PDB-4wsr: The crystal structure of hemagglutinin form A/chicken/New York/14...

ID or keywords:

Entry

Database: PDB / ID: 4wsr

Title

The crystal structure of hemagglutinin form A/chicken/New York/14677-13/1998

Components

Hemagglutinin

Keywords

VIRAL PROTEIN /

Influenza virus /

hemagglutinin / H6

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
Similarity search - Function

Biological species

Influenza A virus

Method

X-RAY DIFFRACTION /

SYNCHROTRON / Resolution: 2.5 Å

Authors

Yang, H. / Carney, P.J. / Chang, J.C. / Villanueva, J.M. / Stevens, J.

Citation

Journal: J.Virol. / Year: 2015
Title: Structure and receptor binding preferences of recombinant hemagglutinins from avian and human h6 and h10 influenza a virus subtypes.
Authors: Yang, H. / Carney, P.J. / Chang, J.C. / Villanueva, J.M. / Stevens, J.

History

Deposition	Oct 28, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 25, 2015	Provider: repository / Type: Initial release
Revision 1.1	Apr 1, 2015	Group: Non-polymer description / Other
Revision 2.0	Jul 29, 2020	Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Source and taxonomy / Structure summary Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / entity_src_gen / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_mod_residue / pdbx_struct_oper_list / pdbx_struct_special_symmetry / struct_asym / struct_conn / struct_site / struct_site_gen Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _chem_comp.type / _entity_src_gen.pdbx_alt_source_flag / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_mod_residue.auth_asym_id / _pdbx_struct_mod_residue.auth_seq_id / _pdbx_struct_mod_residue.label_asym_id / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_special_symmetry.label_asym_id / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_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
Revision 2.1	Dec 27, 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 / 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 / _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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PDBx/mmCIF format	4wsr.cif.gz	1.2 MB	Display	PDBx/mmCIF format
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Validation report

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

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Related structure data

Related structure data	4wssC 4wstC 4wsuC 4wsvC 4wswC 4wsxC C: citing same article (ref.)
Similar structure data	4wsv-d 4m4y-d 4wsu-d 4lxv-1 4kwm-3 4xke-d 5t0b-d 5t0d-d 4xkd-d 2wr5-d 5t08-d 5xl2-d 4xkf-d 3ubq-2 4mhi-1 4cz0-d 10697 4jtv-2 4uny-d 3ku6-1 Search similar-shape structures by Omokage search (details) 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

Related structure data

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#76 - Apr 2006 Hemagglutinin similarity (6) #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

E: Hemagglutinin

D: Hemagglutinin

F: Hemagglutinin

hetero molecules

351 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Hemagglutinin

B: Hemagglutinin

C: Hemagglutinin

hetero molecules

defined by author&software
176 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

E: Hemagglutinin

D: Hemagglutinin

F: Hemagglutinin

hetero molecules

defined by author&software
175 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	252.545, 134.822, 123.093
Angle α, β, γ (deg.)	90.00, 113.23, 90.00
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	B-884- HOH

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: 0 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: 0 / Auth seq-ID: 1 - 498 / Label seq-ID: 5 - 502

NCS ensembles :

ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

#1: Protein

Hemagglutinin /

Mass: 57872.797 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Influenza A virus (A/chicken/New York/14677-13/1998(H6N2))
Strain: A/chicken/New York/14677-13/1998(H6N2) / Gene: HA / Production host:

Trichoplusia ni (cabbage looper) / References: UniProt: Q0A3A5

#2: Polysaccharide

2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

Type: oligosaccharide

/ Mass: 424.401 Da / Num. of mol.: 4 / Source method: obtained synthetically

Descriptor	Type	Program
DGlcpNAcb1-4DGlcpNAcb1-	Glycam Condensed Sequence	GMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1	WURCS	PDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}	LINUCS	PDB-CARE

#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 /

N-Acetylglucosamine

Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 9 / Source method: obtained synthetically / 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 /

Water

Mass: 18.015 Da / Num. of mol.: 1024 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 2.77 Å³/Da / Density % sol: 55.64 %
Crystal grow	Temperature: 293 K / Method: microbatch / Details: 0.2 M ammonium fluoride, 20% (w/v) PEG 3350

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
Detector	Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Mar 20, 2009
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.5→48 Å / Num. obs: 129493 / % possible obs: 99 % / Redundancy: 3.8 % / Net I/σ(I): 30.6

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Processing

Software

Name: REFMAC / Version: 5.8.0049 / Classification: refinement

Refinement

Resolution: 2.5→48 Å / Cor.coef. F_o:F_c: 0.943 / Cor.coef. F_o:F_c free: 0.913 / SU B: 23.103 / SU ML: 0.223 / Cross valid method: THROUGHOUT / ESU R: 0.528 / ESU R Free: 0.28 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.24617	6504	5 %	RANDOM
R_work	0.20997	-	-	-
obs	0.21176	122862	98.86 %	-

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: 67.137 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.05 Å²	0 Å²	-0.83 Å²
2-	-	1.76 Å²	0 Å²
3-	-	-	-0.8 Å²

Refinement step

Cycle: LAST / Resolution: 2.5→48 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	23168	0	238	1024	24430

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.019	23984
X-RAY DIFFRACTION	r_bond_other_d	0.008	0.02	22067
X-RAY DIFFRACTION	r_angle_refined_deg	1.601	1.95	32539
X-RAY DIFFRACTION	r_angle_other_deg	1.499	3	50763
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.138	5	2904
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.063	24.662	1167
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.298	15	4040
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.21	15	133
X-RAY DIFFRACTION	r_chiral_restr	0.091	0.2	3506
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.02	27355
X-RAY DIFFRACTION	r_gen_planes_other	0.007	0.02	5634
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	3.288	4.057	11649
X-RAY DIFFRACTION	r_mcbond_other	3.281	4.056	11648
X-RAY DIFFRACTION	r_mcangle_it	5.23	6.07	14542
X-RAY DIFFRACTION	r_mcangle_other	5.231	6.071	14543
X-RAY DIFFRACTION	r_scbond_it	3.546	4.424	12333
X-RAY DIFFRACTION	r_scbond_other	3.546	4.424	12333
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	5.746	6.499	17996
X-RAY DIFFRACTION	r_long_range_B_refined	9.298	32.775	27831
X-RAY DIFFRACTION	r_long_range_B_other	9.299	32.785	27790
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	27530	0.11
1	2	B	27530	0.11
2	1	A	27338	0.11
2	2	C	27338	0.11
3	1	A	27150	0.12
3	2	E	27150	0.12
4	1	A	27165	0.12
4	2	D	27165	0.12
5	1	A	26678	0.12
5	2	F	26678	0.12
6	1	B	27530	0.11
6	2	C	27530	0.11
7	1	B	26896	0.12
7	2	E	26896	0.12
8	1	B	27127	0.12
8	2	D	27127	0.12
9	1	B	26482	0.13
9	2	F	26482	0.13
10	1	C	27162	0.11
10	2	E	27162	0.11
11	1	C	27139	0.12
11	2	D	27139	0.12
12	1	C	26861	0.12
12	2	F	26861	0.12
13	1	E	26910	0.13
13	2	D	26910	0.13
14	1	E	26687	0.13
14	2	F	26687	0.13
15	1	D	26693	0.13
15	2	F	26693	0.13

LS refinement shell

Resolution: 2.5→2.565 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.34	451	-
R_work	0.307	8526	-
obs	-	-	93.33 %

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	0.2056	-0.0065	-0.0982	0.6295	-0.0316	0.0533	-0.0229	0.0957	-0.0706	-0.0292	-0.0269	0.0071	-0.0161	-0.0348	0.0498	0.1969	0.0034	-0.1098	0.3441	-0.0375	0.2438	-26.6298	54.4842	9.9749
2	0.1165	0.0093	0.0459	0.184	0.0993	0.1035	-0.0028	0.0253	0.0471	0.0622	-0.0306	0.0316	0.1092	0.0211	0.0335	0.2492	0.0016	-0.0826	0.3622	0.02	0.1839	-34.9754	52.1022	38.8756
3	0.1203	-0.0412	-0.1781	0.7409	0.0784	0.273	-0.0527	0.0632	-0.0128	-0.027	-0.0125	0.1205	0.0441	-0.1145	0.0652	0.1285	-0.0293	-0.1649	0.3562	-0.0438	0.278	-56.015	53.8342	17.4235
4	0.0974	0.2419	-0.0743	1.9018	-0.0195	0.1517	0.0349	0.1765	-0.0017	0.0656	0.1126	0.0961	0.0045	-0.2613	-0.1474	0.0361	0.0342	-0.0843	0.4986	0.1543	0.3421	-39.1318	76.3746	-29.5878
5	0.2779	0.1443	-0.2189	0.4051	0.0017	0.2494	0.0891	0.0328	-0.018	0.0441	-0.0152	-0.0261	-0.0047	-0.0234	-0.0738	0.2005	0.0175	-0.1105	0.3166	0.0227	0.2356	-11.6529	74.4793	-17.8657
6	0.1666	0.1214	-0.172	0.5706	0.0994	0.309	-0.0376	0.2384	-0.0019	0.072	0.0304	-0.0848	0.0318	-0.3449	0.0072	0.1306	0.0078	-0.0557	0.4519	0.0162	0.2166	-15.7894	76.6303	-48.1622

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 927
2	X-RAY DIFFRACTION	2	B	1 - 919
3	X-RAY DIFFRACTION	3	C	1 - 875
4	X-RAY DIFFRACTION	4	E	1 - 785
5	X-RAY DIFFRACTION	5	D	1 - 912
6	X-RAY DIFFRACTION	6	F	1 - 2206

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