PDB-2wr3: structure of influenza H2 duck Ontario hemagglutinin with avian r...

ID or keywords:

Entry

Database: PDB / ID: 2wr3

Title

structure of influenza H2 duck Ontario hemagglutinin with avian receptor

Components

HEMAGGLUTININ

Keywords

VIRAL PROTEIN / GLYCOPROTEIN / LIPOPROTEIN / ENVELOPE PROTEIN

Function / homology

Function and homology information

sialate O-acetylesterase activity / sialate O-acetylesterase / viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / membrane
Similarity search - Function

Biological species

UNIDENTIFIED INFLUENZA VIRUS

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.5 Å

Authors

Liu, J. / Stevens, D.J. / Haire, L.F. / Walker, P.A. / Coombs, P.J. / Russell, R.J. / Gamblin, S.J. / Skehel, J.J.

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: From the Cover: Structures of Receptor Complexes Formed by Hemagglutinins from the Asian Influenza Pandemic of 1957.
Authors: Liu, J. / Stevens, D.J. / Haire, L.F. / Walker, P.A. / Coombs, P.J. / Russell, R.J. / Gamblin, S.J. / Skehel, J.J.

History

Deposition	Aug 29, 2009	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Sep 29, 2009	Provider: repository / Type: Initial release
Revision 1.1	May 8, 2011	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Version format compliance
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 / entity_name_com / 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_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / 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_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.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 Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1	Oct 16, 2024	Group: Data collection / Database references / Structure summary Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2wr3.cif.gz	589.9 KB	Display	PDBx/mmCIF format
PDB format	pdb2wr3.ent.gz	488.3 KB	Display	PDB format
PDBx/mmJSON format	2wr3.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	2wr3_validation.pdf.gz	743.7 KB	Display	wwPDB validaton report
Full document	2wr3_full_validation.pdf.gz	800.3 KB	Display
Data in XML	2wr3_validation.xml.gz	69.6 KB	Display
Data in CIF	2wr3_validation.cif.gz	90.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/wr/2wr3 ftp://data.pdbj.org/pub/pdb/validation_reports/wr/2wr3	HTTPS FTP

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Related structure data

Related structure data	2wr0C 2wr1C 2wr2C 2wr4C 2wr5C 2wr7C 2wrbC 2wrcC 2wrdC 2wreC 2wrfC 2wrgC 2wrhC C: citing same article (ref.)
Similar structure data	2wr0-d 2wr2-d 2wr4-d 3ubj-1 4jum-1 4jug-2 4k67-3 4jul-2 6v47-d 2wrf-2 2wrf-1 6ntf-1 3qqb-1 4n64-2 6ida-1 4lkj-1 3ube-2 4jug-1 4n5k-2 4f3z-d 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	#76 - Apr 2006 Hemagglutinin similarity (5) #170 - Feb 2014 Broadly Neutralizing Antibodies similarity (5) #259 - Jul 2021 Designed Proteins and Citizen Science similarity (5) #62 - Feb 2005 Major Histocompatibility Complex similarity (5) #63 - Mar 2005 T-Cell Receptor similarity (5) #200 - Aug 2016 Quasisymmetry in Icosahedral Viruses similarity (1)

Deposited unit

A: HEMAGGLUTININ

B: HEMAGGLUTININ

C: HEMAGGLUTININ

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	86.687, 148.826, 195.974
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein

HEMAGGLUTININ

Mass: 57350.535 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.)

UNIDENTIFIED INFLUENZA VIRUS / References: UniProt: D0VWP9*PLUS

#2: Polysaccharide

N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose / 3'-sialyl-N-acetyllactosamine

Type: oligosaccharide, Oligosaccharide / Class: Substrate analog / Mass: 674.604 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: 3'-sialyl-N-acetyllactosamine

Descriptor	Type	Program
DNeup5Aca2-3DGalpb1-4DGlcpNAcb1-ROH	Glycam Condensed Sequence	GMML 1.0
WURCS=2.0/3,3,2/[a2122h-1b_1-5_2NCC/3=O][a2112h-1b_1-5][Aad21122h-2a_2-6_5NCC/3=O]/1-2-3/a4-b1_b3-c2	WURCS	PDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-Galp]{[(3+2)][a-D-Neup5Ac]{}}}	LINUCS	PDB-CARE

#3: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 377 / Source method: isolated from a natural source / Formula: H₂O

Has protein modification

Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 3.8 Å³/Da / Density % sol: 67.4 % / Description: NONE

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.979
Detector	Type: ADSC CCD / Detector: CCD
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.979 Å / Relative weight: 1
Reflection	Resolution: 2.5→30 Å / Num. obs: 83440 / % possible obs: 99.8 % / Observed criterion σ(I): 2.5 / Redundancy: 7.3 % / B_iso Wilson estimate: 73.5 Å² / R_merge(I) obs: 0.08

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Processing

Software

Name: PHENIX / Version: (PHENIX.REFINE) / Classification: refinement

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.5→29.908 Å / SU ML: 0.36 / σ(F): 0.04 / Phase error: 28.87 / Stereochemistry target values: MLHL

	R_factor	Num. reflection	% reflection
R_free	0.2564	4186	5 %
R_work	0.2182	-	-
obs	0.2201	83440	94.44 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 65.412 Å² / k_sol: 0.317 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-7.9153 Å²	0 Å²	-0 Å²
2-	-	17.9143 Å²	-0 Å²
3-	-	-	-9.999 Å²

Refinement step

Cycle: LAST / Resolution: 2.5→29.908 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11446	0	45	377	11868

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	11783
X-RAY DIFFRACTION	f_angle_d	1.297	15954
X-RAY DIFFRACTION	f_dihedral_angle_d	19.565	4245
X-RAY DIFFRACTION	f_chiral_restr	0.1	1734
X-RAY DIFFRACTION	f_plane_restr	0.005	2073

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 (%)
2.5-2.5284	0.3637	115	0.3423	2171	X-RAY DIFFRACTION	78
2.5284-2.5581	0.3604	140	0.3212	2252	X-RAY DIFFRACTION	82
2.5581-2.5893	0.3418	135	0.3234	2339	X-RAY DIFFRACTION	86
2.5893-2.6221	0.3587	108	0.32	2396	X-RAY DIFFRACTION	85
2.6221-2.6565	0.3827	128	0.3264	2379	X-RAY DIFFRACTION	86
2.6565-2.6929	0.3501	125	0.3165	2448	X-RAY DIFFRACTION	88
2.6929-2.7314	0.3325	128	0.3099	2420	X-RAY DIFFRACTION	89
2.7314-2.7721	0.3223	127	0.3056	2515	X-RAY DIFFRACTION	91
2.7721-2.8154	0.3453	128	0.3026	2586	X-RAY DIFFRACTION	92
2.8154-2.8615	0.3078	151	0.2934	2557	X-RAY DIFFRACTION	93
2.8615-2.9108	0.3367	135	0.3036	2605	X-RAY DIFFRACTION	94
2.9108-2.9637	0.3288	128	0.2942	2633	X-RAY DIFFRACTION	95
2.9637-3.0206	0.327	127	0.2865	2673	X-RAY DIFFRACTION	95
3.0206-3.0822	0.2941	130	0.2849	2663	X-RAY DIFFRACTION	96
3.0822-3.1492	0.3066	143	0.2737	2677	X-RAY DIFFRACTION	97
3.1492-3.2224	0.2962	127	0.2733	2768	X-RAY DIFFRACTION	98
3.2224-3.3029	0.3106	136	0.262	2739	X-RAY DIFFRACTION	98
3.3029-3.392	0.268	159	0.2521	2720	X-RAY DIFFRACTION	99
3.392-3.4917	0.2907	152	0.2459	2752	X-RAY DIFFRACTION	99
3.4917-3.6042	0.2483	178	0.2239	2740	X-RAY DIFFRACTION	99
3.6042-3.7328	0.2616	160	0.205	2743	X-RAY DIFFRACTION	99
3.7328-3.882	0.2273	155	0.1878	2742	X-RAY DIFFRACTION	99
3.882-4.0582	0.2236	159	0.1797	2767	X-RAY DIFFRACTION	99
4.0582-4.2716	0.2003	143	0.1698	2799	X-RAY DIFFRACTION	99
4.2716-4.5384	0.2005	155	0.1542	2819	X-RAY DIFFRACTION	99
4.5384-4.8874	0.1895	151	0.1502	2792	X-RAY DIFFRACTION	100
4.8874-5.3767	0.1983	137	0.1594	2845	X-RAY DIFFRACTION	99
5.3767-6.1488	0.2116	163	0.1726	2843	X-RAY DIFFRACTION	100
6.1488-7.7247	0.2954	126	0.1985	2909	X-RAY DIFFRACTION	100
7.7247-29.9102	0.2185	137	0.2009	2962	X-RAY DIFFRACTION	98

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	1.393	-0.4082	1.166	0.3244	-0.7224	2.037	-0.0081	0.0568	0.1806	-0.0729	-0.3254	-0.1374	0.1907	0.676	0.3106	0.4139	0.1925	0.0719	0.7724	0.178	0.4641	63.1183	-2.6751	34.9907
2	1.1969	-0.1846	1.1235	0.5025	-1.0217	3.1116	0.0374	-0.1815	0.0608	0.0071	-0.3718	-0.0995	-0.0096	0.4621	0.3465	0.3966	-0.003	0.0074	0.5973	0.0897	0.449	49.5254	6.5473	48.2163
3	0.7813	-0.6309	0.7994	0.4078	-1.5272	1.6997	-0.0038	-0.1195	-0.1199	-0.296	-0.1059	0.1132	0.2953	0.0653	0.1174	0.6509	0.1873	0.0396	0.4186	0.1089	0.4973	46.748	-13.4848	42.1489
4	0.0093	-0.2369	0.8993	0.0025	-0.7454	1.2806	-0.2246	-0.1222	-0.1169	0.0215	-0.2507	-0.3124	-0.0858	0.8344	0.5861	0.364	0.087	0.0076	1.0734	0.2111	0.5425	63.982	7.286	25.6551
5	1.9116	-0.8537	1.6561	1.0488	-2.049	0.6899	-0.1919	-0.7211	0.1204	-0.2017	0.0716	0.0062	-0.2056	-0.5276	0.0185	0.6001	0.1148	-0.0286	0.5866	-0.0418	0.3364	36.5132	10.8683	46.4632
6	0.2607	0.4855	0.8446	-1.4017	0.072	1.5183	-0.0454	0.0915	-0.3838	0.0478	0.1117	0.3156	1.0897	0.2045	-0.0718	1.0401	0.2276	-0.046	0.2557	0.0889	0.6227	42.1951	-19.0549	30.2173
7	-0.009	-0.2687	-0.0738	0.745	-0.1316	2.0901	0.0398	0.1957	-0.1302	0.0893	-0.0765	0.0144	-0.0743	0.2359	0.0136	0.4605	0.0175	0.0344	0.5126	-0.0088	0.4431	42.673	15.4025	-12.4806
8	1.3248	-0.8952	0.8169	0.3295	-1.8753	1.1254	-0.1769	-0.1419	-0.1462	-0.0214	0.2541	0.0704	-0.054	-0.1196	-0.0267	0.4261	0.0452	-0.0444	0.3574	0.0028	0.5115	16.5142	31.4438	12.6695
9	0.4918	-1.0702	0.1252	-0.8834	0.5956	1.5409	0.0613	0.1072	-0.1838	0.1677	0.1153	0.1375	0.6745	-0.0348	-0.1888	0.6721	-0.0787	-0.0582	0.4789	-0.0703	0.6643	11.8018	-5.8612	0.2305
10	1.4384	0.7207	0.1885	3.1786	0.5902	-0.2641	-0.1392	0.404	-0.0422	-0.185	0.2544	0.0531	0.0278	0.0104	-0.1214	0.4087	0.0054	0.031	0.4631	0.0128	0.2938	28.6756	18.2399	-25.786
11	1.2106	-0.0042	0.6752	0.4252	-0.6616	1.5616	0.1264	-0.0503	0.279	-0.059	-0.0218	0.0491	-0.0592	-0.1234	-0.0661	0.3892	0.0103	0.0007	0.3468	0.0379	0.5006	10.3919	36.9925	-4.9905
12	1.1639	-1.6323	1.0016	1.6086	-0.1735	1.2323	0.1744	0.0938	-0.06	-0.093	-0.0682	0.1093	0.0067	-0.3568	-0.0378	0.3977	-0.1102	-0.0012	0.523	-0.1382	0.4664	1.4733	5.0964	-12.2713
13	1.1363	0.0605	1.4139	0.1761	-0.3231	2.2519	-0.1922	0.1814	-0.1613	-0.004	0.0162	-0.0294	-0.1539	0.3241	0.1431	0.502	0.0858	0.0535	0.6097	0.0302	0.502	47.9278	9.7178	1.1514
14	0.8778	-0.1667	0.5039	-0.1213	-0.4329	1.0767	-0.0635	-0.1402	0.0749	0.0093	0.0102	-0.0558	-0.1722	-0.0441	0.0632	0.4799	0.0312	-0.0705	0.2914	-0.0119	0.4659	26.2919	24.0163	22.4345
15	1.2605	-0.4003	1.0457	-0.0809	0.1063	1.5275	0.0746	0.1097	-0.3077	0.149	-0.0559	0.1781	0.3462	0.1173	-0.0445	0.6676	-0.02	0.0026	0.4463	0.0455	0.5836	21.667	-7.499	12.3908

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN A AND RESID 330:492
2	X-RAY DIFFRACTION	2	CHAIN B AND RESID 330:492
3	X-RAY DIFFRACTION	3	CHAIN C AND RESID 330:492
4	X-RAY DIFFRACTION	4	CHAIN A AND RESID 5:49
5	X-RAY DIFFRACTION	5	CHAIN B AND RESID 5:49
6	X-RAY DIFFRACTION	6	CHAIN C AND RESID 5:49
7	X-RAY DIFFRACTION	7	CHAIN A AND RESID 50:113
8	X-RAY DIFFRACTION	8	CHAIN B AND RESID 50:113
9	X-RAY DIFFRACTION	9	CHAIN C AND RESID 50:113
10	X-RAY DIFFRACTION	10	CHAIN A AND RESID 114-240
11	X-RAY DIFFRACTION	11	CHAIN B AND RESID 114-240
12	X-RAY DIFFRACTION	12	CHAIN C AND RESID 114-240
13	X-RAY DIFFRACTION	13	CHAIN A AND RESID 241-323
14	X-RAY DIFFRACTION	14	CHAIN B AND RESID 241-323
15	X-RAY DIFFRACTION	15	CHAIN C AND RESID 241-323

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