PDB-4f3z: Crystal structure of a swine H1N2 influenza virus hemagglutinin

ID or keywords:

Entry

Database: PDB / ID: 4f3z

Title

Crystal structure of a swine H1N2 influenza virus hemagglutinin

Components

(Hemagglutinin) x 2

Keywords

VIRAL PROTEIN / viral envelope protein / viral receptor binding and fusion protein / sialic acid

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

Influenza A virus

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.2 Å

Authors

Xu, R. / Wilson, I.A.

Citation

Journal: J.Virol. / Year: 2012
Title: Functional Balance of the Hemagglutinin and Neuraminidase Activities Accompanies the Emergence of the 2009 H1N1 Influenza Pandemic.
Authors: Xu, R. / Zhu, X. / McBride, R. / Nycholat, C.M. / Yu, W. / Paulson, J.C. / Wilson, I.A.

History

Deposition	May 9, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 4, 2012	Provider: repository / Type: Initial release
Revision 1.1	Aug 22, 2012	Group: Database references
Revision 1.2	Jul 29, 2020	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / 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_leaving_atom_flag / _struct_conn.pdbx_role / _struct_ref_seq_dif.details Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3	Sep 13, 2023	Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4	Nov 20, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4f3z.cif.gz	581.7 KB	Display	PDBx/mmCIF format
PDB format	pdb4f3z.ent.gz	485.7 KB	Display	PDB format
PDBx/mmJSON format	4f3z.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/f3/4f3z ftp://data.pdbj.org/pub/pdb/validation_reports/f3/4f3z	HTTPS FTP

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Related structure data

Related structure data	3lzgS S: Starting model for refinement
Similar structure data	4jul-1 3ube-1 4jul-2 3qqb-1 4xkd-d 4lxv-1 5t0b-d 5xrs-2 5t0e-d 1hgj-d 3ubj-1 6v47-d 2wr2-d 5thb-d 2ypg-d 4jum-1 5th0-d 6tvf-1 6twv-2 5t0d-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

D: Hemagglutinin

E: Hemagglutinin

F: Hemagglutinin

hetero molecules

171 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)	93.44, 94.92, 220.53
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: 36626.230 Da / Num. of mol.: 3 / Fragment: HA1 (UNP residues 18-344) / Mutation: G205C, R220C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Influenza A virus / Strain: A/Swine/Indiana/P12439/00(H1N2) / Plasmid: pFASTbac-HT / Production host:

Trichoplusia ni (cabbage looper) / Strain (production host): Hi5 / References: UniProt: Q8QT89

#2: Protein

Hemagglutinin

Mass: 20459.686 Da / Num. of mol.: 3 / Fragment: HA2 (UNP residues 345-520)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Influenza A virus / Strain: A/Swine/Indiana/P12439/00(H1N2) / Plasmid: pFASTbac-HT / Production host:

Trichoplusia ni (cabbage looper) / Strain (production host): Hi5 / References: UniProt: Q8QT89

#3: Sugar

ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE

Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
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

Has protein modification

Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.86 Å³/Da / Density % sol: 56.92 %
Crystal grow	Temperature: 296 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 25% PEG1000, 0.1 M Tris, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 296K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97945 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 1, 2011
Radiation	Monochromator: Side scattering bent cube-root I-beam single crystal, asymmetric cut 4.965 degrees Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97945 Å / Relative weight: 1
Reflection	Resolution: 3.2→35 Å / Num. all: 33469 / Num. obs: 32867 / % possible obs: 98.2 % / Observed criterion σ(I): 1 / Redundancy: 7 % / B_iso Wilson estimate: 43.8 Å² / R_merge(I) obs: 0.165 / Net I/σ(I): 11
Reflection shell	Resolution: 3.2→3.31 Å / Redundancy: 5.3 % / R_sym value: 0.567 / % possible all: 85.7

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Processing

Software

Name	Version	Classification
Blu-Ice		data collection
PHASER		phasing
PHENIX	(phenix.refine: 1.7_650)	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3LZG

3lzg

Resolution: 3.2→34.275 Å / SU ML: 0.28 / σ(F): 0 / Phase error: 28.09 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2933	1569	5.09 %	RANDOM
R_work	0.2339	-	-	-
obs	0.237	30849	93.15 %	-

Solvent computation

Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 3.907 Å² / k_sol: 0.273 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.2925 Å²	-0 Å²	-0 Å²
2-	-	-0.8981 Å²	0 Å²
3-	-	-	-0.3944 Å²

Refinement step

Cycle: LAST / Resolution: 3.2→34.275 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11530	0	14	0	11544

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	12213
X-RAY DIFFRACTION	f_angle_d	0.757	16023
X-RAY DIFFRACTION	f_dihedral_angle_d	18.527	4321
X-RAY DIFFRACTION	f_chiral_restr	0.054	1719
X-RAY DIFFRACTION	f_plane_restr	0.002	2070

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 (%)
3.2-3.3032	0.4168	77	0.32	1327	X-RAY DIFFRACTION	48
3.3032-3.4212	0.3492	126	0.2885	2213	X-RAY DIFFRACTION	79
3.4212-3.558	0.3795	132	0.2954	2761	X-RAY DIFFRACTION	98
3.558-3.7198	0.3056	144	0.2615	2828	X-RAY DIFFRACTION	100
3.7198-3.9156	0.325	163	0.2595	2819	X-RAY DIFFRACTION	100
3.9156-4.1605	0.28	157	0.2225	2812	X-RAY DIFFRACTION	100
4.1605-4.4811	0.2325	144	0.1992	2860	X-RAY DIFFRACTION	100
4.4811-4.9309	0.2654	139	0.1921	2879	X-RAY DIFFRACTION	100
4.9309-5.6417	0.281	147	0.2112	2860	X-RAY DIFFRACTION	100
5.6417-7.0975	0.3249	166	0.2322	2911	X-RAY DIFFRACTION	100
7.0975-34.2768	0.2417	174	0.2173	3010	X-RAY DIFFRACTION	100

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	0.4652	-0.2778	-0.2573	0.511	0.7676	2.3817	0.1243	-0.0596	0.2223	-0.1989	0.081	-0.1557	-0.3767	-0.0472	0	0.3088	0.0083	-0.0056	0.3708	0.025	0.299	-20.0913	-3.1633	16.8541
2	3.3307	-0.087	1.2967	2.7205	0.1567	3.3837	-0.0078	-0.2917	0.6642	0.328	-0.3336	0.4152	-0.516	-0.237	-0	0.5356	0.0114	0.0959	0.5143	-0.1378	0.574	-27.8265	14.7979	50.1382
3	-0.2146	0.7483	1.0037	2.0773	1.3676	1.6887	-0.1293	0.0148	0.0666	-0.1965	-0.2555	0.6964	-0.103	-0.4518	-0	0.2287	0.0321	-0.0347	0.4186	-0.0649	0.448	-22.7437	-4.0252	18.2315
4	2.4539	0.141	0.5645	1.382	0.1713	1.2608	0.161	-0.1037	0.2317	-0.1176	-0.1813	0.2621	-0.4749	-0.2896	-0	0.4082	0.0465	-0.1191	0.3268	-0.0164	0.4443	-22.8943	-28.4545	-8.4646
5	0.2412	0.0008	0.1161	-2.3011	0.2983	2.4441	0.1785	0.1792	-0.1336	-1.357	-0.4213	-0.1468	-0.2385	0.2367	-0	0.0437	-0.2028	-0.2755	0.2801	-0.026	0.4907	-19.7926	-34.1764	-5.4241
6	0.1041	0.2952	0.0467	-0.2364	0.3452	1.776	0.1155	0.105	-0.0795	0.3051	0.1106	-0.1907	0.6177	0.128	-0	0.4347	0.0599	-0.0159	0.1922	-0.0476	0.4317	0.7124	-43.549	14.7877
7	1.223	-0.3721	-0.0966	1.5629	1.8764	-0.6843	-0.1554	-0.0581	-0.1234	0.1609	0.1496	-0.4365	-0.1403	0.4743	0	0.4301	-0.0719	0.0526	0.3381	-0.0265	0.3527	5.1229	-11.4472	47.8224
8	0.8365	0.4009	-0.3505	3.2237	1.6473	4.9106	0.0423	0.0745	0.1676	-0.1063	0.0581	-0.2191	-0.301	0.1022	-0	0.2204	0.0457	-0.0117	0.2809	-0.0201	0.2869	1.1659	3.6889	59.551
9	2.4476	-0.4408	0.0181	-0.8412	1.1494	2.5062	-0.187	0.138	0.4031	-0.4952	0.2306	-0.0531	-0.4578	0.4361	-0	0.3767	-0.1202	0.0212	0.3159	0.0457	0.2762	2.0316	-29.086	27.6624
10	2.9394	0.0706	-0.6159	1.8313	-2.6675	1.9315	-0.014	-0.0159	-0.032	0.412	0.1101	-0.2342	0.1557	0.3958	0	0.1607	-0.016	-0.1621	0.3243	-0.0619	0.3067	-0.3431	-43.2692	2.0947
11	1.0824	-0.2938	-1.0428	1.1905	0.9666	1.5349	-0.0274	0.3165	-0.2223	-0.0796	0.02	0.0091	0.2319	-0.1962	0	0.2928	0.0528	-0.0746	0.2816	0.0441	0.2659	-7.9838	-44.1694	0.8576
12	0.1209	0.4968	-0.2402	-0.4687	0.6081	1.5679	-0.0183	-0.0854	-0.199	0.439	-0.5547	0.591	0.5265	-1.1777	0	0.8756	-0.2106	0.0216	0.7206	-0.1547	0.5959	-34.4858	-31.3914	37.143
13	2.3637	0.1172	0.0179	5.7285	-0.6365	4.2807	-0.0567	-0.3397	-0.0484	0.7321	0.0357	0.4951	0.0034	-0.266	-0	0.7352	-0.1994	0.1823	0.6238	-0.0193	0.4532	-27.4013	-13.8226	69.077
14	-0.1044	-0.3087	-1.1107	1.5737	-0.1516	0.4206	-0.0003	-0.3262	-0.0018	0.7221	-0.5003	0.6998	0.7434	-0.7201	0	0.6213	-0.2777	0.1513	0.8369	-0.1795	0.4925	-33.9534	-35.458	30.0439
15	1.368	-0.6003	-0.88	1.414	-1.2073	0.8124	-0.3358	-0.0923	-0.4382	0.2504	0.0758	0.3407	0.6522	-0.6152	0	0.4756	-0.1954	0.072	0.5534	-0.0948	0.5857	-28.8532	-55.3156	4.0775
16	0.0234	0.0226	-0.0323	-0.0416	0.0715	-0.0357	0.0135	-0.4268	0.0168	0.2985	-0.05	0.9932	-0.2795	-0.4679	0	1.5735	-0.1333	0.0294	1.8368	-0.1261	1.2727	-21.0682	-32.9877	34.3816
17	0.0244	0.9373	0.7682	1.6113	0.2388	-0.5009	-0.09	0.146	-0.1105	-0.1921	-0.0359	0.3206	0.055	-0.1463	0	0.3059	-0.0304	-0.0579	0.3578	-0.079	0.4625	-23.5903	-35.7399	13.8637
18	0.1065	-0.029	0.254	-0.0339	-0.057	0.1905	-0.2037	0.5294	-0.5908	1.5607	-0.3978	0.5123	1.0247	-0.781	-0	1.0981	-0.1187	-0.0547	0.5086	-0.2208	0.9044	-24.0687	-69.7257	-11.6886

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resseq 10:113)
2	X-RAY DIFFRACTION	2	chain 'A' and (resseq 114:247)
3	X-RAY DIFFRACTION	3	chain 'A' and (resseq 248:324)
4	X-RAY DIFFRACTION	4	chain 'B' and (resseq 1:67)
5	X-RAY DIFFRACTION	5	chain 'B' and (resseq 68:171)
6	X-RAY DIFFRACTION	6	chain 'C' and (resseq 9:55)
7	X-RAY DIFFRACTION	7	chain 'C' and (resseq 56:119)
8	X-RAY DIFFRACTION	8	chain 'C' and (resseq 120:260)
9	X-RAY DIFFRACTION	9	chain 'C' and (resseq 261:325)
10	X-RAY DIFFRACTION	10	chain 'D' and (resseq 1:66)
11	X-RAY DIFFRACTION	11	chain 'D' and (resseq 67:174)
12	X-RAY DIFFRACTION	12	chain 'E' and (resseq 11:113)
13	X-RAY DIFFRACTION	13	chain 'E' and (resseq 114:265)
14	X-RAY DIFFRACTION	14	chain 'E' and (resseq 266:325)
15	X-RAY DIFFRACTION	15	chain 'F' and (resseq 1:57)
16	X-RAY DIFFRACTION	16	chain 'F' and (resseq 58:67)
17	X-RAY DIFFRACTION	17	chain 'F' and (resseq 68:134)
18	X-RAY DIFFRACTION	18	chain 'F' and (resseq 135:170)

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