PDB-2wr4: structure of influenza H2 duck Ontario hemagglutinin with human r...

ID or keywords:

Entry

Database: PDB / ID: 2wr4

Title

structure of influenza H2 duck Ontario hemagglutinin with human receptor

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: 2.5 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.Cartn_x / _atom_site.Cartn_y ..._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 23, 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

-
Download

PDBx/mmCIF format	2wr4.cif.gz	594.2 KB	Display	PDBx/mmCIF format
PDB format	pdb2wr4.ent.gz	491.3 KB	Display	PDB format
PDBx/mmJSON format	2wr4.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	2wr4_validation.pdf.gz	903.1 KB	Display	wwPDB validaton report
Full document	2wr4_full_validation.pdf.gz	946 KB	Display
Data in XML	2wr4_validation.xml.gz	70 KB	Display
Data in CIF	2wr4_validation.cif.gz	91.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/wr/2wr4 ftp://data.pdbj.org/pub/pdb/validation_reports/wr/2wr4	HTTPS FTP

-
Related structure data

Related structure data	2wr0C 2wr1C 2wr2C 2wr3C 2wr5C 2wr7C 2wrbC 2wrcC 2wrdC 2wreC 2wrfC 2wrgC 2wrhC C: citing same article (ref.)
Similar structure data	2wr2-d 2wr3-d 6v47-d 2wr0-d 3ubj-1 3ubn-1 3ube-1 6tvb-d 2wrf-2 5tgv-d 5xrs-2 6y5h-d 5xl8-d 4jul-2 4mhj-4 10696 3m6s-1 3ubj-2 3ubn-2 3s12-1 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
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)	86.780, 150.020, 195.740
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-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose / 6'-sialyl-N-acetyllactosamine

Type: oligosaccharide, Oligosaccharide / Class: Glycan component / Mass: 674.604 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: 6'-sialyl-N-acetyllactosamine

Descriptor	Type	Program
DNeup5Aca2-6DGalpb1-4DGlcpNAcb1-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_b6-c2	WURCS	PDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-Galp]{[(6+2)][a-D-Neup5Ac]{}}}	LINUCS	PDB-CARE

#3: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 543 / Source method: isolated from a natural source / Formula: H₂O

Has protein modification

Y

-
Experiment

Experiment	Method: X-RAY DIFFRACTION

-
Sample preparation

Crystal	Density Matthews: 3.7 Å³/Da / Density % sol: 66.78 % / 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: 2.5→30 Å / Num. obs: 84304 / % possible obs: 99.8 % / Observed criterion σ(I): 3.7 / Redundancy: 7.4 % / B_iso Wilson estimate: 62.9 Å² / R_merge(I) obs: 0.08

-
Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.5→19.944 Å / SU ML: 0.37 / σ(F): 1.34 / Phase error: 27.79 / Stereochemistry target values: MLHL

	R_factor	Num. reflection	% reflection
R_free	0.2549	4245	5 %
R_work	0.2193	-	-
obs	0.2211	84304	94.88 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 48.673 Å² / k_sol: 0.292 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.7024 Å²	0 Å²	0 Å²
2-	-	2.4831 Å²	0 Å²
3-	-	-	-1.7807 Å²

Refinement step

Cycle: LAST / Resolution: 2.5→19.944 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11446	0	45	543	12034

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	11783
X-RAY DIFFRACTION	f_angle_d	1.143	15954
X-RAY DIFFRACTION	f_dihedral_angle_d	17.489	4245
X-RAY DIFFRACTION	f_chiral_restr	0.103	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 (%)
2.5002-2.5285	0.4775	34	0.3475	848	X-RAY DIFFRACTION	30
2.5285-2.5582	0.3708	93	0.2989	1556	X-RAY DIFFRACTION	56
2.5582-2.5893	0.3409	101	0.3041	2023	X-RAY DIFFRACTION	73
2.5893-2.6221	0.3416	140	0.2982	2464	X-RAY DIFFRACTION	88
2.6221-2.6565	0.3407	156	0.3051	2705	X-RAY DIFFRACTION	99
2.6565-2.6928	0.3065	145	0.2972	2817	X-RAY DIFFRACTION	100
2.6928-2.7312	0.3481	142	0.2946	2763	X-RAY DIFFRACTION	100
2.7312-2.7718	0.3161	149	0.2911	2778	X-RAY DIFFRACTION	100
2.7718-2.815	0.3269	140	0.2849	2803	X-RAY DIFFRACTION	100
2.815-2.861	0.278	132	0.285	2773	X-RAY DIFFRACTION	100
2.861-2.9102	0.3011	152	0.2871	2810	X-RAY DIFFRACTION	100
2.9102-2.963	0.3545	140	0.2962	2762	X-RAY DIFFRACTION	100
2.963-3.0198	0.3381	145	0.2829	2824	X-RAY DIFFRACTION	100
3.0198-3.0812	0.302	172	0.2805	2764	X-RAY DIFFRACTION	100
3.0812-3.1479	0.3349	148	0.2747	2809	X-RAY DIFFRACTION	100
3.1479-3.2209	0.3123	130	0.2759	2813	X-RAY DIFFRACTION	100
3.2209-3.3011	0.331	141	0.2482	2779	X-RAY DIFFRACTION	100
3.3011-3.3899	0.2714	132	0.253	2833	X-RAY DIFFRACTION	100
3.3899-3.4892	0.3092	153	0.2503	2817	X-RAY DIFFRACTION	100
3.4892-3.6011	0.2687	142	0.2242	2793	X-RAY DIFFRACTION	100
3.6011-3.729	0.2348	158	0.2053	2798	X-RAY DIFFRACTION	100
3.729-3.8773	0.2274	153	0.1984	2811	X-RAY DIFFRACTION	100
3.8773-4.0524	0.2311	156	0.1858	2823	X-RAY DIFFRACTION	100
4.0524-4.2641	0.2326	135	0.1694	2839	X-RAY DIFFRACTION	100
4.2641-4.5283	0.193	140	0.1528	2840	X-RAY DIFFRACTION	100
4.5283-4.8732	0.1809	169	0.149	2821	X-RAY DIFFRACTION	100
4.8732-5.355	0.2178	174	0.1556	2837	X-RAY DIFFRACTION	100
5.355-6.1103	0.191	145	0.167	2874	X-RAY DIFFRACTION	100
6.1103-7.6261	0.2383	167	0.1872	2889	X-RAY DIFFRACTION	100
7.6261-19.9449	0.1747	161	0.1838	2993	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	0.7998	-0.3384	0.6915	0.4231	-0.7544	2.3003	-0.019	-0.0605	0.0779	-0.1212	-0.2487	-0.0274	0.3692	0.821	0.2877	0.3086	0.255	0.089	0.6876	0.1957	0.2882	62.967	-2.7125	34.9374
2	1.2309	-0.2075	0.8021	0.2408	-1.0447	2.8687	-0.0398	-0.3004	0.0863	-0.0338	-0.3746	-0.0376	-0.0472	0.5428	0.3127	0.2548	0.0013	-0.0175	0.4946	0.111	0.3079	49.4389	6.4943	48.1707
3	0.4716	-0.3613	0.5832	0.2234	-1.1842	2.1888	-0.03	-0.0967	-0.1789	-0.328	-0.1181	0.1698	0.6665	0.1877	0.161	0.5608	0.2672	0.091	0.2745	0.1602	0.3097	46.5859	-13.5293	42.0469
4	-0.0574	-0.379	0.4886	-0.2645	-0.6075	1.0664	-0.2291	-0.1431	-0.0386	-0.0012	-0.2192	-0.1251	-0.016	1.1181	0.4931	0.3298	0.103	0.0089	0.9781	0.2566	0.4819	63.8999	7.2263	25.6334
5	2.3348	-0.1759	1.1088	1.0902	-1.5363	0.7626	-0.103	-0.7774	0.2007	-0.4103	0.0458	0.2181	-0.2139	-0.4091	0.1314	0.3153	0.1272	-0.0279	0.3276	-0.078	0.1711	36.5323	10.9197	46.4183
6	0.1613	-0.1069	0.9598	-0.6713	0.0999	1.8177	0.2215	0.4274	-0.4806	-0.0547	-0.0105	0.4738	1.6765	0.0725	-0.5263	1.0978	0.3385	-0.1108	0.1029	0.2174	0.5787	41.9826	-18.93	30.0823
7	0.4129	-0.1285	0.1037	0.207	0.051	1.6453	-0.0501	0.1472	0.0717	0.0847	0.0319	0.0362	-0.2099	0.0869	-0.0024	0.407	0.0202	0.043	0.3097	0.0003	0.3494	42.7795	15.607	-12.4696
8	0.6483	-0.833	0.3928	0.45	-1.566	0.7951	-0.1059	-0.0611	0.0734	0.1201	0.1041	0.04	-0.0178	-0.0335	-0.0081	0.3276	0.0566	-0.0651	0.2314	-0.0128	0.5442	16.6338	31.7502	12.656
9	0.7986	-0.6799	0.2446	-1.554	0.1047	1.378	0.0747	0.0543	-0.2694	-0.0446	-0.0108	-0.1235	0.6284	-0.0454	-0.0753	0.5398	-0.107	-0.0451	0.319	-0.086	0.5286	11.8151	-5.5373	0.1037
10	1.8607	1.6152	0.1836	3.5111	0.3837	0.4734	-0.279	0.5794	0.1124	-0.2801	0.3466	0.4006	0.0227	-0.0105	-0.0663	0.3303	-0.0197	-0.0234	0.3989	0.0471	0.2885	28.9949	18.4384	-25.9369
11	0.6685	0.1217	0.5087	0.9887	-0.3166	1.3858	0.0751	-0.0269	0.1807	-0.1437	0.0187	0.0561	-0.0195	-0.1661	-0.0603	0.2788	0.0146	-0.0493	0.2657	0.0507	0.4661	10.4839	37.2572	-4.9261
12	1.4187	-1.3309	0.3849	0.955	-0.0643	1.7751	0.1238	0.1664	-0.1602	-0.097	-0.1198	0.1008	-0.1008	-0.4336	0.081	0.3334	-0.0852	-0.0031	0.4746	-0.1625	0.3767	1.5992	5.4162	-12.3719
13	1.1858	0.1643	0.4092	0.1694	-0.2297	1.501	-0.1504	0.047	-0.1366	-0.0114	-0.039	-0.027	0.003	0.2859	0.1482	0.3419	0.0714	0.0283	0.298	0.0598	0.3479	48.0128	9.8397	1.1158
14	0.9091	-0.39	0.3379	-0.0125	-0.6543	1.0177	-0.0502	-0.1538	0.0583	0.0421	0.0369	-0.0373	-0.2232	-0.0292	0.0306	0.3605	0.0211	-0.0873	0.1475	-0.0019	0.368	26.3627	24.2691	22.4271
15	0.8057	0.0553	0.8878	-0.1987	0.4155	1.6748	0.1445	-0.026	-0.3478	0.0737	-0.0385	0.1134	0.5991	-0.1132	-0.101	0.6	0.0023	0.008	0.3129	0.0651	0.4456	21.6198	-7.2882	12.2883

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