PDB-4kol: The structure of hemagglutinin from avian-origin H7N9 influenza virus

ID or keywords:

Entry

Database: PDB / ID: 4kol

Title

The structure of hemagglutinin from avian-origin H7N9 influenza virus

Components

Hemagglutinin HA1
Hemagglutinin HA2

Keywords

VIRAL PROTEIN / homotrimer / virus attachment and membrane fusion

Function / homology

Function and homology information

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

Influenza A virus

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.799 Å

Authors

Shi, Y. / Zhang, W. / Wang, F. / Qi, J. / Song, H. / Wu, Y. / Gao, F. / Zhang, Y. / Fan, Z. / Gong, W. ...

Citation

Journal: Science / Year: 2013
Title: Structures and receptor binding of hemagglutinins from human-infecting H7N9 influenza viruses.
Authors: Shi, Y. / Zhang, W. / Wang, F. / Qi, J. / Wu, Y. / Song, H. / Gao, F. / Bi, Y. / Zhang, Y. / Fan, Z. / Qin, C. / Sun, H. / Liu, J. / Haywood, J. / Liu, W. / Gong, W. / Wang, D. / Shu, Y. / ...

History

Deposition	May 12, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 6, 2013	Provider: repository / Type: Initial release
Revision 1.1	Jul 29, 2020	Group: Data collection / Derived calculations / Structure summary Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id Description: Carbohydrate remediation / Provider: repository / Type: Remediation

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4kol.cif.gz	197.4 KB	Display	PDBx/mmCIF format
PDB format	pdb4kol.ent.gz	163.8 KB	Display	PDB format
PDBx/mmJSON format	4kol.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4kol_validation.pdf.gz	459.5 KB	Display	wwPDB validaton report
Full document	4kol_full_validation.pdf.gz	473.5 KB	Display
Data in XML	4kol_validation.xml.gz	20.7 KB	Display
Data in CIF	4kol_validation.cif.gz	27.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ko/4kol ftp://data.pdbj.org/pub/pdb/validation_reports/ko/4kol	HTTPS FTP

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Related structure data

Related structure data	4komC 4konC 4lcxC 4lkgC 4lkhC 4lkiC 4lkjC 4lkkC C: citing same article (ref.)
Similar structure data	4lki-1 6icw-1 6d8b-d 5vjl-1 4lkh-1 4lkg-2 4lkk-1 6icx-1 4lkg-1 6idd-2 4bsg-1 5vjk-1 4n5j-1 6twh-1 2viu-1 6d7u-d 6idb-1 3eyk-1 4bsb-1 5vjm-1 Search similar-shape structures by Omokage search (details) 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 HA1

B: Hemagglutinin HA2

hetero molecules

54.3 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Hemagglutinin HA1

B: Hemagglutinin HA2

hetero molecules

A: Hemagglutinin HA1

B: Hemagglutinin HA2

hetero molecules

A: Hemagglutinin HA1

B: Hemagglutinin HA2

hetero molecules

defined by author&software
163 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	116.898, 116.898, 296.588
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	155
Space group name H-M	H32

Components on special symmetry positions

ID	Model	Components
1	1	B-601- HOH
2	1	B-603- HOH
3	1	B-606- HOH

#1: Protein

Hemagglutinin HA1

Mass: 34195.594 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Influenza A virus / Strain: A/Anhui/1/2013 (H7N9) / Gene: HA / Plasmid: pFastbac1 / Production host:

Trichoplusia ni (cabbage looper) / References: UniProt: V5IRU4*PLUS

#2: Protein

Hemagglutinin HA2

Mass: 19490.309 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Influenza A virus / Strain: A/Anhui/1/2013 (H7N9) / Gene: HA / Plasmid: pFastbac1 / Production host:

Trichoplusia ni (cabbage looper) / References: UniProt: V5IRU3*PLUS

#3: Sugar

ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose

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

#4: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 3.63 Å³/Da / Density % sol: 66.14 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 16% w/v PEG 3350, 0.2 M lithium sulfate, 0.1 M Tris, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 25, 2013
Radiation	Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.799→50 Å / Num. obs: 19421 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shell	Resolution: 2.8→2.9 Å / % possible all: 100

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Processing

Software

Name	Version	Classification
ADSC	Quantum	data collection
PHASER		phasing
PHENIX	(phenix.refine: 1.8_1069)	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.799→39.085 Å / SU ML: 0.47 / σ(F): 1.34 / Phase error: 29.85 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2825	995	5.12 %	RANDOM
R_work	0.2304	-	-	-
all	0.233	19421	-	-
obs	0.233	19421	98.94 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.799→39.085 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3722	0	42	26	3790

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.011	3842
X-RAY DIFFRACTION	f_angle_d	1.554	5182
X-RAY DIFFRACTION	f_dihedral_angle_d	18.756	1423
X-RAY DIFFRACTION	f_chiral_restr	0.09	562
X-RAY DIFFRACTION	f_plane_restr	0.005	684

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 (%)
2.7992-2.9467	0.3813	155	0.3231	2592	X-RAY DIFFRACTION	100
2.9467-3.1313	0.3359	148	0.3063	2614	X-RAY DIFFRACTION	100
3.1313-3.3729	0.3302	149	0.2892	2633	X-RAY DIFFRACTION	100
3.3729-3.7121	0.3203	132	0.2525	2638	X-RAY DIFFRACTION	100
3.7121-4.2487	0.2845	158	0.2185	2628	X-RAY DIFFRACTION	99
4.2487-5.3507	0.2591	121	0.2005	2638	X-RAY DIFFRACTION	98
5.3507-39.0885	0.2399	132	0.2065	2683	X-RAY DIFFRACTION	96

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	0.4058	-0.1356	0.3315	0.4799	-0.0163	0.7606	0.0435	-0.5312	-0.054	0.2837	0.0002	-0.0776	0.0309	0.2141	-0.0103	0.6132	0.0523	-0.1661	0.7556	-0.0043	0.2993	-43.4048	24.4749	37.9758
2	1.194	0.4443	-0.2912	1.2022	0.0447	0.9385	-0.0833	0.4558	0.0226	-0.2351	0.1932	-0.0104	0.0478	-0.1197	0.009	0.1839	-0.0371	0.0469	0.0346	-0.0457	0.2541	-54.6517	10.5463	-12.3427
3	2.0047	0.144	-1.2806	1.8495	0.0388	2.2057	-0.0937	0.2086	-0.3952	-0.3003	0.1082	-0.1048	0.2227	0.3596	-0.0804	0.5662	-0.1007	0.0622	0.5089	-0.0671	0.2795	-51.4157	6.1542	-29.8821
4	0.9101	0.1964	0.3341	0.5897	-0.0308	0.548	0.0924	0.5984	0.1886	-0.5279	0.3426	0.3095	-0.2188	0.013	0.3457	0.5561	-0.156	-0.0344	0.402	0.1171	0.3599	-61.5407	16.1956	-34.1706
5	0.2475	0.0843	0.1768	1.2961	-0.2514	0.2044	0.012	-0.0002	-0.0661	-0.1299	0.1093	-0.038	-0.0509	-0.0441	0.2948	0.7008	0.0442	0.1436	0.2957	0.2051	0.6392	-65.5758	25.7433	-31.1831
6	1.7491	0.6739	-0.5895	0.3721	0.226	2.1876	-0.0362	0.3877	0.1957	-0.3562	0.4339	0.2409	0.041	0.3357	0.1228	0.6279	-0.0798	0.0943	0.3525	0.0269	0.3345	-50.5517	20.6688	-28.1894
7	0.7441	-0.02	-0.1041	0.7616	-0.2219	0.4872	-0.1483	0.3116	0.1191	-0.4014	0.0988	0.5965	-0.0556	-0.1148	-0.0815	0.3285	-0.0786	-0.0871	0.243	0.0049	0.3491	-66.1717	14.1922	-21.3464
8	0.8019	0.0935	0.5154	2.5038	-0.7341	0.5788	0.019	-0.0189	-0.2142	0.3254	-0.0578	-0.2367	0.2868	-0.1199	-0.0479	0.1783	-0.0635	0.0212	0.0632	-0.0181	0.2132	-48.4657	8.142	4.6532
9	1.2376	-0.0342	0.1916	0.9523	0.168	1.6334	-0.1459	-0.5081	-0.3208	0.3293	0.0671	-0.1798	0.3356	-0.1235	-0.2119	0.192	-0.0251	-0.0523	0.239	-0.0357	0.128	-48.0311	21.7052	18.9279
10	5.0249	-0.8897	-2.6891	3.5039	1.3871	4.4201	-0.0743	-0.3016	0.3645	0.3236	-0.1338	-0.0771	-0.6685	-0.3585	-0.0167	1.2014	-0.0336	-0.257	1.3525	0.1287	0.4085	-42.6662	24.9755	50.5343
11	0.1516	-0.1267	0.0968	0.1104	-0.0812	0.0609	0.002	-0.3838	-0.2407	0.2939	-0.0579	-0.2399	0.1169	0.0867	-0.0884	1.2395	0.0129	-0.3496	1.0707	0.4984	0.5229	-46.6065	13.7119	55.421
12	0.6876	-0.0915	0.0194	0.8164	0.0503	0.3118	0.004	-0.3084	-0.1222	0.145	0.0132	0.1423	0.0691	-0.0807	-0.0815	0.8491	-0.1138	-0.1075	0.4975	0.1678	0.3198	-57.6219	16.5402	37.2266
13	1.6001	0.0152	0.7883	1.3881	-0.5739	0.7781	-0.0446	-0.5512	-0.2909	0.5641	0.0935	0.0284	0.3799	-0.2607	-0.1104	0.3367	-0.0465	-0.0065	0.4219	0.1682	0.4559	-60.0416	17.8537	10.5782
14	0.5555	-0.3169	-0.2659	0.1852	0.1047	0.4822	-0.0897	-0.0291	-0.1173	-0.1233	0.0064	-0.1805	0.1076	0.1246	-0.0899	0.3635	-0.0205	0.2679	0.2096	-0.0399	0.2077	-48.2789	23.1955	-7.7716
15	1.6436	0.0629	-0.1786	0.7757	-0.3637	0.5049	0.0252	-0.8196	-0.1252	0.451	0.0448	-0.1303	-0.2001	0.0733	-0.0839	0.2066	0.0626	-0.0531	0.0813	-0.0217	0.177	-53.6036	29.5125	25.8169
16	0.1155	0.1384	-0.1494	0.1497	-0.162	0.1757	0.0374	-0.3241	-0.0926	0.3838	-0.0484	0.0527	0.0218	0.0555	-0.1546	1.6585	0.1062	-0.169	1.3984	0.2569	0.3596	-55.2489	19.6845	65.341
17	2.2773	-1.4213	0.2397	3.6349	-0.3051	0.8341	-0.0847	-0.3929	0.357	0.3216	-0.0437	0.3484	-0.2211	-0.2806	-0.0146	1.304	0.0195	0.0364	1.2158	0.27	0.5578	-58.323	24.1311	76.4701

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 3 through 31 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 32 through 122 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 123 through 142 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 143 through 186 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 187 through 205 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 206 through 228 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 229 through 259 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 260 through 279 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 280 through 316 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 328 through 337 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 338 through 358 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 359 through 376 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 377 through 386 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 387 through 395 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 396 through 446 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 447 through 483 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 484 through 490 )

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