PDB-4lxv: Crystal Structure of the Hemagglutinin from a H1N1pdm A/WASHINGTO...

ID or keywords:

Entry

Database: PDB / ID: 4lxv

Title

Crystal Structure of the Hemagglutinin from a H1N1pdm A/WASHINGTON/5/2011 virus

Components

(Hemagglutinin

) x 2

Keywords

VIRAL PROTEIN /

Hemagglutinin /

pandemic /

influenza

Function / homology

Function and homology information

viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / membrane => GO:0016020 / 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 /

MOLECULAR REPLACEMENT / Resolution: 3 Å

Authors

Yang, H. / Chang, J.C. / Guo, Z. / Carney, P.J. / Shore, D.A. / Donis, R.O. / Cox, N.J. / Villanueva, J.M. / Klimov, A.I. / Stevens, J.

Citation

Journal: J.Virol. / Year: 2014
Title: Structural Stability of Influenza A(H1N1)pdm09 Virus Hemagglutinins.
Authors: Yang, H. / Chang, J.C. / Guo, Z. / Carney, P.J. / Shore, D.A. / Donis, R.O. / Cox, N.J. / Villanueva, J.M. / Klimov, A.I. / Stevens, J.

History

Deposition	Jul 30, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 26, 2014	Provider: repository / Type: Initial release
Revision 1.1	Apr 30, 2014	Group: Database references
Revision 1.2	Dec 10, 2014	Group: Structure summary
Revision 2.0	Jul 29, 2020	Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / 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_unobs_or_zero_occ_atoms / struct_asym / struct_conn / struct_ref_seq_dif / 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 / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _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_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_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 / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details Description: Carbohydrate remediation / Provider: repository / Type: Remediation

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4lxv.cif.gz	1.1 MB	Display	PDBx/mmCIF format
PDB format	pdb4lxv.ent.gz	969 KB	Display	PDB format
PDBx/mmJSON format	4lxv.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

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

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Related structure data

Similar structure data	4uo5-d 4wsu-d 5t0b-d 4xkd-d 3lzg-1 3ubq-2 1rd8-d 4xkg-d 4m4y-d 2wr5-d 4wsv-d 4f3z-d 4gxx-d 3ube-1 5t0d-d 1hgj-d 4we9-1 6n08-d 5t0e-d 2fk0-2 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

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

D: Hemagglutinin

E: Hemagglutinin

F: Hemagglutinin

G: Hemagglutinin

H: Hemagglutinin

I: Hemagglutinin

J: Hemagglutinin

K: Hemagglutinin

L: Hemagglutinin

hetero molecules

350 kDa, 12 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Hemagglutinin

B: Hemagglutinin

C: Hemagglutinin

D: Hemagglutinin

E: Hemagglutinin

F: Hemagglutinin

hetero molecules

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

2

G: Hemagglutinin

H: Hemagglutinin

I: Hemagglutinin

J: Hemagglutinin

K: Hemagglutinin

L: Hemagglutinin

hetero molecules

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

Unit cell

Length a, b, c (Å)	73.241, 226.002, 271.003
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:
NCS domain segments:

Dom-ID	Ens-ID	Auth asym-ID	Auth seq-ID
1	1	A	0 - 322
2	1	C	0 - 322
1	2	A	0 - 322
2	2	E	0 - 322
1	3	A	0 - 322
2	3	G	0 - 322
1	4	A	0 - 322
2	4	I	0 - 322
1	5	A	0 - 322
2	5	K	0 - 322
1	6	C	0 - 322
2	6	E	0 - 322
1	7	C	0 - 322
2	7	G	0 - 322
1	8	C	0 - 322
2	8	I	0 - 322
1	9	C	0 - 322
2	9	K	0 - 322
1	10	E	0 - 322
2	10	G	0 - 322
1	11	E	0 - 322
2	11	I	0 - 322
1	12	E	0 - 322
2	12	K	0 - 322
1	13	G	0 - 322
2	13	I	0 - 322
1	14	G	0 - 322
2	14	K	0 - 322
1	15	I	0 - 322
2	15	K	0 - 322
1	16	B	2 - 172
2	16	D	2 - 172
1	17	B	2 - 172
2	17	F	2 - 172
1	18	B	2 - 172
2	18	H	2 - 172
1	19	B	2 - 172
2	19	J	2 - 172
1	20	B	2 - 172
2	20	L	2 - 172
1	21	D	2 - 172
2	21	F	2 - 172
1	22	D	2 - 172
2	22	H	2 - 172
1	23	D	2 - 172
2	23	J	2 - 172
1	24	D	2 - 172
2	24	L	2 - 172
1	25	F	2 - 172
2	25	H	2 - 172
1	26	F	2 - 172
2	26	J	2 - 172
1	27	F	2 - 172
2	27	L	2 - 172
1	28	H	2 - 172
2	28	J	2 - 172
1	29	H	2 - 172
2	29	L	2 - 172
1	30	J	2 - 172
2	30	L	2 - 172

NCS ensembles :

#1: Protein

Hemagglutinin /

Mass: 36806.480 Da / Num. of mol.: 6 / Fragment: HEMAGGLUTININ HA1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Influenza A virus / Strain: H1N1 PDM09 / Gene: HA / Production host:

trichoplusia ni (cabbage looper) / References: UniProt: J7MFR5

#2: Protein

Hemagglutinin /

Mass: 20829.123 Da / Num. of mol.: 6 / Fragment: HEMAGGLUTININ HA2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Influenza A virus / Strain: H1N1 PDM09 / Gene: HA / Production host:

trichoplusia ni (cabbage looper) / References: UniProt: J7MFR5

#3: 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.: 5
Source method: isolated from a genetically manipulated source

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

#4: Sugar

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

N-Acetylglucosamine

Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 10
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

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.24 Å³/Da / Density % sol: 62.02 %
Crystal grow	Temperature: 293 K / pH: 8 Details: 0.2M Ammonium Tartrate Dibasic 20% PEG3350, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1
Detector	Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 30, 2012
Radiation	Monochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 3→50 Å / % possible obs: 98.4 % / Observed criterion σ(I): 2
Reflection shell	Resolution: 3→3.11 Å / % possible all: 98

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Processing

Software

Name	Version	Classification
HKL-2000		data collection
PHASER		phasing
REFMAC	5.7.0029	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 3→49.78 Å / Cor.coef. F_o:F_c: 0.926 / Cor.coef. F_o:F_c free: 0.915 / SU B: 39.425 / SU ML: 0.299 / Cross valid method: THROUGHOUT / ESU R Free: 0.373 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.23	4494	5 %	RANDOM
R_work	0.205	-	-	-
obs	0.207	85184	98.2 %	-
all	-	78146	-	-

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: 68.422 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.81 Å²	0 Å²	0 Å²
2-	-	-7.32 Å²	0 Å²
3-	-	-	8.13 Å²

Refinement step

Cycle: LAST / Resolution: 3→49.78 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	23460	0	280	0	23740

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.019	24331
X-RAY DIFFRACTION	r_bond_other_d	0.006	0.02	22546
X-RAY DIFFRACTION	r_angle_refined_deg	1.521	1.953	33001
X-RAY DIFFRACTION	r_angle_other_deg	1.158	3.003	51887
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.69	5	2952
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.79	25	1140
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	18.874	15	4104
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.276	15	90
X-RAY DIFFRACTION	r_chiral_restr	0.087	0.2	3595
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	27578
X-RAY DIFFRACTION	r_gen_planes_other	0.005	0.02	5598
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
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it
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	18980	0.07
1	2	C	18980	0.07
2	1	A	18642	0.07
2	2	E	18642	0.07
3	1	A	19647	0.01
3	2	G	19647	0.01
4	1	A	18978	0.07
4	2	I	18978	0.07
5	1	A	18638	0.07
5	2	K	18638	0.07
6	1	C	18787	0.07
6	2	E	18787	0.07
7	1	C	18968	0.07
7	2	G	18968	0.07
8	1	C	19605	0.01
8	2	I	19605	0.01
9	1	C	18790	0.07
9	2	K	18790	0.07
10	1	E	18625	0.07
10	2	G	18625	0.07
11	1	E	18788	0.07
11	2	I	18788	0.07
12	1	E	19666	0.01
12	2	K	19666	0.01
13	1	G	18971	0.07
13	2	I	18971	0.07
14	1	G	18627	0.07
14	2	K	18627	0.07
15	1	I	18794	0.07
15	2	K	18794	0.07
16	1	B	9013	0.07
16	2	D	9013	0.07
17	1	B	8993	0.08
17	2	F	8993	0.08
18	1	B	9237	0.01
18	2	H	9237	0.01
19	1	B	9001	0.07
19	2	J	9001	0.07
20	1	B	8984	0.08
20	2	L	8984	0.08
21	1	D	8938	0.08
21	2	F	8938	0.08
22	1	D	9009	0.07
22	2	H	9009	0.07
23	1	D	9250	0.02
23	2	J	9250	0.02
24	1	D	8929	0.08
24	2	L	8929	0.08
25	1	F	8994	0.08
25	2	H	8994	0.08
26	1	F	8924	0.09
26	2	J	8924	0.09
27	1	F	9307	0.01
27	2	L	9307	0.01
28	1	H	9002	0.07
28	2	J	9002	0.07
29	1	H	8979	0.08
29	2	L	8979	0.08
30	1	J	8919	0.09
30	2	L	8919	0.09

LS refinement shell

Resolution: 3→3.08 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.377	330	-
R_work	0.342	6203	-
obs	-	-	97.93 %

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	0.1945	0.4299	0.0771	1.0965	0.1108	0.1766	0.0731	0.005	-0.0465	0.1911	-0.0051	-0.0444	0.002	0.0723	-0.0681	0.0858	0.0189	-0.0128	0.1816	-0.0293	0.0417	91.1345	243.4524	306.6501
2	0.1604	0.2297	0.0655	0.967	0.1452	0.1886	0.0166	-0.0247	-0.0014	-0.0729	-0.0143	0.1705	-0.1173	-0.0568	-0.0023	0.1102	0.0416	-0.0161	0.1895	0.0012	0.0487	61.3984	254.7337	294.084
3	0.167	0.4524	0.0172	1.4291	0.0531	0.342	-0.0297	0.0804	-0.0474	-0.1719	0.0428	-0.1111	-0.0693	0.1333	-0.0131	0.1186	0.0207	0.0079	0.2457	-0.043	0.0157	87.2765	246.8604	272.6711
4	0.0758	0.1725	0.0655	1.2089	0.5065	0.2781	-0.0407	-0.0677	0.0316	0.0863	-0.0284	0.1862	0.0576	-0.032	0.0692	0.1755	0.0056	0.0001	0.2043	-0.0127	0.0312	52.4483	233.3003	246.632
5	0.0458	0.1838	0.0552	1.4023	0.2596	0.0769	-0.062	-0.0037	0.0052	-0.2708	0.0618	0.1142	-0.0642	0.0322	0.0003	0.2293	-0.0025	-0.0578	0.1448	-0.0124	0.0323	54.3697	244.3471	214.0865
6	0.0967	0.2215	0.1077	1.1869	0.3322	0.2313	0.0417	0.0098	-0.0491	0.078	0.024	-0.2033	-0.0229	0.092	-0.0657	0.1314	-0.009	-0.032	0.178	-0.0243	0.0411	82.9261	234.8479	230.5364
7	0.2407	0.2819	-0.0068	3.5647	-0.3824	0.0444	0.0285	0.0318	-0.0315	-0.1806	-0.017	0.0501	0.032	-0.0012	-0.0115	0.193	0.0012	-0.0613	0.0876	-0.013	0.0228	69.879	195.8409	297.4015
8	1.0476	1.4825	0.0694	3.2009	0.2662	0.0447	0.068	0.0358	-0.0808	0.0339	-0.0538	0.0899	0.0249	-0.0254	-0.0142	0.075	-0.0316	-0.0954	0.1295	0.0019	0.1418	51.3995	202.7563	289.9786
9	0.272	0.6706	0.0911	3.1146	0.7079	0.3158	0.0446	0.0678	-0.0417	-0.0899	-0.0301	0.0789	0.0767	0.0021	-0.0145	0.2009	0.0297	-0.0836	0.1374	-0.0713	0.0614	67.007	198.1651	276.5515
10	0.4474	0.6066	-0.0789	2.5333	0.3949	0.172	-0.0903	0.0632	-0.0979	0.0524	0.0821	-0.2134	0.0195	-0.0067	0.0082	0.2606	-0.0474	-0.0439	0.083	-0.0027	0.0392	50.0363	185.798	223.1805
11	0.4205	0.9156	0.7449	3.0357	1.8116	1.3765	0.1463	0.0045	-0.0454	0.2596	-0.0943	0.0632	0.1998	0.0122	-0.0521	0.1813	-0.0204	-0.0282	0.1361	-0.0156	0.0301	51.2258	192.3353	203.5323
12	0.318	-0.4286	-0.284	3.0375	1.0424	0.4306	0.0724	0.0418	-0.0477	0.0466	-0.0554	-0.163	-0.0236	-0.0358	-0.017	0.1971	0.029	-0.0647	0.1118	-0.008	0.0379	68.6495	186.7384	213.4565

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	0 - 322
2	X-RAY DIFFRACTION	2	C	0 - 322
3	X-RAY DIFFRACTION	3	E	0 - 322
4	X-RAY DIFFRACTION	4	G	0 - 322
5	X-RAY DIFFRACTION	5	I	0 - 322
6	X-RAY DIFFRACTION	6	K	0 - 322
7	X-RAY DIFFRACTION	7	B	2 - 172
8	X-RAY DIFFRACTION	8	D	2 - 172
9	X-RAY DIFFRACTION	9	F	2 - 172
10	X-RAY DIFFRACTION	10	H	2 - 172
11	X-RAY DIFFRACTION	11	J	2 - 172
12	X-RAY DIFFRACTION	12	L	2 - 172

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