PDB-2wr5: structure of influenza H2 duck Ontario hemagglutinin

ID or keywords:

Entry

Database: PDB / ID: 2wr5

Title

structure of influenza H2 duck Ontario hemagglutinin

Components

HEMAGGLUTININ

Keywords

VIRAL PROTEIN / GLYCOPROTEIN / ENVELOPE PROTEIN / LIPROPROTEIN

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: 2.65 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 1.3	Oct 23, 2024	Group: Data collection / Database references ...Data collection / Database references / Other / 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 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	2wr5.cif.gz	583.3 KB	Display	PDBx/mmCIF format
PDB format	pdb2wr5.ent.gz	485.5 KB	Display	PDB format
PDBx/mmJSON format	2wr5.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	2wr5_validation.pdf.gz	448.4 KB	Display	wwPDB validaton report
Full document	2wr5_full_validation.pdf.gz	487.7 KB	Display
Data in XML	2wr5_validation.xml.gz	62.3 KB	Display
Data in CIF	2wr5_validation.cif.gz	79.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/wr/2wr5 ftp://data.pdbj.org/pub/pdb/validation_reports/wr/2wr5	HTTPS FTP

-
Related structure data

Related structure data	2wr0C 2wr1C 2wr2C 2wr3C 2wr4C 2wr7C 2wrbC 2wrcC 2wrdC 2wreC 2wrfC 2wrgC 2wrhC C: citing same article (ref.)
Similar structure data	2wrf-1 2wr1-d 4juh-d 4wsv-d 6tzb-d 4lxv-1 5vmf-d 4juk-1 4gxx-d 4juj-d 1jsi-2 6v47-d 4wsu-d 4lkg-1 10697 5xl2-d 6idd-2 2yp9-1 3ubj-1 4w8n-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

-
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

172 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)	86.980, 150.880, 195.560
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: isolated from a natural source / Source: (natural) UNIDENTIFIED INFLUENZA VIRUS / References: UniProt: D0VWP9*PLUS
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 162 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

-
Experiment

Experiment	Method: X-RAY DIFFRACTION

-
Sample preparation

Crystal	Density Matthews: 3.95 Å³/Da / Density % sol: 68.61 % / Description: NONE

-
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: 2.65→30 Å / Num. obs: 69020 / % possible obs: 98.8 % / Observed criterion σ(I): 2.6 / Redundancy: 4.8 % / B_iso Wilson estimate: 78.9 Å² / R_merge(I) obs: 0.07

-
Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.65→29.865 Å / SU ML: 0.37 / σ(F): 1.34 / Phase error: 28.78 / Stereochemistry target values: MLHL

	R_factor	Num. reflection	% reflection
R_free	0.2612	3442	5 %
R_work	0.2265	-	-
obs	0.2282	69020	91.55 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 47.292 Å² / k_sol: 0.287 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-4.1251 Å²	0 Å²	0 Å²
2-	-	5.2515 Å²	0 Å²
3-	-	-	-1.1264 Å²

Refinement step

Cycle: LAST / Resolution: 2.65→29.865 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11442	0	0	162	11604

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	11736
X-RAY DIFFRACTION	f_angle_d	1.147	15885
X-RAY DIFFRACTION	f_dihedral_angle_d	17.49	4215
X-RAY DIFFRACTION	f_chiral_restr	0.097	1719
X-RAY DIFFRACTION	f_plane_restr	0.004	2070

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 (%)
2.6505-2.6868	0.3233	42	0.3187	733	X-RAY DIFFRACTION	26
2.6868-2.7251	0.3346	83	0.335	1381	X-RAY DIFFRACTION	49
2.7251-2.7658	0.4209	94	0.3337	1774	X-RAY DIFFRACTION	63
2.7658-2.809	0.3429	118	0.3225	2221	X-RAY DIFFRACTION	77
2.809-2.855	0.3469	124	0.3245	2481	X-RAY DIFFRACTION	89
2.855-2.9042	0.3852	129	0.3183	2848	X-RAY DIFFRACTION	99
2.9042-2.9569	0.3197	152	0.3226	2801	X-RAY DIFFRACTION	100
2.9569-3.0138	0.3413	139	0.3088	2834	X-RAY DIFFRACTION	100
3.0138-3.0752	0.3234	146	0.3076	2820	X-RAY DIFFRACTION	100
3.0752-3.142	0.3383	152	0.3046	2811	X-RAY DIFFRACTION	100
3.142-3.215	0.3256	160	0.2826	2846	X-RAY DIFFRACTION	100
3.215-3.2953	0.2974	170	0.265	2806	X-RAY DIFFRACTION	100
3.2953-3.3843	0.2821	147	0.2547	2845	X-RAY DIFFRACTION	100
3.3843-3.4837	0.2897	147	0.2537	2872	X-RAY DIFFRACTION	100
3.4837-3.596	0.2859	160	0.2336	2819	X-RAY DIFFRACTION	100
3.596-3.7243	0.242	153	0.2231	2807	X-RAY DIFFRACTION	100
3.7243-3.8731	0.2805	161	0.2097	2879	X-RAY DIFFRACTION	100
3.8731-4.049	0.2254	140	0.1983	2861	X-RAY DIFFRACTION	100
4.049-4.2619	0.2154	143	0.1809	2857	X-RAY DIFFRACTION	100
4.2619-4.5281	0.2109	141	0.1721	2860	X-RAY DIFFRACTION	99
4.5281-4.8763	0.1906	155	0.16	2866	X-RAY DIFFRACTION	99
4.8763-5.3645	0.2195	161	0.1707	2853	X-RAY DIFFRACTION	99
5.3645-6.1349	0.2167	137	0.1769	2899	X-RAY DIFFRACTION	99
6.1349-7.7072	0.2563	147	0.2048	2949	X-RAY DIFFRACTION	99
7.7072-29.8665	0.2464	141	0.2382	2855	X-RAY DIFFRACTION	92

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	1.5632	0.668	1.4447	0.4881	0.6275	2.6781	-0.0114	0.0761	0.1196	0.0245	-0.1122	0.0074	0.292	-0.8129	0.1449	0.3747	-0.2728	0.0688	0.9009	-0.1713	0.361	-62.9917	-2.8939	-34.4785
2	1.5261	0.0439	1.3294	0.2581	0.9809	4.0509	0.0319	0.2717	0.0791	0.054	-0.4183	0.0688	0.0929	-0.6295	0.3403	0.3404	-0.0277	0.0091	0.574	-0.075	0.4139	-49.4734	6.4142	-47.9206
3	0.6424	0.4305	0.8921	0.4779	1.6367	3.5476	0.1118	0.0138	-0.1357	0.4179	-0.1442	-0.1108	0.8841	-0.3709	0.0824	0.6981	-0.3201	0.0356	0.3583	-0.0767	0.4136	-46.4312	-13.7729	-41.7087
4	-0.2951	-0.302	1.2409	0.3181	0.6955	0.9647	-0.1437	-0.0377	-0.131	0.0184	-0.2671	0.2871	-0.0281	-1.3966	0.4482	0.4342	-0.1817	0.0196	1.4951	-0.2456	0.625	-63.9483	7.2285	-25.222
5	1.8263	-0.2617	1.8858	0.8612	1.5732	1.7725	-0.0394	0.7756	0.2589	0.3697	-0.0354	-0.2101	-0.2126	0.5179	0.136	0.5459	-0.1687	-0.0311	0.5752	0.0648	0.34	-36.4339	10.8528	-46.3188
6	0.1625	-1.2042	0.6729	-0.4929	-0.2389	2.5232	0.1836	-0.181	-0.2664	-0.0749	0.2125	-0.2854	1.6172	-0.1789	-0.4139	1.209	-0.3866	-0.1498	0.3689	-0.1103	0.8085	-41.8409	-19.2319	-29.667
7	0.3861	-0.2552	0.4731	0.6753	0.4501	2.8693	0.0806	-0.14	0.2467	-0.2946	0.0583	0.0393	-0.6068	-0.338	-0.1629	0.5222	-0.001	0.0772	0.4091	-0.0228	0.4301	-42.5821	15.9146	12.7438
8	1.1629	0.7798	0.454	-0.8224	2.4252	1.7191	0.0195	0.1094	-0.0376	-0.2894	0.0184	-0.0746	0.022	0.0557	-0.1127	0.382	-0.0821	-0.096	0.2413	0.0018	0.6403	-16.3797	31.8079	-12.6632
9	1.2381	0.9211	0.5944	-0.69	0.1076	1.8785	-0.0298	-0.0219	-0.1891	0.0273	0.1168	0.0281	0.3832	0.0287	-0.1302	0.5738	0.0404	-0.0331	0.4943	0.0719	0.6347	-11.7496	-5.6787	0.2173
10	3.1076	-0.6693	0.9618	4.0254	-0.5624	0.3255	-0.1448	-0.7868	0.0773	0.1925	0.2116	-0.0376	-0.0874	0.1022	-0.05	0.461	-0.0431	0.0715	0.5457	-0.0716	0.2864	-28.847	18.5997	26.3303
11	2.2847	-1.0038	1.1518	1.2599	-0.0069	3.3393	0.1395	-0.1149	0.3405	0.2177	-0.0149	-0.0612	0.0189	0.0525	-0.1299	0.3139	-0.0349	-0.0224	0.2506	-0.1066	0.5463	-10.2241	37.3565	4.9567
12	2.136	1.8266	0.5031	1.602	-0.2547	1.789	0.158	-0.0722	-0.1061	0.1217	-0.1563	-0.111	-0.0705	0.3867	0.0706	0.3467	0.0587	0.0013	0.5488	0.1369	0.3701	-1.4688	5.4119	12.6116
13	2.0015	0.5165	0.9867	0.3527	0.7568	3.1862	-0.1852	-0.1997	-0.1041	0.0244	-0.0535	0.0909	-0.1682	-0.7012	0.2122	0.4225	-0.0472	0.0358	0.4224	-0.0556	0.4074	-47.9794	10.0347	-0.7981
14	0.9691	0.7377	1.0773	0.0396	1.3883	2.1362	-0.1399	0.0788	0.0305	-0.1802	0.0691	0.0609	-0.4776	-0.0089	0.0387	0.5661	-0.0477	-0.111	0.2413	-0.027	0.586	-26.1516	24.3008	-22.4245
15	0.8161	0.5458	0.7581	0.4008	0.1279	1.7876	-0.0292	0.0839	-0.1292	-0.1069	0.0121	-0.0813	0.4757	0.1695	-0.0189	0.6391	-0.0434	-0.0067	0.4658	-0.0229	0.493	-21.5344	-7.4767	-11.967

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

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi