PDB-2wr1: structure of influenza H2 hemagglutinin with human receptor

ID or keywords:

Entry

Database: PDB / ID: 2wr1

Title

structure of influenza H2 hemagglutinin with human 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 / apical plasma membrane / 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
Similarity search - Function

Biological species

UNIDENTIFIED INFLUENZA VIRUS

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.1 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 / pdbx_validate_close_contact / 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 / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_seq_id_1 / _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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2wr1.cif.gz	603.9 KB	Display	PDBx/mmCIF format
PDB format	pdb2wr1.ent.gz	503 KB	Display	PDB format
PDBx/mmJSON format	2wr1.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/wr/2wr1 ftp://data.pdbj.org/pub/pdb/validation_reports/wr/2wr1	HTTPS FTP

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Related structure data

Related structure data	2wr0C 2wr2C 2wr3C 2wr4C 2wr5C 2wr7C 2wrbC 2wrcC 2wrdC 2wreC 2wrfC 2wrgC 2wrhC C: citing same article (ref.)
Similar structure data	2wr5-d 2wrf-1 4wsv-d 4juh-d 2wr0-d 6tzb-d 6bkq-d 4wea-1 5vtx-d 4xkd-d 6idd-2 4unx-d 4lkg-1 6nhq-d 5t6n-d 2wr2-d 2yp9-1 5vmf-d 4jul-2 4juk-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	#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

177 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)	69.565, 141.457, 199.505
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 / Non-polymers , 2 types, 1240 molecules ABC

#1: Protein	HEMAGGLUTININ / Mass: 57593.816 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) UNIDENTIFIED INFLUENZA VIRUS / References: UniProt: D0VWP8*PLUS
#7: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 1237 / Source method: isolated from a natural source / Formula: H₂O

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Sugars , 5 types, 8 molecules

#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.: 2
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
[][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{[(6+2)][a-D-Neup5Ac]{}}}	LINUCS	PDB-CARE

#3: 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-ROH	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
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}	LINUCS	PDB-CARE

#4: Polysaccharide

beta-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4) ...

Type: oligosaccharide

/ Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source

Descriptor	Type	Program
DManpb1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROH	Glycam Condensed Sequence	GMML 1.0
WURCS=2.0/2,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2-2/a4-b1_b4-c1_c3-d1	WURCS	PDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp3Me]{}}}	LINUCS	PDB-CARE

#5: Polysaccharide

alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...

Type: oligosaccharide

/ Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source

Descriptor	Type	Program
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROH	Glycam Condensed Sequence	GMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c3-d1	WURCS	PDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}	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.: 3
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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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 2.68 Å³/Da / Density % sol: 53.7 % / 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: 2.1→30 Å / Num. obs: 115302 / % possible obs: 99.8 % / Observed criterion σ(I): 3.7 / Redundancy: 6.4 % / B_iso Wilson estimate: 41.4 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: 2.1→30 Å / SU ML: 0.3 / σ(F): 1.33 / Phase error: 24.02 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2297	5780	5 %
R_work	0.1958	-	-
obs	0.1975	115302	99.83 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 69.61 Å² / k_sol: 0.356 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.8908 Å²	-0 Å²	0 Å²
2-	-	-0.3299 Å²	0 Å²
3-	-	-	1.2207 Å²

Refinement step

Cycle: LAST / Resolution: 2.1→30 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11605	0	252	1237	13094

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.021	12169
X-RAY DIFFRACTION	f_angle_d	1.608	16475
X-RAY DIFFRACTION	f_dihedral_angle_d	17.707	4503
X-RAY DIFFRACTION	f_chiral_restr	0.125	1820
X-RAY DIFFRACTION	f_plane_restr	0.009	2113

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 (%)
2.1-2.1239	0.2978	192	0.2705	3576	X-RAY DIFFRACTION	100
2.1239-2.1488	0.3307	215	0.2552	3575	X-RAY DIFFRACTION	100
2.1488-2.175	0.2885	175	0.2466	3670	X-RAY DIFFRACTION	100
2.175-2.2026	0.3314	190	0.2455	3576	X-RAY DIFFRACTION	100
2.2026-2.2315	0.2688	178	0.2292	3649	X-RAY DIFFRACTION	100
2.2315-2.2621	0.2629	188	0.2157	3595	X-RAY DIFFRACTION	100
2.2621-2.2944	0.2649	188	0.217	3634	X-RAY DIFFRACTION	100
2.2944-2.3286	0.2539	187	0.2145	3644	X-RAY DIFFRACTION	100
2.3286-2.365	0.2607	191	0.222	3591	X-RAY DIFFRACTION	100
2.365-2.4038	0.253	208	0.2155	3648	X-RAY DIFFRACTION	100
2.4038-2.4452	0.3077	184	0.2233	3598	X-RAY DIFFRACTION	100
2.4452-2.4896	0.269	199	0.217	3645	X-RAY DIFFRACTION	100
2.4896-2.5375	0.2698	166	0.2197	3630	X-RAY DIFFRACTION	100
2.5375-2.5893	0.2571	188	0.22	3637	X-RAY DIFFRACTION	100
2.5893-2.6455	0.3172	197	0.2229	3630	X-RAY DIFFRACTION	100
2.6455-2.707	0.2791	199	0.2158	3608	X-RAY DIFFRACTION	100
2.707-2.7747	0.2486	188	0.2076	3667	X-RAY DIFFRACTION	100
2.7747-2.8497	0.2439	188	0.1986	3604	X-RAY DIFFRACTION	100
2.8497-2.9334	0.2687	189	0.2106	3671	X-RAY DIFFRACTION	100
2.9334-3.028	0.2705	200	0.2073	3670	X-RAY DIFFRACTION	100
3.028-3.1362	0.2289	166	0.2001	3657	X-RAY DIFFRACTION	100
3.1362-3.2616	0.2204	216	0.1903	3627	X-RAY DIFFRACTION	100
3.2616-3.4098	0.207	175	0.1851	3666	X-RAY DIFFRACTION	100
3.4098-3.5893	0.2187	206	0.1764	3663	X-RAY DIFFRACTION	100
3.5893-3.8138	0.18	211	0.1635	3664	X-RAY DIFFRACTION	100
3.8138-4.1076	0.173	199	0.1579	3681	X-RAY DIFFRACTION	100
4.1076-4.5197	0.1831	214	0.161	3677	X-RAY DIFFRACTION	100
4.5197-5.1708	0.197	193	0.1642	3713	X-RAY DIFFRACTION	100
5.1708-6.5037	0.2208	205	0.188	3763	X-RAY DIFFRACTION	100
6.5037-30.003	0.2118	185	0.2011	3893	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	0.806	0.859	1.5456	0.9703	1.5708	3.3528	0.0414	0.0406	-0.0965	0.0351	0.0752	-0.1227	-0.0452	0.262	-0.0871	0.2454	-0.0449	0.0051	0.3538	-0.0295	0.2813	29.8422	24.4024	42.657
2	0.5602	0.4871	0.9643	1.3437	2.0409	3.3344	-0.0602	-0.1433	0.0421	-0.0113	-0.0575	0.0841	-0.1005	-0.2337	0.1019	0.2866	0.0122	0.0234	0.2597	0.0144	0.2369	9.6536	26.0129	49.4425
3	0.738	0.8697	0.8803	1.8203	1.5729	1.729	-0.0515	0.0212	0.0439	-0.0227	0.0484	-0.0034	-0.2252	0.0652	0.0217	0.3378	-0.0263	0.0084	0.2081	0.0053	0.2247	17.8097	40.2847	36.7141
4	-0.6553	0.3895	-0.0059	1.3571	1.5633	1.625	0.0151	0.0373	-0.1658	-0.066	0.3298	-0.3831	-0.0874	0.5363	-0.3249	0.2884	-0.066	-0.0082	0.5186	-0.0927	0.37	34.983	21.0326	31.2568
5	0.0176	0.1615	0.4567	0.2769	0.8743	1.3032	0.0967	-0.1595	-0.0285	0.1554	-0.0703	-0.0102	0.2339	-0.3514	-0.028	0.415	-0.0616	0.0125	0.3778	0.0191	0.2375	6.0958	13.2599	48.1574
6	0.1931	0.4869	0.6858	0.9321	1.0877	1.421	-0.1218	0.0112	0.0544	-0.282	0.0693	0.1245	-0.5321	0.0086	0.0302	0.5297	0.0135	-0.019	0.276	-0.0053	0.3644	6.96	41.2438	27.8756
7	-0.3626	0.3775	0.353	0.4852	0.3068	1.3179	-0.0378	0.0442	-0.0311	-0.0039	0.0629	-0.1987	-0.1087	0.2882	-0.0362	0.1948	-0.0056	0.0204	0.3061	-0.0345	0.2834	22.3204	-8.6297	-0.3255
8	1.4966	0.7081	1.2143	0.5913	0.4746	0.7927	0.0279	-0.3274	0.1543	0.1047	-0.1358	-0.0797	0.1015	-0.1851	0.1014	0.2093	-0.0552	0.0227	0.2948	0.0218	0.2954	-14.4507	-7.5337	13.4746
9	0.9978	0.3964	1.1563	0.0323	0.7508	2.9039	-0.1148	-0.1854	0.1229	-0.0936	0.0002	0.0628	-0.5048	-0.0774	0.0787	0.4114	0.0021	-0.0065	0.2786	0.0096	0.2847	-1.9412	21.3487	-10.9166
10	0.7876	0.0032	0.0821	1.2969	0.0937	2.1052	0.0253	0.0916	-0.093	-0.0228	0.0024	-0.0477	0.104	0.0975	-0.0101	0.1709	-0.0201	0.0396	0.2161	-0.0137	0.2368	12.0416	-18.8624	-13.1933
11	1.1293	0.3186	0.0575	1.0561	-0.1311	1.5355	-0.0251	0.121	-0.054	-0.0468	-0.0447	0.2884	0.1655	-0.3395	0.0588	0.1627	-0.0635	0.0275	0.2479	-0.0046	0.2884	-19.9271	-13.4389	-4.3385
12	1.6517	-0.169	-0.3794	0.9866	-0.1651	1.5953	0.0829	0.1468	-0.0947	-0.2245	-0.053	0.057	-0.0718	-0.0512	-0.0323	0.2924	0.0168	0.006	0.2199	0.0271	0.2232	-3.734	7.6007	-24.4523
13	0.1416	0.1489	0.0855	0.4351	0.5056	0.7556	0.0477	-0.0743	-0.0754	0.0131	0.1312	-0.1789	-0.0262	0.1418	-0.1503	0.2109	-0.0226	0.0091	0.2823	-0.0444	0.2705	23.7048	0.467	12.3455
14	0.4141	0.4198	0.7042	0.6299	0.8237	1.5586	0.0973	-0.1283	0.027	0.1071	-0.1266	0.0629	0.0934	-0.3466	0.0175	0.2079	-0.0517	0.0057	0.2863	-0.0097	0.278	-7.5398	2.4996	23.4239
15	0.192	0.1168	0.4007	1.0433	1.2233	2.516	-0.1044	-0.0353	0.0125	-0.2316	-0.0302	0.0386	-0.5054	-0.0089	0.1138	0.312	-0.012	0.0027	0.2337	0.0092	0.2137	4.2828	26.4179	2.8209

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 6:49
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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Protein / Non-polymers , 2 types, 1240 molecules ABC

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Sugars , 5 types, 8 molecules

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Experimental details

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Experiment

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Sample preparation

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Data collection

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Processing

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About Yorodumi

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

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Aug 12, 2020. Covid-19 info

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Yorodumi