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- PDB-2vqz: Structure of the cap-binding domain of influenza virus polymerase... -

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Basic information

Entry
Database: PDB / ID: 2vqz
TitleStructure of the cap-binding domain of influenza virus polymerase subunit PB2 with bound m7GTP
ComponentsPOLYMERASE BASIC PROTEIN 2
KeywordsTRANSCRIPTION / RNA-DEPENDENT RNA POLYMERASE / PB2 SUBUNIT / INFLUENZA VIRUS / CAP-BINDING DOMAIN
Function / homology
Function and homology information


cap snatching / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / 7-methylguanosine mRNA capping / host cell mitochondrion / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / virion component / symbiont-mediated suppression of host gene expression / viral RNA genome replication / RNA-directed RNA polymerase activity / DNA-templated transcription ...cap snatching / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / 7-methylguanosine mRNA capping / host cell mitochondrion / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / virion component / symbiont-mediated suppression of host gene expression / viral RNA genome replication / RNA-directed RNA polymerase activity / DNA-templated transcription / host cell nucleus / RNA binding
Similarity search - Function
Influenza RNA-dependent RNA polymerase subunit PB2 / PB2, C-terminal / : / : / Influenza RNA polymerase PB2 N-terminal region / Influenza RNA polymerase PB2 second domain / : / Influenza RNA polymerase PB2 middle domain / : / Influenza RNA polymerase PB2 C-terminal domain ...Influenza RNA-dependent RNA polymerase subunit PB2 / PB2, C-terminal / : / : / Influenza RNA polymerase PB2 N-terminal region / Influenza RNA polymerase PB2 second domain / : / Influenza RNA polymerase PB2 middle domain / : / Influenza RNA polymerase PB2 C-terminal domain / : / Influenza RNA polymerase PB2 6th domain / : / Influenza RNA polymerase PB2 CAP binding domain / : / Influenza RNA polymerase PB2 helical domain
Similarity search - Domain/homology
7N-METHYL-8-HYDROGUANOSINE-5'-TRIPHOSPHATE / Polymerase basic protein 2
Similarity search - Component
Biological speciesINFLUENZA A VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsGuilligay, D. / Tarendeau, F. / Resa-Infante, P. / Coloma, R. / Crepin, T. / Sehr, P. / Lewis, J. / Ruigrok, R.W.H. / Ortin, J. / Hart, D.J. / Cusack, S.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2008
Title: The Structural Basis for CAP Binding by Influenza Virus Polymerase Subunit Pb2.
Authors: Guilligay, D. / Tarendeau, F. / Resa-Infante, P. / Coloma, R. / Crepin, T. / Sehr, P. / Lewis, J. / Ruigrok, R.W.H. / Ortin, J. / Hart, D.J. / Cusack, S.
History
DepositionMar 21, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 13, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ncs_dom_lim / 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_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_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: POLYMERASE BASIC PROTEIN 2
B: POLYMERASE BASIC PROTEIN 2
D: POLYMERASE BASIC PROTEIN 2
E: POLYMERASE BASIC PROTEIN 2
F: POLYMERASE BASIC PROTEIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,28110
Polymers96,5845
Non-polymers2,6965
Water4,900272
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8630 Å2
ΔGint-33.9 kcal/mol
Surface area45720 Å2
MethodPQS
Unit cell
Length a, b, c (Å)92.200, 94.440, 220.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21D
31E
41A

NCS domain segments:

Ens-ID: 1 / Refine code: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PHEPHEPHEPHEBB323 - 3306 - 13
21PHEPHEPHEPHEDC323 - 3306 - 13
31PHEPHEPHEPHEED323 - 3306 - 13
41PHEPHEPHEPHEAA323 - 3306 - 13
12THRTHRARGARGBB333 - 34016 - 23
22THRTHRARGARGDC333 - 34016 - 23
32THRTHRARGARGED333 - 34016 - 23
42THRTHRARGARGAA333 - 34016 - 23
13GLNGLNLYSLYSBB350 - 36833 - 51
23GLNGLNLYSLYSDC350 - 36833 - 51
33GLNGLNLYSLYSED350 - 36833 - 51
43GLNGLNLYSLYSAA350 - 36833 - 51
14ALAALALYSLYSBB370 - 38953 - 72
24ALAALALYSLYSDC370 - 38953 - 72
34ALAALALYSLYSED370 - 38953 - 72
44ALAALALYSLYSAA370 - 38953 - 72
15SERSERGLUGLUBB393 - 40776 - 90
25SERSERGLUGLUDC393 - 40776 - 90
35SERSERGLUGLUED393 - 40776 - 90
45SERSERGLUGLUAA393 - 40776 - 90
16ILEILEPHEPHEBB411 - 42094 - 103
26ILEILEPHEPHEDC411 - 42094 - 103
36ILEILEPHEPHEED411 - 42094 - 103
46ILEILEPHEPHEAA411 - 42094 - 103
17LEULEULEULEUBB428 - 434111 - 117
27LEULEULEULEUDC428 - 434111 - 117
37LEULEULEULEUED428 - 434111 - 117
47LEULEULEULEUAA428 - 434111 - 117
18LYSLYSILEILEBB443 - 451126 - 134
28LYSLYSILEILEDC443 - 451126 - 134
38LYSLYSILEILEED443 - 451126 - 134
48LYSLYSILEILEAA443 - 451126 - 134
19ASPASPLYSLYSBB455 - 482138 - 165
29ASPASPLYSLYSDC455 - 482138 - 165
39ASPASPLYSLYSED455 - 482138 - 165
49ASPASPLYSLYSAA455 - 482138 - 165

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.03383, -0.98769, 0.15271), (0.98823, -0.01025, 0.15261), (-0.14916, 0.15608, 0.97642)36.57726, -34.4912, 5.48464
3given(0.01201, 0.98432, -0.17597), (-0.98182, 0.04495, 0.18443), (0.18945, 0.17056, 0.96696)34.76315, 34.62057, -6.8038
4given(-0.99985, 0.01703, 0.00014), (-0.01605, -0.94478, 0.3273), (0.0057, 0.32725, 0.94492)70.41152, 0.54119, -0.09479
5given(0.50069, -0.62346, 0.60051), (0.41085, 0.78177, 0.46909), (-0.76191, 0.01185, 0.64757)38.3766, -26.32042, -9.00428

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Components

#1: Protein
POLYMERASE BASIC PROTEIN 2 / RNA-DIRECTED RNA POLYMERASE SUBUNIT P3 / PB2 CAP-BINDING DOMAIN


Mass: 19316.877 Da / Num. of mol.: 5 / Fragment: CAP-BINDING DOMAIN, RESIDUES 318-483 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) INFLUENZA A VIRUS / Strain: A/VICTORIA/3/1975(H3N2) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21-CODONPLUS-RIL / References: UniProt: P31345
#2: Chemical
ChemComp-MGT / 7N-METHYL-8-HYDROGUANOSINE-5'-TRIPHOSPHATE


Mass: 539.223 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C11H20N5O14P3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 272 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, ARG 389 TO LYS ENGINEERED RESIDUE IN CHAIN B, ARG 389 TO LYS ...ENGINEERED RESIDUE IN CHAIN A, ARG 389 TO LYS ENGINEERED RESIDUE IN CHAIN B, ARG 389 TO LYS ENGINEERED RESIDUE IN CHAIN D, ARG 389 TO LYS ENGINEERED RESIDUE IN CHAIN E, ARG 389 TO LYS ENGINEERED RESIDUE IN CHAIN F, ARG 389 TO LYS
Has protein modificationY
Nonpolymer details7N-METHYL-8-HYDROGUANOSINE-5'-TRIPHOSPHATE (MGT): CO-CRYSTALLISED SELENOMETHIONINE (MSE): ...7N-METHYL-8-HYDROGUANOSINE-5'-TRIPHOSPHATE (MGT): CO-CRYSTALLISED SELENOMETHIONINE (MSE): SELENOMETHIONATED FOR STRUCTURE DETERMINATION
Sequence detailsMUTATION R389K IN OUR SEQUENCE COMPARED TO DATABASE.

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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: 2.51 Å3/Da / Density % sol: 51 % / Description: NONE
Crystal growpH: 4.6
Details: 1 MICROLITRE OF PROTEIN SOLUTION AT 11 MG PER ML IN 50 MM TRIS-HCL (PH 8.0), 200 MM NACL, 2 MM DTT, 5 MM M7GTP WITH AN EQUAL VOLUME OF A SOLUTION CONTAINING 0.1 M CITRIC ACID PH 4.6, 1.6-1.8 M SODIUM FORMATE.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 8, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 40785 / % possible obs: 98.4 % / Observed criterion σ(I): 0 / Redundancy: 3.48 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 8.59
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 3.38 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 1.79 / % possible all: 97.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
autoSHARPphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.3→29.53 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.92 / SU B: 13.245 / SU ML: 0.16 / Cross valid method: THROUGHOUT / ESU R: 0.317 / ESU R Free: 0.227 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.235 2165 5 %RANDOM
Rwork0.186 ---
obs0.189 40781 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.47 Å2
Baniso -1Baniso -2Baniso -3
1-0.44 Å20 Å20 Å2
2--0.68 Å20 Å2
3----1.12 Å2
Refinement stepCycle: LAST / Resolution: 2.3→29.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6413 0 165 272 6850
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0226764
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5191.9879116
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2675823
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.37923.199297
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.121151291
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6471562
X-RAY DIFFRACTIONr_chiral_restr0.0930.21027
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024923
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.20.22631
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2920.24496
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1730.2321
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3330.2124
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2050.217
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7281.54221
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.12426577
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.09532920
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.2324.52539
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 965 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Btight positional0.050.05
2Dtight positional0.040.05
3Etight positional0.050.05
4Atight positional0.060.05
1Btight thermal1.465
2Dtight thermal1.425
3Etight thermal1.175
4Atight thermal1.465
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.312 148
Rwork0.25 2984
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)
12.35330.0348-0.07731.70750.50352.25710.00550.17250.1938-0.08210.0154-0.05490.02160.1221-0.0208-0.1550.0176-0.0298-0.19290.0184-0.106735.14119.855-23.497
21.91720.0348-0.24232.6126-0.1863.626-0.07290.1999-0.0806-0.07710.02690.21530.1325-0.34380.046-0.1896-0.0381-0.0171-0.1182-0.0637-0.097812.475-3.558-19.412
32.5312-0.2516-0.07233.5830.16582.76860.02810.3485-0.0276-0.3438-0.1013-0.18150.0548-0.15090.0732-0.20070.00080.035-0.1084-0.0105-0.162958.884-3.426-19.48
43.71940.62740.29482.49291.00252.9822-0.04840.3196-0.2371-0.19860.0864-0.05610.12080.1243-0.038-0.0768-0.02330.0636-0.2139-0.0476-0.080435.657-25.932-15.28
52.43390.4947-0.06994.76011.52314.8718-0.04890.5805-0.1649-0.22690.0375-0.02930.28720.31810.01140.02770.0164-0.01460.2406-0.0766-0.121729.655-7.617-50.496
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A320 - 483
2X-RAY DIFFRACTION1A1
3X-RAY DIFFRACTION2B320 - 483
4X-RAY DIFFRACTION2B1
5X-RAY DIFFRACTION3D319 - 483
6X-RAY DIFFRACTION3D1
7X-RAY DIFFRACTION4E320 - 483
8X-RAY DIFFRACTION4E1
9X-RAY DIFFRACTION5F322 - 483
10X-RAY DIFFRACTION5F1

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