PDB-4b7q: H1N1 2009 Pandemic Influenza Virus: Resistance of the I223R Neura...

ID or keywords:

Entry

Database: PDB / ID: 4b7q

Title

H1N1 2009 Pandemic Influenza Virus: Resistance of the I223R Neuraminidase Mutant Explained by Kinetic and Structural Analysis

Components

NEURAMINIDASE

Keywords

HYDROLASE / NEURAMINIDASE INHIBITOR / NAI / NAIS / OSELTAMIVIR / ANTIVIRAL RESISTANCE

Function / homology

Function and homology information

exo-alpha-(2->3)-sialidase activity / exo-alpha-(2->6)-sialidase activity / exo-alpha-(2->8)-sialidase activity / exo-alpha-sialidase / viral budding from plasma membrane / carbohydrate metabolic process / host cell plasma membrane / virion membrane / membrane / metal ion binding
Similarity search - Function

Biological species

INFLUENZA A VIRUS

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.728 Å

Authors

Liu, J. / van der Vries, E. / Vachieri, S.G. / Xiong, X. / Collins, P.J. / Walker, P.A. / Haire, L.F. / Hay, A.J. / Schutten, M. / Osterhaus, A.D.M.E. ...

Citation

Journal: Plos Pathog. / Year: 2012
Title: H1N1 2009 Pandemic Influenza Virus: Resistance of the I223R Neuraminidase Mutant Explained by Kinetic and Structural Analysis
Authors: Van Der Vries, E. / Collins, P.J. / Vachieri, S.G. / Xiong, X. / Liu, J. / Walker, P.A. / Haire, L.F. / Hay, A.J. / Schutten, M. / Osterhaus, A.D.M.E. / Martin, S.R. / Boucher, C.A.B. / ...

History

Deposition	Aug 21, 2012	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Oct 3, 2012	Provider: repository / Type: Initial release
Revision 1.1	Oct 10, 2012	Group: Database references
Revision 1.2	Jul 29, 2020	Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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 Description: Carbohydrate remediation / Provider: repository / Type: Remediation

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4b7q.cif.gz	600.9 KB	Display	PDBx/mmCIF format
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PDBx/mmJSON format	4b7q.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	4b7q_validation.pdf.gz	1.7 MB	Display	wwPDB validaton report
Full document	4b7q_full_validation.pdf.gz	1.8 MB	Display
Data in XML	4b7q_validation.xml.gz	60.6 KB	Display
Data in CIF	4b7q_validation.cif.gz	82.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/b7/4b7q ftp://data.pdbj.org/pub/pdb/validation_reports/b7/4b7q	HTTPS FTP

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Related structure data

Related structure data	4b7jC 4b7mC 4b7nC 4b7rC C: citing same article (ref.)
Similar structure data	4b7j-1 6d96-1 2hty-2 3cl2-1 3ti4-1 3ti5-1 3cl2-2 6g02-1 3o9j-1 3ti3-1 3cye-1 2hu4-2 2hty-1 4mju-1 5nzn-d 2hu0-1 4ks5-1 4wa4-1 2hu0-2 4ks1-1 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#113 - May 2009 Influenza Neuraminidase similarity (6) #231 - Mar 2019 Measles Virus Proteins similarity (1)

Deposited unit

A: NEURAMINIDASE

B: NEURAMINIDASE

C: NEURAMINIDASE

D: NEURAMINIDASE

hetero molecules

210 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by software

Unit cell

Length a, b, c (Å)	82.650, 148.820, 166.600
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein

NEURAMINIDASE

Mass: 51638.676 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Details: ZANAMIVIR LIGAND BOUND
Source: (natural)

INFLUENZA A VIRUS (A/CALIFORNIA/07/2009(H1N1))
References: UniProt: C7FH46

#2: Sugar

ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose

Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Formula: C₈H₁₅NO₆

Identifier	Type	Program
DGlcpNAcb	CONDENSED IUPAC CARBOHYDRATE SYMBOL	GMML 1.0
N-acetyl-b-D-glucopyranosamine	COMMON NAME	GMML 1.0
b-D-GlcpNAc	IUPAC CARBOHYDRATE SYMBOL	PDB-CARE 1.0
GlcNAc	SNFG CARBOHYDRATE SYMBOL	GMML 1.0

#3: Sugar

ChemComp-ZMR / ZANAMIVIR / MODIFIED SIALIC ACID

Type: D-saccharide / Mass: 332.310 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₂H₂₀N₄O₇ / Comment: medication, inhibitor*YM

#4: Chemical

ChemComp-CA / CALCIUM ION

Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca

#5: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 386 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.48 Å³/Da / Density % sol: 50.39 % / Description: NONE
Crystal grow	Details: 15% PEG3350, 0.1M BIS-TRIS PROPANE AND 0.1M SODIUM ACETATE BUFFER (PH 4.6)

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Data collection

Diffraction	Mean temperature: 77 K
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Type: DIAMOND / Wavelength: 0.9763
Detector	Type: ADSC QUANTUM / Detector: CCD / Date: May 10, 2010
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9763 Å / Relative weight: 1
Reflection	Resolution: 2.73→82.65 Å / Num. obs: 55091 / % possible obs: 99.2 % / Observed criterion σ(I): 2 / Redundancy: 6.8 % / B_iso Wilson estimate: 35.14 Å² / R_merge(I) obs: 0.2 / Net I/σ(I): 6.1
Reflection shell	Resolution: 2.73→2.8 Å / Redundancy: 6.4 % / R_merge(I) obs: 0.54 / Mean I/σ(I) obs: 2.5 / % possible all: 99

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Processing

Software

Name	Version	Classification
PHENIX	(PHENIX.REFINE: 1.8_1069)	refinement
DENZO		data reduction
SCALA		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.728→55.494 Å / SU ML: 0.37 / σ(F): 1.34 / Phase error: 26.03 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2581	2790	5.1 %
R_work	0.174	-	-
obs	0.1783	54976	99.02 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.728→55.494 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11976	0	209	386	12571

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	12548
X-RAY DIFFRACTION	f_angle_d	1.205	17016
X-RAY DIFFRACTION	f_dihedral_angle_d	13.915	4460
X-RAY DIFFRACTION	f_chiral_restr	0.078	1800
X-RAY DIFFRACTION	f_plane_restr	0.005	2200

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.7276-2.7747	0.3154	140	0.1973	2571	X-RAY DIFFRACTION	99
2.7747-2.8251	0.3058	146	0.1912	2525	X-RAY DIFFRACTION	98
2.8251-2.8795	0.3111	161	0.1853	2554	X-RAY DIFFRACTION	99
2.8795-2.9382	0.2899	145	0.1965	2605	X-RAY DIFFRACTION	100
2.9382-3.0021	0.3322	143	0.1893	2565	X-RAY DIFFRACTION	100
3.0021-3.0719	0.3149	123	0.1982	2604	X-RAY DIFFRACTION	99
3.0719-3.1488	0.3105	129	0.1969	2618	X-RAY DIFFRACTION	100
3.1488-3.2339	0.2906	152	0.192	2570	X-RAY DIFFRACTION	100
3.2339-3.329	0.3279	139	0.1939	2603	X-RAY DIFFRACTION	99
3.329-3.4365	0.2663	115	0.1816	2638	X-RAY DIFFRACTION	99
3.4365-3.5593	0.2528	133	0.1748	2589	X-RAY DIFFRACTION	99
3.5593-3.7018	0.2638	141	0.1695	2576	X-RAY DIFFRACTION	99
3.7018-3.8702	0.2426	137	0.1694	2587	X-RAY DIFFRACTION	99
3.8702-4.0742	0.2258	152	0.1588	2572	X-RAY DIFFRACTION	98
4.0742-4.3293	0.228	122	0.1417	2621	X-RAY DIFFRACTION	98
4.3293-4.6635	0.1931	141	0.1477	2597	X-RAY DIFFRACTION	98
4.6635-5.1325	0.218	131	0.1465	2627	X-RAY DIFFRACTION	98
5.1325-5.8744	0.243	145	0.1626	2672	X-RAY DIFFRACTION	100
5.8744-7.3984	0.226	130	0.1815	2697	X-RAY DIFFRACTION	99
7.3984-55.5051	0.2487	165	0.1929	2795	X-RAY DIFFRACTION	99

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	0.0415	-0.1901	-0.1127	0.1442	0.0482	-0.02	0.0415	-0.0076	0.0253	0.0565	-0.0915	-0.1186	0.054	-0.1567	-0.0001	0.3365	-0.006	0.0643	0.2042	0.0082	0.2269	20.0846	12.2881	-29.4714
2	0.0673	-0.0279	0.1753	0.0851	-0.234	0.3171	-0.0432	0.0581	0.0827	0.0434	0.0239	-0.057	-0.1571	-0.0141	-0	0.3148	0.0019	-0.0161	0.1577	0.0249	0.2627	16.4087	27.4726	-34.2121
3	0.0281	-0.0225	0.0493	0.0435	-0.016	0.0826	-0.1741	0.0432	0.1621	0.2193	0.0335	-0.2239	-0.0596	0.4765	-0.005	0.3305	-0.0444	-0.0223	0.2727	-0.0015	0.3241	33.8015	28.3389	-24.2435
4	0.1301	-0.0923	0.1545	0.1216	0.054	0.1309	-0.16	0.0759	0.0927	0.0676	0.1226	-0.1458	-0.0996	0.2722	-0.0042	0.262	-0.0091	0.0066	0.2302	0.0093	0.2383	27.4153	14.7757	-25.2325
5	-0.0445	-0.1193	-0.0843	0.1514	-0.0824	0.0781	0.0144	0.0385	0.0929	0.0233	0.0456	-0.0208	-0.0611	0.0559	0	0.2158	-0.0123	-0.0124	0.2503	0.0219	0.2484	23.2151	-3.1805	-11.571
6	0.2485	0.2831	0.3347	0.1105	0.0192	0.3696	0.0172	-0.0846	0.0118	0.0757	-0.0171	-0.0289	0.008	0.0453	-0	0.1869	0.0172	0.0091	0.2154	-0.0061	0.1902	30.5695	-4.487	1.7981
7	0.0041	-0.032	0.007	0.0377	0.0547	-0.0139	-0.0082	-0.1679	0.1981	0.0212	0.0619	0.0848	0.04	0.0241	0	0.2163	0.0302	0.007	0.2073	-0.0092	0.2681	6.5278	-20.4865	-21.5343
8	0.0184	-0.0255	0.0089	0.0344	0.0022	0.0151	-0.0921	0.0414	0.0712	0.1079	-0.033	-0.0772	0.0227	0.0508	0	0.2196	0.0363	0.0332	0.2107	-0.0019	0.1776	7.6576	-15.2952	-15.4204
9	0.1148	0.0332	-0.0224	0.0334	0.027	0.0367	0.0899	-0.163	-0.0724	0.1654	-0.0809	-0.0281	0.0237	-0.0838	-0.0003	0.2073	0.0064	-0.0013	0.1552	-0.023	0.1921	4.4156	-28.7094	-3.68
10	0.0074	0.0069	-0.0388	0.1073	-0.0802	0.0091	0.1182	-0.1228	-0.079	0.0255	-0.0154	0.0817	0.0329	-0.0704	0.0032	0.1778	-0.0228	0.0256	0.2089	0.0075	0.1777	-5.655	-37.9832	-17.0286
11	0.0802	0.0751	-0.0674	0.066	-0.0543	0.1405	0.1737	0.2674	-0.0761	0.028	0.1601	0.0724	-0.0119	-0.1296	0.0124	0.2953	-0.0233	-0.0063	0.2131	-0.0157	0.3377	-7.5768	-37.1098	-27.7296
12	0.1428	0.1428	-0.0711	0.2507	-0.0838	0.1414	0.1658	0.3835	0.0511	0.0152	-0.0651	-0.0391	0.0557	-0.1676	0.0157	0.2035	0.0174	0.0612	0.2269	0.004	0.1813	1.398	-24.3981	-27.5257
13	0.0127	-0.0005	-0.0614	0.0573	0.0105	0.0246	0.1309	0.1146	-0.0559	0.0205	-0.085	0.0625	-0.038	0.0427	0.0006	0.2037	0.0222	0.0362	0.2297	0.0021	0.1632	2.0972	-2.8124	-39.658
14	0.0181	-0.0711	0.0801	0.0921	-0.1028	0.0469	-0.0891	-0.0577	0.1735	-0.0819	0.068	0.0944	-0.0303	-0.2152	0	0.2292	-0.0478	0.028	0.2767	0.0091	0.2719	-5.6481	-9.4441	-33.1424
15	0.0049	-0.0125	-0.0133	0.0523	-0.0398	0.0235	0.0202	0.2448	0.0419	0.0012	-0.0229	0.0291	-0.1267	-0.0585	0.0001	0.1789	-0.0022	0.0235	0.3593	0.0575	0.2935	-15.3478	-8.866	-41.8576
16	0.014	0.0539	-0.0487	0.2674	0.0711	0.0282	0.0061	0.0068	0.0908	-0.0965	0.0812	0.2241	-0.1582	-0.2404	-0.0031	0.2006	-0.0213	0.044	0.3398	0.0332	0.304	-19.2658	-4.4819	-47.0723
17	0.0358	-0.0176	-0.0351	0.6249	0.3272	0.1822	0.0292	-0.0864	0.047	-0.2835	0.0342	-0.153	-0.1872	-0.0576	0.0735	0.2593	0.0467	-0.0697	0.4011	0.1715	0.2751	-12.7287	0.6416	-60.2212
18	0.0461	0.081	0.015	0.0929	0.026	0.0441	-0.0734	0.201	0.0716	-0.1169	0.0696	0.0625	0.0244	-0.1987	-0.0001	0.2285	-0.0025	0.0013	0.2774	0.0794	0.2295	-5.7583	8.5631	-56.4149
19	0.0784	0.0229	0.0383	-0.0137	0.0117	0.1578	0.0345	-0.0073	0.1926	-0.1816	0.0772	-0.0715	-0.018	-0.0507	0.0002	0.2192	0.0264	0.0233	0.1877	0.0027	0.1864	3.5139	3.5901	-45.5723

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(CHAIN A AND RESID 83:156)
2	X-RAY DIFFRACTION	2	(CHAIN A AND RESID 157:349)
3	X-RAY DIFFRACTION	3	(CHAIN A AND RESID 350:402)
4	X-RAY DIFFRACTION	4	(CHAIN A AND RESID 403:469)
5	X-RAY DIFFRACTION	5	(CHAIN B AND RESID 83:189)
6	X-RAY DIFFRACTION	6	(CHAIN B AND RESID 190:469)
7	X-RAY DIFFRACTION	7	(CHAIN C AND RESID 83:156)
8	X-RAY DIFFRACTION	8	(CHAIN C AND RESID 157:189)
9	X-RAY DIFFRACTION	9	(CHAIN C AND RESID 190:279)
10	X-RAY DIFFRACTION	10	(CHAIN C AND RESID 280:376)
11	X-RAY DIFFRACTION	11	(CHAIN C AND RESID 377:402)
12	X-RAY DIFFRACTION	12	(CHAIN C AND RESID 403:469)
13	X-RAY DIFFRACTION	13	(CHAIN D AND RESID 83:156)
14	X-RAY DIFFRACTION	14	(CHAIN D AND RESID 157:217)
15	X-RAY DIFFRACTION	15	(CHAIN D AND RESID 218:245)
16	X-RAY DIFFRACTION	16	(CHAIN D AND RESID 246:311)
17	X-RAY DIFFRACTION	17	(CHAIN D AND RESID 312:349)
18	X-RAY DIFFRACTION	18	(CHAIN D AND RESID 350:402)
19	X-RAY DIFFRACTION	19	(CHAIN D AND RESID 403:469)

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