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- PDB-3zed: X-ray structure of the birnavirus VP1-VP3 complex -

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Basic information

Entry
Database: PDB / ID: 3zed
TitleX-ray structure of the birnavirus VP1-VP3 complex
Components
  • CAPSID PROTEIN VP3
  • RNA-DIRECTED RNA POLYMERASE
KeywordsVIRAL PROTEIN / VIRUS MORPHOGENESIS
Function / homology
Function and homology information


T=13 icosahedral viral capsid / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / serine-type peptidase activity / viral genome replication / virion component / host cell cytoplasm / RNA-directed RNA polymerase / RNA-directed RNA polymerase activity / GTP binding / structural molecule activity ...T=13 icosahedral viral capsid / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / serine-type peptidase activity / viral genome replication / virion component / host cell cytoplasm / RNA-directed RNA polymerase / RNA-directed RNA polymerase activity / GTP binding / structural molecule activity / proteolysis / metal ion binding
Similarity search - Function
VP1, C-terminal extension domain / Infectious bursal virus vp1 polymerase fold / Infectious bursal virus vp1 polymerase domain / Helix Hairpins - #300 / Birnavirus RNA-directed RNA polymerase, palm domain / RNA-directed RNA polymerase, C-terminal, birnavirus / RNA-directed RNA polymerase, thumb domain, birnavirus / RNA-directed RNA polymerase, palm domain superfamily, Birnavirus / RNA-directed RNA polymerase, thumb domain superfamily, Birnavirus / Birnavirus RNA dependent RNA polymerase (VP1), palm domain ...VP1, C-terminal extension domain / Infectious bursal virus vp1 polymerase fold / Infectious bursal virus vp1 polymerase domain / Helix Hairpins - #300 / Birnavirus RNA-directed RNA polymerase, palm domain / RNA-directed RNA polymerase, C-terminal, birnavirus / RNA-directed RNA polymerase, thumb domain, birnavirus / RNA-directed RNA polymerase, palm domain superfamily, Birnavirus / RNA-directed RNA polymerase, thumb domain superfamily, Birnavirus / Birnavirus RNA dependent RNA polymerase (VP1), palm domain / Birnavirus RNA dependent RNA polymerase (VP1), thumb domain / Birnavirus RNA dependent RNA polymerase (VP1), C-terminal / RdRp of Birnaviridae dsRNA viruses catalytic domain profile. / Birnavirus VP3, domain 2 / Birnavirus VP3, domain 1 / Birnavirus VP2 protein / Birnavirus VP3 protein / Birnavirus VP4 protease domain / Birnavirus VP2 protein / Birnavirus VP3 protein / Birnavirus VP4 protein / Birnavirus VP4 protease domain profile. / Helix hairpin bin / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / Helix Hairpins / Helix non-globular / Special / Viral coat protein subunit / Helix Hairpins / DNA/RNA polymerase superfamily / Alpha-Beta Complex / Up-down Bundle / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / Structural polyprotein / RNA-directed RNA polymerase
Similarity search - Component
Biological speciesINFECTIOUS PANCREATIC NECROSIS VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsBahar, M.W. / Sarin, L.P. / Graham, S.C. / Pang, J. / Bamford, D.H. / Stuart, D.I. / Grimes, J.M.
CitationJournal: J.Virol. / Year: 2013
Title: Structure of a Vp1-Vp3 Complex Suggests How Birnaviruses Package the Vp1 Polymerase.
Authors: Bahar, M.W. / Sarin, L.P. / Graham, S.C. / Pang, J. / Bamford, D.H. / Stuart, D.I. / Grimes, J.M.
History
DepositionDec 4, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 16, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2013Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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_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 / _struct_conn.pdbx_dist_value / _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_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: RNA-DIRECTED RNA POLYMERASE
B: RNA-DIRECTED RNA POLYMERASE
C: RNA-DIRECTED RNA POLYMERASE
D: CAPSID PROTEIN VP3
E: CAPSID PROTEIN VP3
F: CAPSID PROTEIN VP3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)369,14215
Polymers368,6316
Non-polymers5119
Water19,9791109
1
B: RNA-DIRECTED RNA POLYMERASE
E: CAPSID PROTEIN VP3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,9554
Polymers122,8772
Non-polymers782
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1560 Å2
ΔGint-4.2 kcal/mol
Surface area31120 Å2
MethodPISA
2
C: RNA-DIRECTED RNA POLYMERASE
F: CAPSID PROTEIN VP3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,0475
Polymers122,8772
Non-polymers1703
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1840 Å2
ΔGint-3.8 kcal/mol
Surface area31230 Å2
MethodPISA
3
A: RNA-DIRECTED RNA POLYMERASE
D: CAPSID PROTEIN VP3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,1396
Polymers122,8772
Non-polymers2624
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1750 Å2
ΔGint-8.2 kcal/mol
Surface area38080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.270, 341.870, 59.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.9944, -0.006196, 0.1051), (-0.005245, 0.9999, 0.009326), (-0.1051, 0.008723, -0.9944)-58.84, -55.01, 0.5366
2given(-0.9862, 0.06055, -0.1539), (-0.04017, -0.9904, -0.1323), (-0.1604, -0.1243, 0.9792)-114.2, -113.3, -15.93
3given(-0.9918, -0.05551, 0.1155), (-0.04569, 0.9952, 0.08602), (-0.1198, 0.08004, -0.9896)-58.61, -55.06, -0.2593
4given(-0.9841, 0.08372, -0.1567), (-0.05822, -0.9853, -0.1607), (-0.1679, -0.149, 0.9745)-112.7, -114.1, -18.2

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Components

#1: Protein RNA-DIRECTED RNA POLYMERASE / RDRP / PROTEIN VP1 / VP1 POLYMERASE


Mass: 95632.492 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) INFECTIOUS PANCREATIC NECROSIS VIRUS / Strain: JASPER / Production host: ESCHERICHIA COLI B (bacteria) / Strain (production host): B834(DE3) / References: UniProt: P22173, RNA-directed RNA polymerase
#2: Protein CAPSID PROTEIN VP3


Mass: 27244.477 Da / Num. of mol.: 3 / Fragment: VP3 C-TERMINAL PEPTIDE RESIDUES 735-972
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) INFECTIOUS PANCREATIC NECROSIS VIRUS / Strain: JASPER / Production host: ESCHERICHIA COLI B (bacteria) / Strain (production host): B834(DE3) / References: UniProt: P05844
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: K
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1109 / 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: 2.32 Å3/Da / Density % sol: 47.04 % / Description: NONE
Crystal growpH: 7.5
Details: 20% (W/V) POLYETHYLENE GLYCOL 3350 AND 0.2M POTASSIUM FLUORIDE, pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9173
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 30, 2011 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9173 Å / Relative weight: 1
ReflectionResolution: 2.2→68.4 Å / Num. obs: 123796 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 6.7 % / Biso Wilson estimate: 46.48 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 12
Reflection shellResolution: 2.2→2.26 Å / Redundancy: 6.6 % / Mean I/σ(I) obs: 1.2 / % possible all: 99.2

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Processing

Software
NameVersionClassification
BUSTER2.11.2refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2YI9

2yi9


Resolution: 2.2→59.13 Å / Cor.coef. Fo:Fc: 0.9539 / Cor.coef. Fo:Fc free: 0.9392 / SU R Cruickshank DPI: 0.254 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.265 / SU Rfree Blow DPI: 0.187 / SU Rfree Cruickshank DPI: 0.186
RfactorNum. reflection% reflectionSelection details
Rfree0.2145 6202 5.01 %RANDOM
Rwork0.1793 ---
obs0.181 123689 99.63 %-
Displacement parametersBiso mean: 55.66 Å2
Baniso -1Baniso -2Baniso -3
1-5.2703 Å20 Å20 Å2
2--2.0945 Å20 Å2
3----7.3648 Å2
Refine analyzeLuzzati coordinate error obs: 0.308 Å
Refinement stepCycle: LAST / Resolution: 2.2→59.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18145 0 24 1109 19278
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0118590HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9925322HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d8552SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes493HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2643HARMONIC5
X-RAY DIFFRACTIONt_it18590HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.12
X-RAY DIFFRACTIONt_other_torsion2.76
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion2496SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies3HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact22269SEMIHARMONIC4
LS refinement shellResolution: 2.2→2.26 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2578 461 5.17 %
Rwork0.2287 8451 -
all0.2302 8912 -
obs--99.63 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.99650.1981-0.12630.7242-0.07030.5688-0.03350.0514-0.0444-0.02530.06270.06110.035-0.0131-0.0292-0.0590.0090.018-0.06970.0289-0.1294-43.9457-75.81479.3
21.8348-0.2969-0.11081.6226-0.23510.62210.10410.12710.2856-0.03740.06010.2374-0.1714-0.0136-0.1642-0.1904-0.00240.0375-0.18980.02-0.0637-15.5582-20.9081-7.3043
32.67351.0980.44751.77420.25170.52420.13210.2335-0.38320.16250.082-0.19540.04210.0528-0.2142-0.23660.0393-0.0087-0.16450.0103-0.1154-74.9532-35.97918.9643
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN C

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