PDB-2w69: Influenza polymerase fragment

ID or keywords:

Entry

Database: PDB / ID: 2w69

Title

Influenza polymerase fragment

Components

POLYMERASE ACIDIC PROTEIN

Keywords

TRANSCRIPTION / RNA-DEPENDENT / RNA POLYMERASE

Function / homology

Function and homology information

cap snatching / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / endonuclease activity / host cell cytoplasm / Hydrolases; Acting on ester bonds / viral translational frameshifting / viral RNA genome replication / DNA-templated transcription / host cell nucleus / RNA binding / metal ion binding
Similarity search - Function

Biological species

INFLUENZA A VIRUS

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.05 Å

Authors

Dias, A. / Bouvier, D. / Crepin, T. / McCarthy, A.A. / Hart, D.J. / Baudin, F. / Cusack, S. / Ruigrok, R.W.H.

Citation

Journal: Nature / Year: 2009
Title: The CAP-Snatching Endonuclease of Influenza Virus Polymerase Resides in the Pa Subunit
Authors: Dias, A. / Bouvier, D. / Crepin, T. / Mccarthy, A.A. / Hart, D.J. / Baudin, F. / Cusack, S. / Ruigrok, R.W.H.

History

Deposition	Dec 17, 2008	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Feb 3, 2009	Provider: repository / Type: Initial release
Revision 1.1	Jun 30, 2011	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Version format compliance
Revision 1.3	May 8, 2024	Group: 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_struct_conn_angle / 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_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.ptnr1_symmetry / _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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _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

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	2w69.cif.gz	255.8 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	2w69_validation.pdf.gz	460.2 KB	Display	wwPDB validaton report
Full document	2w69_full_validation.pdf.gz	465.6 KB	Display
Data in XML	2w69_validation.xml.gz	24 KB	Display
Data in CIF	2w69_validation.cif.gz	33.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/w6/2w69 ftp://data.pdbj.org/pub/pdb/validation_reports/w6/2w69	HTTPS FTP

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Related structure data

Similar structure data	5lsv-d 4ueb-3 4o7v-d 4bq1-1 1aoe-2 4o7n-d 5gig-d 3dl0-2 3mbr-d 2yeg-2 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#40 - Apr 2003 RNA Polymerase similarity (1)

Deposited unit

A: POLYMERASE ACIDIC PROTEIN

B: POLYMERASE ACIDIC PROTEIN

D: POLYMERASE ACIDIC PROTEIN

hetero molecules

76.9 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: POLYMERASE ACIDIC PROTEIN

hetero molecules

defined by author&software
25.6 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: POLYMERASE ACIDIC PROTEIN

hetero molecules

defined by author&software
25.6 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

D: POLYMERASE ACIDIC PROTEIN

hetero molecules

defined by author&software
25.7 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	67.130, 67.130, 302.950
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	96
Space group name H-M	P4₃2₁2

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
1	2	B
2	2	D

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Refine code	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	1	MET	MET	CYS	CYS	1	A	A	1 - 8	8 - 15
2	1	1	MET	MET	CYS	CYS	1	B	B	1 - 8	8 - 15
1	2	1	MET	MET	ALA	ALA	1	A	A	12 - 17	19 - 24
2	2	1	MET	MET	ALA	ALA	1	B	B	12 - 17	19 - 24
1	3	1	ASN	ASN	CYS	CYS	1	A	A	33 - 45	40 - 52
2	3	1	ASN	ASN	CYS	CYS	1	B	B	33 - 45	40 - 52
1	4	1	TYR	TYR	ARG	ARG	1	A	A	110 - 116	117 - 123
2	4	1	TYR	TYR	ARG	ARG	1	B	B	110 - 116	117 - 123
1	5	1	VAL	VAL	LEU	LEU	1	A	A	122 - 132	129 - 139
2	5	1	VAL	VAL	LEU	LEU	1	B	B	122 - 132	129 - 139
1	6	1	HIS	HIS	PHE	PHE	1	A	A	144 - 150	151 - 157
2	6	1	HIS	HIS	PHE	PHE	1	B	B	144 - 150	151 - 157
1	7	1	GLU	GLU	LEU	LEU	1	A	A	154 - 163	161 - 170
2	7	1	GLU	GLU	LEU	LEU	1	B	B	154 - 163	161 - 170
1	8	1	ARG	ARG	ARG	ARG	1	A	A	174 - 192	181 - 199
2	8	1	ARG	ARG	ARG	ARG	1	B	B	174 - 192	181 - 199
1	1	2	ASN	ASN	CYS	CYS	2	B	B	33 - 45	40 - 52
2	1	2	ASN	ASN	CYS	CYS	2	D	C	33 - 45	40 - 52
1	2	2	GLY	GLY	GLU	GLU	2	B	B	121 - 133	128 - 140
2	2	2	GLY	GLY	GLU	GLU	2	D	C	121 - 133	128 - 140
1	3	2	HIS	HIS	PHE	PHE	2	B	B	144 - 150	151 - 157
2	3	2	HIS	HIS	PHE	PHE	2	D	C	144 - 150	151 - 157
1	4	2	TYR	TYR	ASP	ASP	2	B	B	161 - 164	168 - 171
2	4	2	TYR	TYR	ASP	ASP	2	D	C	161 - 164	168 - 171
1	5	2	ARG	ARG	ALA	ALA	2	B	B	168 - 183	175 - 190
2	5	2	ARG	ARG	ALA	ALA	2	D	C	168 - 183	175 - 190

NCS ensembles :

ID
1
2

NCS oper:

ID	Code	Matrix	Vector
1	given	(0.999084, 0.018206, -0.038729), (0.042701, -0.483982, 0.874036), (-0.002831, -0.874889, -0.484316)	-19.164, -38.382, 171.137
2	given	(0.996557, -0.082915, 0.000361), (-0.040548, -0.491132, -0.870141), (0.072325, 0.86713, -0.492802)	24.6072, 129.4225, 117.8326

#1: Protein	POLYMERASE ACIDIC PROTEIN / INFLUENZA POLYMERASE PA SUBUNIT / RNA-DIRECTED RNA POLYMERASE SUBUNIT P2 Mass: 25300.637 Da / Num. of mol.: 3 / Fragment: N-TERMINAL DOMAIN, RESIDUES 1-209 Source method: isolated from a genetically manipulated source Source: (gene. exp.) INFLUENZA A VIRUS / Strain: A/VICTORIA/3/1975 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): RIL CODONPLUS / References: UniProt: P31343
#2: Chemical	ChemComp-MN / MANGANESE (II) ION Mass: 54.938 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mn
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO₄
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 151 / Source method: isolated from a natural source / Formula: H₂O
Sequence details	ADDITIONAL GMGSGMA AT N-TERMINUS

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.35 Å³/Da / Density % sol: 47.7 % / Description: NONE
Crystal grow	pH: 8 Details: PROTEIN SOLUTION WAS AT 5-10 MG.ML-1 IN 20 MM TRIS-HCL PH 8.0, 100 MM NACL, 2.5 MM MNCL2. THE RESERVOIR COMPOSITION WAS 100 MM MES PH 6.0, 1.2 M LI2SO4, 10 MM MG ACETATE, 3 % ETHYLENE GLYCOL.

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9755
Detector	Type: ADSC CCD / Detector: CCD / Date: Nov 8, 2008
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9755 Å / Relative weight: 1
Reflection	Resolution: 2.05→50 Å / Num. obs: 41831 / % possible obs: 93.2 % / Observed criterion σ(I): 0 / Redundancy: 4.84 % / R_merge(I) obs: 0.06 / Net I/σ(I): 17.6
Reflection shell	Resolution: 2.05→2.1 Å / Redundancy: 5.64 % / R_merge(I) obs: 0.69 / Mean I/σ(I) obs: 2.2 / % possible all: 99.4

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Processing

Software

Name	Version	Classification
XDS		data reduction
XSCALE		data scaling
SHELXD		phasing
SHARP		phasing
REFMAC	5.2.0019	refinement

Refinement

Method to determine structure:

SAD
Starting model: NONE

Resolution: 2.05→75.81 Å / Cor.coef. F_o:F_c: 0.943 / Cor.coef. F_o:F_c free: 0.914 / SU B: 11.611 / SU ML: 0.156 / Cross valid method: THROUGHOUT / ESU R: 0.231 / ESU R Free: 0.201 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.268	2118	5.1 %	RANDOM
R_work	0.217	-	-	-
obs	0.22	39713	93.2 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 45.8 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.36 Å²	0 Å²	0 Å²
2-	-	-0.36 Å²	0 Å²
3-	-	-	0.71 Å²

Refinement step

Cycle: LAST / Resolution: 2.05→75.81 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4721	0	45	151	4917

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.022	4869
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	3354
X-RAY DIFFRACTION	r_angle_refined_deg	1.363	1.946	6555
X-RAY DIFFRACTION	r_angle_other_deg	0.981	3	8117
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.789	5	573
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.576	23.977	259
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.069	15	895
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.457	15	37
X-RAY DIFFRACTION	r_chiral_restr	0.081	0.2	701
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	5348
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	1043
X-RAY DIFFRACTION	r_nbd_refined	0.215	0.2	1019
X-RAY DIFFRACTION	r_nbd_other	0.194	0.2	3369
X-RAY DIFFRACTION	r_nbtor_refined	0.178	0.2	2308
X-RAY DIFFRACTION	r_nbtor_other	0.084	0.2	2563
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.18	0.2	179
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.239	0.2	25
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.274	0.2	50
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.192	0.2	5
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	1.59	2	3179
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	2.247	3	4635
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	1.426	2	2210
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	1.974	3	1918
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-ID	Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	1	A	1143	tight positional	0.06	0.05
1	2	B	1143	tight positional	0.06	0.05
2	1	B	317	tight positional	0.04	0.05
2	2	D	317	tight positional	0.04	0.05
2	1	B	443	medium positional	0.24	0.5
2	2	D	443	medium positional	0.24	0.5
1	1	A	1143	tight thermal	0.17	0.5
1	2	B	1143	tight thermal	0.17	0.5
2	1	B	317	tight thermal	0.18	0.5
2	2	D	317	tight thermal	0.18	0.5
2	1	B	443	medium thermal	0.69	2
2	2	D	443	medium thermal	0.69	2

LS refinement shell

Resolution: 2.05→2.1 Å / Total num. of bins used: 20 /

	R_factor	Num. reflection
R_free	0.32	169
R_work	0.278	3094

Refinement TLS params.

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

ID	L11 (°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)
1	2.6068	1.0612	0.015	2.0135	-0.1527	2.5508	-0.1001	0.2362	-0.0361	-0.1237	0.1658	0.0784	0.083	-0.25	-0.0657	0.034	-0.0193	0.0298	0.132	0.0543	-0.0452	0.438	31.922	84.534
2	2.8576	0.1958	-0.8397	2.1021	-0.3874	3.1067	0.0073	-0.2765	0.2133	0.0189	0.088	-0.1481	0.0012	0.2691	-0.0953	0.0404	0.021	0.0303	0.0842	-0.0277	-0.0604	22.539	42.142	102.741
3	2.5483	0.0117	0.0498	2.0767	0.6732	8.2665	-0.2912	-0.3117	-0.2484	0.2341	-0.4001	-0.1232	0.6684	-0.3291	0.6913	0.157	-0.0869	0.111	0.1217	-0.016	0.1402	-22.477	20.893	102.372

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	0 - 196
2	X-RAY DIFFRACTION	1	A	301 - 402
3	X-RAY DIFFRACTION	2	B	0 - 196
4	X-RAY DIFFRACTION	2	B	301 - 403
5	X-RAY DIFFRACTION	3	D	0 - 196
6	X-RAY DIFFRACTION	3	D	301 - 403

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