PDB-2wrh: structure of H1 duck albert hemagglutinin with human receptor

ID or keywords:

Entry

Database: PDB / ID: 2wrh

Title

structure of H1 duck albert hemagglutinin with human receptor

Components

HEMAGGLUTININ HA1 CHAIN
HEMAGGLUTININ HA2 CHAIN

Keywords

VIRAL PROTEIN /

ENVELOPE PROTEIN /

GLYCOPROTEIN /

LIPOPROTEIN

Function / homology

Function and homology information

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 / virion membrane /

membrane
Similarity search - Function

Biological species

INFLUENZA A VIRUS

Method

X-RAY DIFFRACTION / OTHER / Resolution: 3 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: 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	Sep 1, 2009	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Sep 29, 2009	Provider: repository / Type: Initial release
Revision 1.1	Nov 28, 2012	Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description / Version format compliance
Revision 1.2	Jul 29, 2020	Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / struct_site / struct_site_gen Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name Description: Carbohydrate remediation / Provider: repository / Type: Remediation

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2wrh.cif.gz	565 KB	Display	PDBx/mmCIF format
PDB format	pdb2wrh.ent.gz	474.1 KB	Display	PDB format
PDBx/mmJSON format	2wrh.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/2wrh ftp://data.pdbj.org/pub/pdb/validation_reports/wr/2wrh	HTTPS FTP

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Related structure data

Related structure data	2wr0C 2wr1C 2wr2C 2wr3C 2wr4C 2wr5C 2wr7C 2wrbC 2wrcC 2wrdC 2wreC 2wrfC 2wrgC C: citing same article (ref.)
Similar structure data	2wrg-d 3htt-1 5vmf-d 4ju0-1 4juj-d 2wrf-1 3hto-1 1rv0-d 4yy7-2 4juh-d 2wr1-d 4jtv-2 1ru7-1 2wr5-d 5t6n-d 1ru7-2 4yy9-1 2wrf-2 6ona-d 4k66-1 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) #113 - May 2009 Influenza Neuraminidase similarity (1) #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)

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)
#113 - May 2009
Influenza Neuraminidase
similarity (1)
#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

H: HEMAGGLUTININ HA1 CHAIN

I: HEMAGGLUTININ HA2 CHAIN

J: HEMAGGLUTININ HA1 CHAIN

K: HEMAGGLUTININ HA2 CHAIN

L: HEMAGGLUTININ HA1 CHAIN

M: HEMAGGLUTININ HA2 CHAIN

hetero molecules

183 kDa, 6 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)	103.416, 155.538, 157.876
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID
1	1
2	1
3	1
1	2
2	2
3	2

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Selection details
1	1	1	CHAIN H AND (RESSEQ 7:42 OR RESSEQ 44:323 )
2	1	1	CHAIN J AND (RESSEQ 7:42 OR RESSEQ 44:323 )
3	1	1	CHAIN L AND (RESSEQ 7:42 OR RESSEQ 44:323 )
1	1	2	CHAIN I AND (RESSEQ 501:660 )
2	1	2	CHAIN K AND (RESSEQ 501:660 )
3	1	2	CHAIN M AND (RESSEQ 501:660 )

NCS ensembles :

ID
1
2

#1: Protein

HEMAGGLUTININ HA1 CHAIN

Mass: 35728.895 Da / Num. of mol.: 3 / Fragment: RESIDUES 18-343 / Source method: isolated from a natural source
Source: (natural)

INFLUENZA A VIRUS (A/MALLARD/ALBERTA/35/1976(H1N1))
References: UniProt: Q9WCE0, UniProt: P26562*PLUS

#2: Protein

HEMAGGLUTININ HA2 CHAIN

Mass: 25064.057 Da / Num. of mol.: 3 / Fragment: RESIDUES 345-566 / Source method: isolated from a natural source
Source: (natural)

INFLUENZA A VIRUS (A/MALLARD/ALBERTA/35/1976(H1N1))
References: UniProt: Q9WCE0, UniProt: P26562*PLUS

#3: Sugar

ChemComp-SIA / N-acetyl-alpha-neuraminic acid /

Sialic acid

Type: D-saccharide, alpha linking / Mass: 309.270 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C₁₁H₁₉NO₉

Identifier	Type	Program
DNeup5Aca	CONDENSED IUPAC CARBOHYDRATE SYMBOL	GMML 1.0
N-acetyl-a-D-neuraminic acid	COMMON NAME	GMML 1.0
a-D-Neup5Ac	IUPAC CARBOHYDRATE SYMBOL	PDB-CARE 1.0
Neu5Ac	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: 4 Å³/Da / Density % sol: 69.02 % / Description: NONE

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: ROTATING ANODE / Wavelength: 1.5418
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.5418 Å / Relative weight: 1
Reflection	Resolution: 3→20 Å / Num. obs: 47954 / % possible obs: 98 % / Observed criterion σ(I): 2.4 / Redundancy: 3 % / B_iso Wilson estimate: 65.06 Å² / R_merge(I) obs: 0.07

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Processing

Software

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

Refinement

Method to determine structure: OTHER
Starting model: NONE

Resolution: 3→19.984 Å / SU ML: 0.39 / σ(F): 0.03 / Phase error: 24.28 / Stereochemistry target values: MLHL

	R_factor	Num. reflection	% reflection
R_free	0.2517	2453	5.1 %
R_work	0.2289	-	-
obs	0.2301	47954	93.15 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 33.339 Å² / k_sol: 0.301 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	7.7407 Å²	0 Å²	0 Å²
2-	-	9.4025 Å²	0 Å²
3-	-	-	-17.1431 Å²

Refinement step

Cycle: LAST / Resolution: 3→19.984 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11271	0	61	0	11332

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.014	11643
X-RAY DIFFRACTION	f_angle_d	1.208	15813
X-RAY DIFFRACTION	f_dihedral_angle_d	18.708	4098
X-RAY DIFFRACTION	f_chiral_restr	0.086	1723
X-RAY DIFFRACTION	f_plane_restr	0.003	2061

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Type	Rms dev position (Å)
1	1	H	2438	X-RAY DIFFRACTION	POSITIONAL
1	2	J	2438	X-RAY DIFFRACTION	POSITIONAL	0.046
1	3	L	2438	X-RAY DIFFRACTION	POSITIONAL	0.043
2	1	I	1274	X-RAY DIFFRACTION	POSITIONAL
2	2	K	1274	X-RAY DIFFRACTION	POSITIONAL	0.064
2	3	M	1274	X-RAY DIFFRACTION	POSITIONAL	0.051

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 (%)
3-3.0575	0.3561	117	0.3268	2198	X-RAY DIFFRACTION	82
3.0575-3.1197	0.2999	124	0.3195	2299	X-RAY DIFFRACTION	86
3.1197-3.1873	0.3111	134	0.2915	2301	X-RAY DIFFRACTION	87
3.1873-3.2611	0.308	137	0.2906	2391	X-RAY DIFFRACTION	89
3.2611-3.3423	0.28	128	0.2713	2415	X-RAY DIFFRACTION	90
3.3423-3.4322	0.2493	147	0.2674	2457	X-RAY DIFFRACTION	92
3.4322-3.5327	0.2902	132	0.2632	2486	X-RAY DIFFRACTION	93
3.5327-3.6461	0.2906	148	0.2502	2535	X-RAY DIFFRACTION	95
3.6461-3.7755	0.2858	121	0.2353	2586	X-RAY DIFFRACTION	95
3.7755-3.9256	0.263	148	0.2225	2574	X-RAY DIFFRACTION	96
3.9256-4.1028	0.2302	133	0.2036	2638	X-RAY DIFFRACTION	96
4.1028-4.3171	0.2153	138	0.1995	2620	X-RAY DIFFRACTION	97
4.3171-4.5845	0.2201	144	0.1883	2653	X-RAY DIFFRACTION	98
4.5845-4.9335	0.2208	140	0.1919	2668	X-RAY DIFFRACTION	97
4.9335-5.421	0.235	125	0.207	2705	X-RAY DIFFRACTION	98
5.421-6.185	0.2662	142	0.2139	2682	X-RAY DIFFRACTION	98
6.185-7.7171	0.2531	156	0.2244	2656	X-RAY DIFFRACTION	96
7.7171-19.9843	0.2009	139	0.2039	2637	X-RAY DIFFRACTION	91

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	1.3524	1.8066	-1.219	3.1836	-1.8937	1.7103	-0.1292	0.0777	-0.2752	0.0078	0.0791	-0.4436	0.2615	-0.0056	0.0523	0.5278	0.1184	-0.0697	0.4872	-0.0451	0.5634	-10.2943	-28.3826	28.4676
2	1.6651	0.9614	-1.8916	0.5558	-1.7496	3.6033	0.158	-0.1462	0.0239	0.1521	-0.0388	-0.0286	-0.3768	0.0047	-0.0983	0.5362	0.0929	0.0151	0.3288	-0.0536	0.483	-16.8442	-10.7959	38.5769
3	2.5955	1.7849	-1.5022	1.7787	-1.0963	1.7154	-0.0757	0.3538	-0.1302	-0.0231	0.2155	0.054	0.094	-0.4154	-0.1722	0.4866	0.0329	-0.0291	0.5796	-0.029	0.4367	-27.1188	-17.4471	21.0271
4	1.3968	-0.2325	-0.3592	1.3579	-1.3259	0.5624	0.0992	-0.4652	-0.2476	0.1082	-0.2974	-0.6723	0.3292	0.3174	0.1035	0.5853	0.1444	-0.0103	0.4735	-0.0711	0.6769	3.0811	-25.534	28.6178
5	0.9718	1.2677	-0.4727	1.1289	-0.6589	0.1911	0.1304	0.1123	0.3961	0.3991	0.244	0.1945	-0.4726	-0.0768	-0.264	0.7245	0.1492	0.0962	0.558	-0.0411	0.6412	-16.5285	2.1325	35.287
6	0.1325	1.0618	-0.085	0.7943	-0.5157	0.846	-0.2428	0.1437	-0.0768	-0.5596	0.2699	-0.0682	0.6245	-0.3886	-0.0193	0.6866	-0.1037	0.0072	0.7014	-0.0169	0.6797	-23.3764	-17.5643	7.8941
7	0.4071	1.9006	-1.2421	0.6347	-0.6587	0.6227	-0.171	-0.748	-0.3658	-0.0603	-0.2107	-0.7018	0.0205	0.4432	0.399	0.5823	0.1306	0.2263	1.1165	-0.0521	1.1566	29.6224	-6.4465	-1.1564
8	0.886	2.0751	-0.1405	0.1176	-2.0734	0.759	0.1817	-0.09	0.0337	0.2083	-0.1652	0.1215	-0.6102	0.1492	0.0151	0.9039	-0.1477	-0.1087	0.5291	-0.0494	0.7606	15.0666	26.6827	16.5638
9	0.6205	1.0283	-0.5714	0.7743	-1.5496	0.6937	-0.1386	0.0736	-0.0966	-0.3121	0.4023	-0.1462	0.8104	0.1011	-0.2927	0.682	-0.1456	0.07	0.6893	-0.0885	0.4201	-2.2891	12.5071	-16.7307
10	0.6717	1.9469	-0.32	2.2807	0.4455	2.7892	-0.3955	0.1583	-0.3453	-0.2933	-0.1479	-0.6439	-0.14	0.7211	0.537	0.746	-0.0327	0.1845	1.0324	-0.0344	1.1718	36.4824	6.0495	-14.1921
11	3.5779	-0.426	0.0035	1.5967	-0.3155	1.916	0.236	0.3427	-0.3294	-0.1581	0.0119	-0.2566	-0.2308	0.5412	-0.2651	0.7027	-0.157	-0.1264	0.7501	-0.0933	0.7112	28.8375	32.5976	4.3675
12	1.7885	-1.4421	-1.9336	3.8096	1.4691	2.1398	-0.3859	0.0665	0.3418	-0.569	0.6006	-0.458	-0.4435	0.2786	-0.2131	0.7205	-0.3004	0.0711	0.8017	-0.1626	0.5678	10.808	25.4558	-22.5598
13	1.4773	1.0246	-0.649	0.5774	-0.5223	0.9465	-0.1867	0.1725	-0.4286	-0.246	-0.0606	-0.5042	0.3209	0.1344	0.232	0.6612	0.1008	0.1401	0.687	-0.0654	0.8707	17.2246	-12.0673	6.2425
14	0.4129	1.4332	-0.8088	2.7297	-1.3735	0.9162	0.2656	-0.1231	-0.196	0.6655	-0.0771	-0.167	-0.4066	0.2423	-0.1979	0.5732	0.0109	-0.1065	0.4691	-0.0715	0.4085	6.9195	14.8184	22.2453
15	-0.1105	0.4863	-0.62	1.407	-1.4331	2.8905	-0.3213	0.3353	-0.0249	0.0998	0.538	-0.0589	-0.0068	-0.487	-0.2193	0.4983	-0.0006	0.0003	0.5361	-0.0607	0.5069	-8.6994	4.8759	-4.8579

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN I AND RESID 501:660
2	X-RAY DIFFRACTION	2	CHAIN K AND RESID 501:660
3	X-RAY DIFFRACTION	3	CHAIN M AND RESID 501:660
4	X-RAY DIFFRACTION	4	CHAIN H AND RESID 7:49
5	X-RAY DIFFRACTION	5	CHAIN J AND RESID 7:49
6	X-RAY DIFFRACTION	6	CHAIN L AND RESID 7:49
7	X-RAY DIFFRACTION	7	CHAIN H AND RESID 50:113
8	X-RAY DIFFRACTION	8	CHAIN J AND RESID 50:113
9	X-RAY DIFFRACTION	9	CHAIN L AND RESID 50:113
10	X-RAY DIFFRACTION	10	CHAIN H AND RESID 114-240
11	X-RAY DIFFRACTION	11	CHAIN J AND RESID 114-240
12	X-RAY DIFFRACTION	12	CHAIN L AND RESID 114-240
13	X-RAY DIFFRACTION	13	CHAIN H AND RESID 241-323
14	X-RAY DIFFRACTION	14	CHAIN J AND RESID 241-323
15	X-RAY DIFFRACTION	15	CHAIN L AND RESID 241-323

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