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- PDB-4chf: Crystal structure of the putative cap-binding domain of the PB2 s... -

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Basic information

Entry
Database: PDB / ID: 4chf
TitleCrystal structure of the putative cap-binding domain of the PB2 subunit of Thogoto virus polymerase (form 2)
ComponentsPOLYMERASE BASIC PROTEIN 2
KeywordsVIRAL PROTEIN
Function / homology
Function and homology information


cap snatching / 7-methylguanosine mRNA capping / virion component / host cell nucleus
Similarity search - Function
: / : / Polymerase basic protein 2 (PB2), '627' domain / Polymerase basic protein 2, cap-binding domain / : / Influenza RNA polymerase PB2 helical domain
Similarity search - Domain/homology
Polymerase basic protein 2
Similarity search - Component
Biological speciesTHOGOTO VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsGuilligay, D. / Kadlec, J. / Crepin, T. / Lunardi, T. / Bouvier, D. / Kochs, G. / Ruigrok, R.W.H. / Cusack, S.
CitationJournal: Plos One / Year: 2014
Title: Comparative Structural and Functional Analysis of Orthomyxovirus Polymerase CAP-Snatching Domains.
Authors: Guilligay, D. / Kadlec, J. / Crepin, T. / Lunardi, T. / Bouvier, D. / Kochs, G. / Ruigrok, R.W.H. / Cusack, S.
History
DepositionDec 1, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 5, 2014Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: POLYMERASE BASIC PROTEIN 2
B: POLYMERASE BASIC PROTEIN 2


Theoretical massNumber of molelcules
Total (without water)38,6362
Polymers38,6362
Non-polymers00
Water00
1
A: POLYMERASE BASIC PROTEIN 2


Theoretical massNumber of molelcules
Total (without water)19,3181
Polymers19,3181
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: POLYMERASE BASIC PROTEIN 2


Theoretical massNumber of molelcules
Total (without water)19,3181
Polymers19,3181
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)101.440, 101.440, 106.020
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212

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Components

#1: Protein POLYMERASE BASIC PROTEIN 2 / RNA-DIRECTED RNA POLYMERASE SUBUNIT P3


Mass: 19318.199 Da / Num. of mol.: 2 / Fragment: PUTATIVE CAP-BINDING DOMAIN, RESIDUES 323-486
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THOGOTO VIRUS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): CODON PLUS-RIL / References: UniProt: Q9YNA4
Sequence detailsEXTRA GAMA AT N-TERMINUS AFTER HIS-TAG CLEAVAGE

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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: 3.61 Å3/Da / Density % sol: 65.9 % / Description: NONE
Crystal growpH: 6
Details: 100 MM BIS-TRIS PH 6.0, 100 MM MGCL2 AND 22 % PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 20, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 11610 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 10.2 % / Biso Wilson estimate: 39.83 Å2 / Rmerge(I) obs: 0.22 / Net I/σ(I): 12.9
Reflection shellResolution: 3→3.11 Å / Redundancy: 10.4 % / Rmerge(I) obs: 0.95 / Mean I/σ(I) obs: 3.8 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: THOGOTO PB2 PUTATIVE CAP-BINDING DOMAIN FORM 1

Resolution: 3→46.982 Å / SU ML: 0.36 / σ(F): 1.34 / Phase error: 19.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2158 553 4.8 %
Rwork0.1996 --
obs0.2004 11607 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3→46.982 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2628 0 0 0 2628
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032710
X-RAY DIFFRACTIONf_angle_d0.8463657
X-RAY DIFFRACTIONf_dihedral_angle_d13.6561024
X-RAY DIFFRACTIONf_chiral_restr0.031386
X-RAY DIFFRACTIONf_plane_restr0.003470
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0001-3.30190.28881420.26252683X-RAY DIFFRACTION100
3.3019-3.77950.25531440.20952710X-RAY DIFFRACTION100
3.7795-4.76110.16141400.17442733X-RAY DIFFRACTION100
4.7611-46.98750.20241270.1862928X-RAY DIFFRACTION100
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)
11.981-1.63240.4592.9029-0.23480.53790.06180.3279-0.1144-0.32-0.17030.0721-0.0625-0.0320.06410.2055-0.0078-0.03930.1991-0.00570.2489-0.5261-23.3295-54.3418
26.07250.7965-2.77332.3919-1.18952.7680.39840.06040.32090.36830.00350.097-0.5836-0.1436-0.35840.26360.0033-0.03180.2362-0.03580.1282-5.3306-15.9467-41.7339
32.8108-0.5460.06152.6858-0.10291.1759-0.0366-0.0126-0.50010.24810.13730.34420.17720.0813-0.10020.25380.005-0.0490.21190.06640.34871.9784-31.6737-45.9714
44.3504-2.46150.36664.00240.62461.8399-0.1577-0.49230.16460.70090.1149-0.10160.1335-0.0660.02990.37790.07010.00180.34450.02880.1981-2.1723-17.4315-32.7891
54.51770.58851.45193.0098-0.47226.573-0.05730.03150.58390.56790.2538-0.181-0.0696-0.26990.38060.29690.1110.00890.32940.00940.2729-5.243-10.7049-36.4116
62.78920.441-1.61016.16213.5013.2583-0.227-0.3303-0.07680.7905-0.2242-0.324-0.24450.74010.1590.4757-0.0424-0.16540.32430.09490.295717.1377-24.935-8.0746
74.61352.12890.76582.28611.57451.60430.1432-0.51550.00830.73710.0847-0.3191-0.45850.7443-0.23340.57060.0549-0.03010.4466-0.09360.16792.97-22.1103-3.206
81.84221.5843-0.61462.6549-0.13361.32830.2325-0.26180.16510.5214-0.1930.1868-0.21320.1065-0.01360.2991-0.0017-0.08180.333-0.00620.24682.3799-27.4329-8.5615
93.3844-0.3212-1.38082.2092-0.27633.1549-0.02760.09250.28960.219-0.2219-0.3905-0.49620.59270.26650.3961-0.0584-0.11070.43430.05880.301217.3045-19.5424-18.9948
103.63252.9278-1.16993.74410.7822.8118-0.1131-0.1066-0.1667-0.0293-0.21070.13310.0413-0.01820.24420.32430.0032-0.09140.2930.03850.27614.2784-32.0119-17.0341
113.2158-0.17980.10381.4903-0.28032.83770.13420.6260.4604-0.3863-0.2327-0.4257-0.18580.25530.15930.44190.0492-0.02770.53740.15130.324314.1313-18.4565-29.2071
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 325 THROUGH 386 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 387 THROUGH 403 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 404 THROUGH 445 )
4X-RAY DIFFRACTION4CHAIN A AND (RESID 446 THROUGH 474 )
5X-RAY DIFFRACTION5CHAIN A AND (RESID 475 THROUGH 485 )
6X-RAY DIFFRACTION6CHAIN B AND (RESID 326 THROUGH 340 )
7X-RAY DIFFRACTION7CHAIN B AND (RESID 341 THROUGH 349 )
8X-RAY DIFFRACTION8CHAIN B AND (RESID 350 THROUGH 376 )
9X-RAY DIFFRACTION9CHAIN B AND (RESID 377 THROUGH 403 )
10X-RAY DIFFRACTION10CHAIN B AND (RESID 404 THROUGH 445 )
11X-RAY DIFFRACTION11CHAIN B AND (RESID 446 THROUGH 485 )

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