PDB-4b7r: H1N1 2009 Pandemic Influenza Virus: Resistance of the I223R Neura...

ID or keywords:

Entry

Database: PDB / ID: 4b7r

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 /

ZANAMIVIR / RESISTANCE / 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: 1.9 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 17, 2013	Group: Atomic model / Derived calculations / Non-polymer description
Revision 2.0	Jul 29, 2020	Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Structure summary Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_asym / struct_conn / struct_site / struct_site_gen Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _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.ptnr2_label_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.value / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _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	4b7r.cif.gz	611.8 KB	Display	PDBx/mmCIF format
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PDBx/mmJSON format	4b7r.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/b7/4b7r ftp://data.pdbj.org/pub/pdb/validation_reports/b7/4b7r	HTTPS FTP

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Related structure data

Related structure data	4b7jC 4b7mC 4b7nC 4b7qC C: citing same article (ref.)
Similar structure data	4b7m-1 5nzf-d 5nz4-2 5nze-1 5hug-1 6g02-2 6g02-1 5nwe-d 4b7j-1 4b7n-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) #226 - Oct 2018 Aminoglycoside Antibiotics and Resistance similarity (1) #231 - Mar 2019 Measles Virus Proteins similarity (1)

Deposited unit

A: NEURAMINIDASE

B: NEURAMINIDASE

C: NEURAMINIDASE

D: NEURAMINIDASE

hetero molecules

176 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

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Protein , 1 types, 4 molecules ABCD

#1: Protein	NEURAMINIDASE / Mass: 42640.551 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Details: OSELTAMIVIR LIGAND BOUND Source: (natural) INFLUENZA A VIRUS (A/CALIFORNIA/07/2009(H1N1)) References: UniProt: C7FH46

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Sugars , 2 types, 13 molecules

#2: Polysaccharide

2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

Type: oligosaccharide

/ Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source

Descriptor	Type	Program
DGlcpNAcb1-4DGlcpNAcb1-	Glycam Condensed Sequence	GMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1	WURCS	PDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}	LINUCS	PDB-CARE

#6: Sugar

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

N-Acetylglucosamine

Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 12
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

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Non-polymers , 4 types, 972 molecules

#3: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#4: Chemical	ChemComp-G39 / (3R,4R,5S)-4-(acetylamino)-5-amino-3-(pentan-3-yloxy)cyclohex-1-ene-1-carboxylic acid / Oseltamivir carboxylate / Oseltamivir Mass: 284.351 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₄H₂₄N₂O₄ / Comment: medication, antivirus*YM
#5: Chemical	ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES Mass: 238.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₈H₁₈N₂O₄S / Comment: pH buffer*YM
#7: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 956 / Source method: isolated from a natural source / Formula: H₂O

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Details

Sequence details	RESIDUES 1-82 WERE PROTEOLYTICALY CLEAVED USING BROMELAIN DURING PURIFICATION

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.05 Å³/Da / Density % sol: 59.66 % / 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 / Beamline: I02 / Wavelength: 0.9795
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 24, 2010
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9795 Å / Relative weight: 1
Reflection	Resolution: 1.9→30 Å / Num. obs: 163254 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 6.4 % / B_iso Wilson estimate: 28.07 Å² / R_merge(I) obs: 0.12 / Net I/σ(I): 13.5
Reflection shell	Resolution: 1.9→1.99 Å / Redundancy: 4.8 % / R_merge(I) obs: 0.73 / Mean I/σ(I) obs: 3 / % possible all: 98

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Processing

Software

Name	Version	Classification
PHENIX	(PHENIX.REFINE)	refinement
DENZO		data reduction
SCALEPACK		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.9→29.818 Å / SU ML: 0.17 / σ(F): 100 / Phase error: 17.4 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1732	8184	5 %
R_work	0.1457	-	-
obs	0.1471	163045	99.66 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 34.056 Å² / k_sol: 0.353 e/Å³

Displacement parameters

B_iso mean: 28.6 Å²

Refinement step

Cycle: LAST / Resolution: 1.9→29.818 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11976	0	344	956	13276

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	12685
X-RAY DIFFRACTION	f_angle_d	1.19	17201
X-RAY DIFFRACTION	f_dihedral_angle_d	14.779	4571
X-RAY DIFFRACTION	f_chiral_restr	0.087	1817
X-RAY DIFFRACTION	f_plane_restr	0.005	2206

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 (%)
1.9-1.9216	0.3045	229	0.3005	4844	X-RAY DIFFRACTION	94
1.9216-1.9442	0.2647	259	0.2259	5024	X-RAY DIFFRACTION	98
1.9442-1.9679	0.2504	268	0.2038	5041	X-RAY DIFFRACTION	99
1.9679-1.9928	0.1979	245	0.183	5180	X-RAY DIFFRACTION	100
1.9928-2.019	0.2238	261	0.1756	5112	X-RAY DIFFRACTION	100
2.019-2.0467	0.2076	267	0.1731	5130	X-RAY DIFFRACTION	100
2.0467-2.0759	0.225	277	0.1805	5142	X-RAY DIFFRACTION	100
2.0759-2.1069	0.2115	236	0.1621	5179	X-RAY DIFFRACTION	100
2.1069-2.1398	0.195	270	0.1482	5141	X-RAY DIFFRACTION	100
2.1398-2.1749	0.1719	251	0.1489	5133	X-RAY DIFFRACTION	100
2.1749-2.2124	0.1862	280	0.1557	5139	X-RAY DIFFRACTION	100
2.2124-2.2526	0.227	302	0.1924	5143	X-RAY DIFFRACTION	100
2.2526-2.2959	0.1979	271	0.1631	5099	X-RAY DIFFRACTION	100
2.2959-2.3427	0.1938	280	0.1495	5156	X-RAY DIFFRACTION	100
2.3427-2.3936	0.1857	283	0.1453	5129	X-RAY DIFFRACTION	100
2.3936-2.4493	0.1916	304	0.1459	5146	X-RAY DIFFRACTION	100
2.4493-2.5105	0.1792	289	0.147	5141	X-RAY DIFFRACTION	100
2.5105-2.5784	0.1793	307	0.1459	5103	X-RAY DIFFRACTION	100
2.5784-2.6542	0.192	271	0.1474	5158	X-RAY DIFFRACTION	100
2.6542-2.7398	0.176	241	0.1511	5204	X-RAY DIFFRACTION	100
2.7398-2.8377	0.1777	276	0.1455	5183	X-RAY DIFFRACTION	100
2.8377-2.9512	0.1958	290	0.1457	5181	X-RAY DIFFRACTION	100
2.9512-3.0854	0.1618	274	0.138	5175	X-RAY DIFFRACTION	100
3.0854-3.2478	0.1728	273	0.1405	5192	X-RAY DIFFRACTION	100
3.2478-3.451	0.1571	266	0.1348	5236	X-RAY DIFFRACTION	100
3.451-3.717	0.1501	268	0.13	5232	X-RAY DIFFRACTION	100
3.717-4.0903	0.1393	291	0.1219	5204	X-RAY DIFFRACTION	100
4.0903-4.6802	0.1314	253	0.1132	5318	X-RAY DIFFRACTION	100
4.6802-5.8891	0.1529	308	0.1324	5296	X-RAY DIFFRACTION	100
5.8891-29.8221	0.1758	294	0.1632	5500	X-RAY DIFFRACTION	100

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	0.4863	0.0236	0.267	0.6021	-0.0983	0.5109	-0.0241	-0.005	0.0791	0.0593	-0.0192	-0.0454	-0.115	0.0262	0.0604	0.2237	-0.0032	0.0119	0.208	0.0218	0.2328	20.1654	12.3301	-29.5125
2	0.7447	-0.0888	0.3222	0.4948	-0.0719	0.8443	-0.0797	0.0127	0.2013	0.0636	-0.0303	-0.0698	-0.299	0.0555	0.11	0.3012	0.0014	-0.0224	0.1828	0.0349	0.2622	16.5206	27.5103	-34.2489
3	0.7499	0.1521	0.097	1.0115	0.0537	1.133	-0.0299	0.005	0.2924	0.1033	-0.0561	-0.3209	-0.4	0.2746	0.0696	0.3623	-0.09	-0.0752	0.2709	0.0453	0.3634	33.9933	28.377	-24.2802
4	0.6247	0.0347	0.6	0.6053	-0.1901	0.6625	-0.0837	0.0046	0.1156	0.0894	0.0402	-0.1267	-0.1354	0.1674	0.0526	0.237	-0.0238	-0.008	0.1986	0.0339	0.2417	27.5312	14.8155	-25.2962
5	0.2995	-0.02	0.0862	0.604	-0.0001	0.4413	-0.0311	0.0437	0.0521	0.0171	-0.0017	0.0269	-0.0641	-0.0135	0.0245	0.2003	0.01	-0.0105	0.2198	0.0015	0.2124	23.334	-3.1573	-11.5442
6	0.4644	0.0553	0.2386	0.456	0.0288	0.8541	-0.0279	-0.0016	0.0431	0.1009	-0.0121	-0.0714	-0.0231	0.073	0.0387	0.1863	0.0111	-0.0092	0.1801	-0.0066	0.1784	30.7506	-4.5194	1.8146
7	0.5412	0.3152	0.3383	0.4854	-0.0678	0.4449	-0.0058	-0.0432	0.0417	0.0347	-0.0057	0.0364	-0.0049	-0.0469	0.0056	0.184	0.0172	0.0242	0.1888	-0.0167	0.1865	6.5886	-20.4943	-21.4465
8	0.4991	0.0165	0.0275	0.1681	0.1067	0.3699	-0.0687	0.0525	0.0762	0.0566	-0.0354	0.0711	-0.029	-0.1464	0.0907	0.216	0.0104	0.0131	0.2145	-0.0103	0.2302	7.7836	-15.3185	-15.3532
9	0.594	0.1932	0.0123	0.5828	0.1051	0.4978	0.0589	-0.0935	-0.0166	0.1528	-0.0334	0.0592	0.0958	-0.1035	-0.0307	0.2448	-0.0097	0.0178	0.2098	-0.0003	0.1852	4.5403	-28.7159	-3.6097
10	0.6167	0.2718	0.4018	0.6595	-0.1403	0.6563	0.063	-0.0476	-0.0771	0.0866	-0.0219	0.0808	0.1699	-0.1048	-0.0407	0.2133	-0.0268	0.0208	0.1715	-0.0012	0.1815	-5.6377	-38.0229	-17.0224
11	0.7388	0.4273	-0.0904	0.7903	-0.3268	0.9203	-0.0789	0.2133	-0.183	-0.0706	0.0824	0.0637	0.1593	-0.1817	0.0141	0.2413	-0.0202	0.014	0.2388	-0.0431	0.2401	-7.5842	-37.0855	-27.6917
12	0.5796	0.2867	0.3622	0.7389	-0.3804	1.0676	0.0347	0.0952	0.0066	-0.0054	-0.0126	0.006	0.0508	-0.0636	-0.0301	0.1874	-0.0067	0.0095	0.169	-0.0153	0.1747	1.472	-24.3875	-27.4426
13	0.3111	0.186	0.0565	0.5806	-0.2867	0.3885	0.0005	-0.0095	0.0121	-0.0044	-0.002	0.0352	-0.0396	-0.0533	0.0039	0.2124	0.0285	0.0127	0.2362	0.0028	0.1901	2.0909	-2.8327	-39.7167
14	0.3474	-0.0189	-0.0816	0.5168	-0.3832	0.4684	0.0153	-0.0102	0.1031	0.033	0.0231	0.0471	-0.0309	-0.0533	-0.0613	0.2134	0.0201	0.0186	0.2337	-0.0005	0.2202	-5.662	-9.3997	-33.1433
15	0.8322	-0.3466	-0.5024	1.5641	0.331	1.0681	0.0524	0.0027	0.0878	0.0186	0.017	0.2311	-0.0629	-0.3186	-0.0497	0.1745	0.0131	0.0041	0.2713	0.0261	0.2373	-15.3422	-8.907	-41.9254
16	0.4703	0.0379	0.0039	0.6633	-0.244	0.5911	0.0043	-0.031	0.0471	0.0046	0.0733	0.2234	-0.0674	-0.2782	-0.0681	0.1999	0.0122	0.0063	0.3285	0.0368	0.2886	-19.1907	-4.4719	-47.1605
17	0.8083	0.3729	-0.1332	0.7886	-0.5211	0.7103	-0.0342	0.3338	0.0478	-0.2188	0.0293	0.1117	0.0055	-0.2128	-0.0276	0.2253	0.0301	-0.0236	0.3553	0.0375	0.2516	-12.6082	0.733	-60.3692
18	0.9846	0.0122	-0.0996	0.6768	0.1412	0.5111	-0.0162	0.3217	0.1629	-0.1387	0.0086	0.083	-0.1301	-0.1375	0.0174	0.2132	0.0473	0.0019	0.25	0.0531	0.2088	-5.6462	8.6073	-56.5159
19	0.7331	0.2956	0.3325	0.8279	-0.2988	0.5901	0.0449	0.0602	0.1126	-0.0995	-0.0166	-0.0078	-0.0728	-0.0031	-0.0356	0.1989	0.0201	0.0156	0.2125	0.0237	0.1747	3.5273	3.5855	-45.6374

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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