PDB-4bgz: Crystal Structure of H5 (tyTy) Influenza Virus Haemagglutinin

ID or keywords:

Entry

Database: PDB / ID: 4bgz

Title

Crystal Structure of H5 (tyTy) Influenza Virus Haemagglutinin

Components

HAEMAGGLUTININ HA1
HEMAGGLUTININ

Keywords

VIRAL PROTEIN / N-GLYCOSYLATION / VIRUS RECEPTOR / BIRD FLU

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 VIRUS

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.68 Å

Authors

Xiong, X. / Coombs, P. / Martin, S.R. / Liu, J. / Xiao, H. / McCauley, J.W. / Locher, K. / Walker, P.A. / Collins, P.J. / Kawaoka, Y. ...

Citation

Journal: Nature / Year: 2013
Title: Receptor Binding by a Ferret-Transmissible H5 Avian Influenza Virus.
Authors: Xiong, X. / Coombs, P. / R Martin, S. / Liu, J. / Xiao, H. / Mccauley, J.W. / Locher, K. / Walker, P.A. / Collins, P.J. / Kawaoka, Y. / Skehel, J.J. / Gamblin, S.J.

History

Deposition	Mar 29, 2013	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Apr 24, 2013	Provider: repository / Type: Initial release
Revision 1.1	May 8, 2013	Group: Database references
Revision 1.2	May 15, 2013	Group: Database references
Revision 1.3	May 22, 2013	Group: Database references
Revision 1.4	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_conn / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5	Oct 23, 2024	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_entry_details / pdbx_modification_feature / struct_ncs_dom_lim Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4bgz.cif.gz	578.1 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	4bgz_validation.pdf.gz	502 KB	Display	wwPDB validaton report
Full document	4bgz_full_validation.pdf.gz	514.6 KB	Display
Data in XML	4bgz_validation.xml.gz	59.6 KB	Display
Data in CIF	4bgz_validation.cif.gz	78.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/bg/4bgz ftp://data.pdbj.org/pub/pdb/validation_reports/bg/4bgz	HTTPS FTP

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Related structure data

Related structure data	4bgwC 4bgxC 4bgyC 4bh0C 4bh1C 4bh2C 4bh3C 4bh4C C: citing same article (ref.)
Similar structure data	4bgw-1 4k63-3 4bh0-d 4k63-4 4k64-1 3zp1-1 4k67-1 3zpa-1 4bgy-1 5ajm-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: HAEMAGGLUTININ HA1

C: HEMAGGLUTININ

D: HAEMAGGLUTININ HA1

E: HEMAGGLUTININ

F: HAEMAGGLUTININ HA1

hetero molecules

170 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)	70.482, 228.492, 71.324
Angle α, β, γ (deg.)	90.00, 113.88, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	C
1	2	A
2	2	E
1	3	C
2	3	E
1	4	B
2	4	D
1	5	B
2	5	F
1	6	D
2	6	F

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	ASP	ASP	ASN	ASN	A	A	1 - 319	2 - 320
2	1	ASP	ASP	ASN	ASN	C	C	1 - 319	2 - 320
1	2	ASP	ASP	ARG	ARG	A	A	1 - 318	2 - 319
2	2	ASP	ASP	ARG	ARG	E	E	1 - 318	2 - 319
1	3	ASP	ASP	ARG	ARG	C	C	1 - 318	2 - 319
2	3	ASP	ASP	ARG	ARG	E	E	1 - 318	2 - 319
1	4	ILE	ILE	ASN	ASN	B	B	10 - 154	10 - 154
2	4	ILE	ILE	ASN	ASN	D	D	10 - 154	10 - 154
1	5	ILE	ILE	ARG	ARG	B	B	10 - 153	10 - 153
2	5	ILE	ILE	ARG	ARG	F	F	10 - 153	10 - 153
1	6	ILE	ILE	ARG	ARG	D	D	10 - 153	10 - 153
2	6	ILE	ILE	ARG	ARG	F	F	10 - 153	10 - 153

NCS ensembles :

ID
1
2
3
4
5
6

#1: Protein

HEMAGGLUTININ / HAEMAGGLUTININ HA1

Mass: 36978.715 Da / Num. of mol.: 3 / Fragment: HA1 TRYPSIN RELEASED ECTODOMAIN, RESIDUES 17-338
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

INFLUENZA VIRUS / Strain: A/TURKEY/TURKEY/1/2005(H5N1) / Plasmid: PACGP67A / Cell line (production host): SF9 / Production host:

SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: Q207Z6

#2: Protein

HAEMAGGLUTININ HA1

Mass: 19126.004 Da / Num. of mol.: 3 / Fragment: HA2 TRYPSIN RELEASED ECTODOMAIN, RESIDUES 347-512
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

INFLUENZA VIRUS / Strain: A/TURKEY/TURKEY/1/2005 (H5N1) / Plasmid: PACGP67A / Cell line (production host): SF9 / Production host:

SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: Q207Z6

#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.: 4
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: Chemical

ChemComp-PO4 / PHOSPHATE ION

Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO₄

#5: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 398 / Source method: isolated from a natural source / Formula: H₂O

Has protein modification

Y

Sequence details

MULTIBASIC SITE REMOVED

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.13 Å³/Da / Density % sol: 60.65 % / Description: NONE
Crystal grow	Details: BIS-TRIS PROPANE PH 7.5, 0.05 - 0.15 M K/NAPO4 (PH 7.0), 15-18% PEG 3350

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 10, 2012
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9763 Å / Relative weight: 1
Reflection	Resolution: 2.68→114.2 Å / Num. obs: 57647 / % possible obs: 100 % / Observed criterion σ(I): 2.1 / Redundancy: 3.5 % / R_merge(I) obs: 0.09 / Net I/σ(I): 10
Reflection shell	Resolution: 2.68→2.82 Å / Redundancy: 3.4 % / R_merge(I) obs: 0.68 / Mean I/σ(I) obs: 2.1 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.7.0032	refinement
XDS		data reduction
SCALA		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.68→114.25 Å / Cor.coef. F_o:F_c: 0.937 / Cor.coef. F_o:F_c free: 0.9 / SU B: 26.205 / SU ML: 0.285 / Cross valid method: THROUGHOUT / ESU R: 0.668 / ESU R Free: 0.305 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.24392	2926	5.1 %	RANDOM
R_work	0.21388	-	-	-
obs	0.21544	54721	99.98 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 95.428 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.94 Å²	0 Å²	-1.05 Å²
2-	-	6.89 Å²	0 Å²
3-	-	-	-3.94 Å²

Refinement step

Cycle: LAST / Resolution: 2.68→114.25 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11016	0	76	398	11490

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.005	0.019	11353
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	10413
X-RAY DIFFRACTION	r_angle_refined_deg	1.042	1.939	15413
X-RAY DIFFRACTION	r_angle_other_deg	0.781	3.003	23869
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.126	5	1390
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.341	25.185	569
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.914	15	1886
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.373	15	52
X-RAY DIFFRACTION	r_chiral_restr	0.056	0.2	1664
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.02	13111
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	2693
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.86	2.748	5578
X-RAY DIFFRACTION	r_mcbond_other	0.86	2.748	5577
X-RAY DIFFRACTION	r_mcangle_it	1.5	4.122	6962
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	1.094	2.886	5775
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	A	19376	0.06
1	2	C	19376	0.06
2	1	A	19350	0.05
2	2	E	19350	0.05
3	1	C	19338	0.06
3	2	E	19338	0.06
4	1	B	6802	0.08
4	2	D	6802	0.08
5	1	B	6648	0.1
5	2	F	6648	0.1
6	1	D	6760	0.11
6	2	F	6760	0.11

LS refinement shell

Resolution: 2.68→2.75 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.378	198	-
R_work	0.354	4091	-
obs	-	-	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	0.4884	-0.4281	-1.9357	18.2157	10.4283	12.4546	-0.2827	0.1476	-0.4607	-0.982	-0.2071	-0.8968	0.9321	-0.5764	0.4898	1.6813	0.2023	0.0756	0.3173	-0.2826	1.6472	15.9938	-54.3284	-25.3027
2	2.5546	0.3144	-0.1726	3.134	0.7634	2.1503	-0.1336	-0.3051	-0.1539	-0.111	0.3124	-0.3653	0.121	0.6199	-0.1788	0.0439	0.0709	0.0388	0.602	-0.0428	0.0958	34.1156	-1.4565	-9.5758
3	0.38	0.2306	-0.007	0.1437	0.0097	0.0754	-0.8405	0.3594	-0.1399	-0.5578	0.4409	-0.0746	0.1776	0.1488	0.3996	3.4477	-0.0484	0.2204	1.3922	-0.4696	1.6778	15.323	-50.733	-34.7334
4	0.8352	2.6697	1.4169	18.748	9.6313	7.8711	0.1062	-0.0636	-0.5933	0.694	-0.0152	-1.354	1.4363	0.7635	-0.0911	0.4457	0.2481	0.198	0.286	0.198	0.6035	15.7569	-16.7457	-6.711
5	5.3493	7.8072	8.2722	12.3903	12.6099	13.7662	0.6311	0.4829	-0.0078	0.6008	-0.3805	0.8777	1.2972	-0.2253	-0.2505	2.2443	0.0347	0.0084	1.3476	-0.5916	1.7635	6.9197	-51.1231	-30.3065
6	1.1518	-0.101	0.2902	0.015	-0.0157	0.09	0.0636	0.3838	0.4807	0.0716	-0.1047	-0.0739	0.0955	-0.0134	0.0411	2.7263	-0.2166	0.1852	2.0904	-0.402	1.646	5.9768	-70.4904	-44.9203
7	12.3836	1.1639	1.798	4.2475	2.9518	2.7299	0.3169	0.0948	-1.6182	-1.2335	-0.1895	0.4187	0.3186	-0.7416	-0.1274	3.0007	-0.5854	-0.6939	1.693	-0.4364	1.4871	-6.2891	-39.1826	-41.1485
8	2.0239	0.7183	0.8718	2.6599	1.7167	4.5727	-0.0769	0.4317	0.2149	-0.4598	-0.025	0.2075	-0.601	-0.2597	0.1019	0.1367	0.0983	-0.0585	0.2759	0.0341	0.1467	0.2461	11.4086	-13.4717
9	1.8343	-0.0725	-0.1901	0.0462	-0.0268	0.0613	0.1817	0.1477	-0.9785	-0.0921	-0.0802	0.3072	0.2385	0.0452	-0.1015	2.7626	-0.2892	-0.5714	2.1021	-0.5526	2.1869	-14.9472	-40.7079	-35.7433
10	6.0831	6.6273	3.8755	12.0901	7.6282	6.4555	-0.4632	0.6169	-0.0524	-0.693	0.2289	0.4099	0.2085	0.3046	0.2343	0.2956	0.0562	-0.0282	0.243	-0.0415	0.1122	10.0655	-10.548	-15.5086
11	1.174	-1.267	-0.5299	1.393	0.5824	0.4126	-0.9646	-0.5987	-0.8261	1.1247	1.0046	0.7791	0.9138	0.3248	-0.04	2.513	-0.1714	-0.2084	1.8932	-0.3739	2.6939	-7.3307	-45.3745	-31.8972
12	0.0003	0.0012	-0.0016	0.0178	-0.0116	0.0137	0.0203	0.0025	-0.0104	0.0495	-0.0913	-0.1774	-0.1323	0.0703	0.0709	1.9001	0.0119	0.0152	1.9736	0.0796	2.4828	-20.4859	-63.1878	-43.3442
13	4.4593	2.4894	0.8044	17.8739	1.064	0.1742	0.0619	-0.0096	0.523	-0.2709	-0.152	1.4273	0.0248	-0.0593	0.0901	1.2929	-0.3555	0.2658	0.6693	-0.0721	0.9477	-13.2329	-50.8226	-12.8212
14	1.809	0.0488	-0.3644	2.2132	1.7017	3.8132	-0.2533	-0.3483	-0.2321	0.5672	0.0949	0.1501	1.0939	0.4273	0.1584	0.4034	0.1207	0.0761	0.2696	0.0466	0.1058	9.5869	-6.6313	16.8028
15	0.1866	-0.8921	-0.2724	4.584	1.4414	0.5037	0.0519	-0.0573	0.1818	0.1048	0.3847	-1.498	0.2984	0.1576	-0.4366	1.6665	-0.2553	-0.0896	1.0154	-0.116	1.5811	-5.8151	-56.3816	-10.151
16	1.8137	4.4776	1.5235	22.5289	6.694	4.7152	-0.0107	-0.142	-0.2499	0.2006	-0.4032	0.9381	0.5974	-0.5078	0.4139	0.1487	-0.0051	0.0817	0.223	-0.0121	0.2646	4.0823	-13.5834	-5.3976
17	0.6302	4.1819	0.6973	34.7876	8.2319	2.7653	-0.0039	-0.0494	-0.1966	-0.1462	0.1663	-0.6768	0.0731	0.3406	-0.1624	1.0564	-0.2063	0.0919	0.6203	-0.0884	0.9088	-4.4233	-52.8137	-18.9181
18	1.5204	3.9743	-0.6136	11.9911	-1.2335	0.3405	-0.2881	0.4847	-0.3138	-0.9239	0.1502	-0.3036	0.0174	-0.4694	0.1379	1.491	-0.0974	-0.0448	1.023	-0.1148	1.3062	-10.449	-76.461	-22.6277

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 32
2	X-RAY DIFFRACTION	2	A	33 - 320
3	X-RAY DIFFRACTION	3	B	10 - 64
4	X-RAY DIFFRACTION	4	B	65 - 95
5	X-RAY DIFFRACTION	5	B	96 - 125
6	X-RAY DIFFRACTION	6	B	126 - 157
7	X-RAY DIFFRACTION	7	C	1 - 32
8	X-RAY DIFFRACTION	8	C	33 - 320
9	X-RAY DIFFRACTION	9	D	10 - 64
10	X-RAY DIFFRACTION	10	D	65 - 95
11	X-RAY DIFFRACTION	11	D	96 - 125
12	X-RAY DIFFRACTION	12	D	126 - 157
13	X-RAY DIFFRACTION	13	E	1 - 32
14	X-RAY DIFFRACTION	14	E	33 - 320
15	X-RAY DIFFRACTION	15	F	10 - 64
16	X-RAY DIFFRACTION	16	F	65 - 95
17	X-RAY DIFFRACTION	17	F	96 - 125
18	X-RAY DIFFRACTION	18	F	126 - 157

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