 Å2 / Biso mean: 62.8606 Å2 / Biso min: 29.1 Å2
Baniso -1Baniso -2Baniso -3
1-5.295 Å20 Å20 Å2
2--5.295 Å20 Å2
3----10.59 Å2
Refinement stepCycle: LAST / Resolution: 2.7→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7491 302 50 478 8321
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_d1.466
LS refinement shell
Resolution (Å)Rfactor RworkNum. reflection RworkRefine-IDTotal num. of bins used% reflection obs (%)
2.7-2.80.403943755X-RAY DIFFRACTION1051.4
2.8-2.910.393453772X-RAY DIFFRACTION1063.1
2.91-3.040.38566398X-RAY DIFFRACTION1078.1
3.04-3.20.36272081X-RAY DIFFRACTION1084.6
3.2-3.40.320372607X-RAY DIFFRACTION1085.3
3.4-3.660.303872629X-RAY DIFFRACTION1085.3
3.66-4.030.255974975X-RAY DIFFRACTION1088.1
4.03-4.620.191679823X-RAY DIFFRACTION1093.7
4.62-5.810.165781582X-RAY DIFFRACTION1095.9
5.81-400.163482396X-RAY DIFFRACTION1096.8
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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