PDB-2wrc: the structure of influenza H2 human singapore hemagglutinin

ID or keywords:

Entry

Database: PDB / ID: 2wrc

Title

the structure of influenza H2 human singapore hemagglutinin

Components

HEMAGGLUTININ

Keywords

VIRAL PROTEIN / GLYCOPROTEIN / LIPOPROTEIN / ENVELOPE PROTEIN

Function / homology

Function and homology information

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 / virion membrane / membrane
Similarity search - Function

Biological species

UNIDENTIFIED INFLUENZA VIRUS

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 2.706 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	Sep 1, 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	Nov 6, 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

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Download

PDBx/mmCIF format	2wrc.cif.gz	572.6 KB	Display	PDBx/mmCIF format
PDB format	pdb2wrc.ent.gz	482.1 KB	Display	PDB format
PDBx/mmJSON format	2wrc.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	2wrc_validation.pdf.gz	452.3 KB	Display	wwPDB validaton report
Full document	2wrc_full_validation.pdf.gz	488.8 KB	Display
Data in XML	2wrc_validation.xml.gz	57.4 KB	Display
Data in CIF	2wrc_validation.cif.gz	72.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/wr/2wrc ftp://data.pdbj.org/pub/pdb/validation_reports/wr/2wrc	HTTPS FTP

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Related structure data

Related structure data	2wr0C 2wr1C 2wr2C 2wr3C 2wr4C 2wr5C 2wr7C 2wrbC 2wrdC 2wreC 2wrfC 2wrgC 2wrhC C: citing same article (ref.)
Similar structure data	5vmg-d 4ju0-2 5vmc-d 2wr7-d 4k65-1 4k66-2 7kna-d 5vmj-d 4kdq-d 1rvz-2 5w6r-1 6ona-d 4k63-2 4k62-1 6wcr-1 4k62-3 4cqw-d 4k66-1 4bgx-1 6n41-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

171 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)	79.950, 122.460, 222.910
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 A AND (RESSEQ 9:323 )
2	1	1	CHAIN B AND (RESSEQ 5:323 )
3	1	1	CHAIN C AND (RESSEQ 7:323 )
1	1	2	CHAIN A AND (RESSEQ 330:487 )
2	1	2	CHAIN B AND (RESSEQ 330:492 )
3	1	2	CHAIN C AND (RESSEQ 330:478 )

NCS ensembles :

ID
1
2

#1: Protein	HEMAGGLUTININ Mass: 57164.238 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) UNIDENTIFIED INFLUENZA VIRUS / References: UniProt: Q67333*PLUS
Has protein modification	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 3.46 Å³/Da / Density % sol: 64.17 % / 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: 2.7→30 Å / Num. obs: 46459 / % possible obs: 92.5 % / Observed criterion σ(I): 1.7 / Redundancy: 2.6 % / B_iso Wilson estimate: 78.02 Å² / R_merge(I) obs: 0.16

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: NONE

Resolution: 2.706→29.522 Å / SU ML: 0.42 / σ(F): 1.33 / Phase error: 36.63 / Stereochemistry target values: MLHL

	R_factor	Num. reflection	% reflection
R_free	0.301	2336	5 %
R_work	0.2668	-	-
obs	0.2685	46459	76.79 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 51.249 Å² / k_sol: 0.303 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	10.8574 Å²	0 Å²	0 Å²
2-	-	-0.6845 Å²	0 Å²
3-	-	-	-10.1729 Å²

Refinement step

Cycle: LAST / Resolution: 2.706→29.522 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11265	0	0	0	11265

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	11536
X-RAY DIFFRACTION	f_angle_d	0.932	15585
X-RAY DIFFRACTION	f_dihedral_angle_d	16.747	4184
X-RAY DIFFRACTION	f_chiral_restr	0.061	1674
X-RAY DIFFRACTION	f_plane_restr	0.004	2026

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Type	Rms dev position (Å)
1	1	A	2462	X-RAY DIFFRACTION	POSITIONAL
1	2	B	2462	X-RAY DIFFRACTION	POSITIONAL	0.031
1	3	C	2462	X-RAY DIFFRACTION	POSITIONAL	0.026
2	1	A	1267	X-RAY DIFFRACTION	POSITIONAL
2	2	B	1267	X-RAY DIFFRACTION	POSITIONAL	0.032
2	3	C	1198	X-RAY DIFFRACTION	POSITIONAL	0.027

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 (%)
2.7062-2.7614	0.4583	6	0.4015	178	X-RAY DIFFRACTION	5
2.7614-2.8214	0.4189	24	0.3962	451	X-RAY DIFFRACTION	14
2.8214-2.887	0.3697	40	0.4012	859	X-RAY DIFFRACTION	26
2.887-2.9591	0.4458	70	0.4029	1437	X-RAY DIFFRACTION	43
2.9591-3.039	0.4144	106	0.4171	2094	X-RAY DIFFRACTION	63
3.039-3.1283	0.4305	144	0.3891	2590	X-RAY DIFFRACTION	78
3.1283-3.2292	0.4607	169	0.3811	3100	X-RAY DIFFRACTION	93
3.2292-3.3445	0.4409	171	0.3519	3362	X-RAY DIFFRACTION	100
3.3445-3.4782	0.3403	164	0.3415	3353	X-RAY DIFFRACTION	99
3.4782-3.6362	0.3305	188	0.3076	3328	X-RAY DIFFRACTION	99
3.6362-3.8275	0.293	178	0.2978	3307	X-RAY DIFFRACTION	99
3.8275-4.0668	0.2954	185	0.2648	3294	X-RAY DIFFRACTION	98
4.0668-4.3798	0.2639	182	0.2445	3332	X-RAY DIFFRACTION	98
4.3798-4.8189	0.2617	185	0.1982	3324	X-RAY DIFFRACTION	98
4.8189-5.5123	0.2095	170	0.196	3401	X-RAY DIFFRACTION	99
5.5123-6.93	0.2529	185	0.2127	3452	X-RAY DIFFRACTION	100
6.93-29.5233	0.2728	169	0.2421	3261	X-RAY DIFFRACTION	90

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	0.7974	0.2632	-0.5896	0.4573	-0.862	4.8909	0.4012	-0.8191	0.0151	0.3977	-0.0757	-0.4683	-0.2981	1.4956	0.0732	0.1806	-0.4701	-0.0261	1.0585	0.0196	0.482	45.3654	-4.2756	13.8576
2	0.5154	-0.7616	-1.0384	2.7309	1.8464	5.0362	0.2709	-0.2328	0.0596	0.3091	-0.1214	-0.0168	-0.9275	-0.2349	0.0001	0.347	-0.1178	0.15	0.4312	0.0221	0.4263	25.204	1.9543	10.6459
3	0.1051	0.0626	0.0809	1.1165	1.1077	1.9741	0.231	-0.2972	0.2107	-0.1689	-0.0249	-0.0636	-1.5449	0.8195	-0.0044	0.9714	-0.5451	0.2516	0.5318	-0.1417	0.5181	40.7221	13.6669	3.1462
4	-0.6196	-0.2864	-0.9686	2.4601	0.8469	1.0221	0.2351	-1.3297	-0.1766	-0.3491	0.3565	-0.6121	-0.1845	1.2714	0.0867	0.1759	-0.2814	-0.1737	1.7271	-0.1622	0.7191	55.7495	-9.1162	4.5195
5	-0.3919	-0.8678	-1.8702	0.3568	0.6045	0.7965	-0.0495	-0.1609	0.1475	0.3976	-0.2735	0.3449	-0.1834	-0.5617	-0.2196	0.2185	-0.1085	0.1636	0.5477	0.0155	0.446	20.724	-9.3033	5.5459
6	0.9212	1.785	-0.484	0.5242	0.8247	1.3559	0.679	0.4842	0.7692	0.2154	-0.2333	0.0466	-1.8931	0.1555	0.0068	1.5505	-0.2216	0.3181	0.1941	-0.074	0.7133	37.5729	17.222	-8.4394
7	1.1224	1.1936	0.0896	1.65	1.6812	0.1052	-0.0437	0.0877	0.2387	0.1025	0.1303	-0.8069	-0.0104	1.2959	-0.0117	0.4794	0.5833	0.15	0.9654	0.0204	0.8981	56.7839	-34.2656	-29.2309
8	1.3856	-0.2177	2.2571	1.9942	1.2749	3.7211	0.0598	-0.263	-0.1616	-0.1092	-0.2434	0.0249	0.6957	-0.8656	0.0008	0.4155	-0.1357	0.0236	0.3977	0.0451	0.5186	18.5972	-25.0814	-36.8557
9	1.3841	0.1298	0.0292	1.1235	-0.8137	2.128	-0.0878	-0.186	-0.0057	-0.6156	0.141	-0.0509	-1.448	0.9231	-0.0006	0.876	-0.2329	0.2382	0.5409	0.0697	0.5909	47.6758	0.2628	-47.2117
10	1.3621	1.1446	0.6091	1.69	1.1954	1.7679	-0.0658	0.6244	-0.0152	-0.2902	0.3487	-0.4262	1.157	0.9371	0.0364	0.7461	0.553	0.3166	0.7051	-0.019	0.8492	52.5514	-42.1387	-46.6123
11	1.2574	-0.753	0.2871	4.6731	-1.5086	5.2674	-0.0311	0.3397	-0.0652	-1.2922	-0.0831	-0.1388	0.6543	-0.5091	-0.0039	0.8164	-0.1084	0.0346	0.314	0.0514	0.4974	23.3872	-29.3705	-55.3135
12	4.1332	-1.0717	-0.4419	1.6998	-0.3584	3.4045	0.1714	0.1218	-0.0972	-1.2347	0.0118	-0.4426	-0.2424	1.1976	0.0005	0.8423	-0.0315	0.2523	0.6315	0.0408	0.5597	51.1587	-12.6723	-61.4458
13	1.2185	-0.0022	-0.4744	1.0317	0.6918	2.2362	0.2873	-0.4059	-0.0645	0.2674	0.0587	-0.6795	0.833	1.0631	-0.0004	0.3817	0.2524	0.0896	0.7781	0.1122	0.6221	52.4621	-25.4744	-16.9036
14	0.3478	0.3379	0.1396	1.3263	0.8472	3.3705	-0.0367	-0.0098	0.0733	-0.1603	-0.2678	0.1629	0.33	-0.8984	-0.0002	0.2063	0.0118	0.0233	0.36	-0.0039	0.4643	21.0856	-16.5948	-23.8839
15	0.1155	0.2047	0.1351	1.5311	0.5001	2.3958	0.298	-0.1215	0.0823	-0.3837	-0.0082	-0.2682	-1.2819	1.0199	-0.0006	0.7786	-0.2767	0.2389	0.5918	0.0274	0.5075	46.3407	3.467	-31.889

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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