PDB-4cqv: Crystal structure of H5 (tyTy) Del133/Ile155Thr Mutant Haemagglutinin

ID or keywords:

Entry

Database: PDB / ID: 4cqv

Title

Crystal structure of H5 (tyTy) Del133/Ile155Thr Mutant Haemagglutinin

Components

HAEMAGGLUTININ HA1
HAEMAGGLUTININ HA2

Keywords

VIRAL PROTEIN / SIALIC ACID / GLYCOPROTEIN / VIRUS RECEPTOR / AVIAN FLU / SIALYLLACTOSAMINE / 3SLN / 3'SLN / 6SLN / 6'SLN / LSTA

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: 2.86 Å

Authors

Xiong, X. / Xiao, H. / Martin, S.R. / Coombs, P.J. / Liu, J. / Collins, P.J. / Vachieri, S.G. / Walker, P.A. / Lin, Y.P. / McCauley, J.W. ...

Citation

Journal: Virology / Year: 2014
Title: Enhanced Human Receptor Binding by H5 Haemagglutinins.
Authors: Xiong, X. / Xiao, H. / Martin, S.R. / Coombs, P.J. / Liu, J. / Collins, P.J. / Vachieri, S.G. / Walker, P.A. / Lin, Y.P. / Mccauley, J.W. / Gamblin, S.J. / Skehel, J.J.

History

Deposition	Feb 21, 2014	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	May 28, 2014	Provider: repository / Type: Initial release
Revision 1.1	Jun 11, 2014	Group: Database references
Revision 1.2	Jul 29, 2020	Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Other / Structure summary Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / 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 1.3	Dec 20, 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 13, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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Validation report

Summary document	4cqv_validation.pdf.gz	505.7 KB	Display	wwPDB validaton report
Full document	4cqv_full_validation.pdf.gz	519.4 KB	Display
Data in XML	4cqv_validation.xml.gz	53.2 KB	Display
Data in CIF	4cqv_validation.cif.gz	72.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/cq/4cqv ftp://data.pdbj.org/pub/pdb/validation_reports/cq/4cqv	HTTPS FTP

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Related structure data

Related structure data	4cqpC 4cqqC 4cqrC 4cqsC 4cquC 4cqwC 4cqxC 4cqyC 4cqzC 4cr0C 5ajmC 4bgzS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	4k64-3 4k62-4 4jun-d 4yy7-2 4jug-1 2wrf-2 4yy9-1 2wr0-d 3qqe-1 4jum-1 4k66-4 4k67-3 4jul-2 4k65-3 4jug-2 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: HAEMAGGLUTININ HA1

B: HAEMAGGLUTININ HA2

C: HAEMAGGLUTININ HA1

D: HAEMAGGLUTININ HA2

E: HAEMAGGLUTININ HA1

F: HAEMAGGLUTININ HA2

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)	87.407, 117.251, 101.003
Angle α, β, γ (deg.)	90.00, 92.52, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein

HAEMAGGLUTININ HA1

Mass: 37010.672 Da / Num. of mol.: 3
Fragment: HA1 OF TRYPSIN RELEASED ECTODOMAIN, RESIDUES 17-342
Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

INFLUENZA A VIRUS (A/TURKEY/TURKEY/1/2005(H5N1))
Variant: DEL133/ILE155THR MUTANT / Plasmid: PACGP67A / Cell line (production host): SF9 / Production host:

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

#2: Protein

HAEMAGGLUTININ HA2

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

INFLUENZA A VIRUS (A/TURKEY/TURKEY/1/2005(H5N1))
Variant: DEL133/ILE155THR MUTANT / 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.: 8
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.: 6 / Source method: obtained synthetically / Formula: PO₄

#5: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 224 / 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: 2.25 Å³/Da / Density % sol: 45 % / 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: 0.98
Detector	Type: ADSC QUANTUM 315r / Detector: CCD
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.98 Å / Relative weight: 1
Reflection	Resolution: 2.86→70.03 Å / Num. obs: 46268 / % possible obs: 98.3 % / Observed criterion σ(I): 2 / Redundancy: 3 % / R_merge(I) obs: 0.08 / Net I/σ(I): 8.8
Reflection shell	Resolution: 2.86→3.01 Å / Redundancy: 3 % / R_merge(I) obs: 0.52 / Mean I/σ(I) obs: 2 / % possible all: 99

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Processing

Software

Name	Version	Classification
REFMAC	5.7.0032	refinement
xia2		data reduction
SCALA		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4BGZ

4bgz

Resolution: 2.86→70.13 Å / Cor.coef. F_o:F_c: 0.945 / Cor.coef. F_o:F_c free: 0.912 / SU B: 32.202 / SU ML: 0.304 / Cross valid method: THROUGHOUT / ESU R Free: 0.374 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. WITH TLS ADDED

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.24444	2341	5.1 %	RANDOM
R_work	0.19529	-	-	-
obs	0.19778	43919	98.15 %	-

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: 79.448 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	5.45 Å²	-0 Å²	-4.35 Å²
2-	-	-2.81 Å²	0 Å²
3-	-	-	-2.44 Å²

Refinement step

Cycle: LAST / Resolution: 2.86→70.13 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11610	0	142	224	11976

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.006	0.019	12039
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	11041
X-RAY DIFFRACTION	r_angle_refined_deg	1.17	1.949	16334
X-RAY DIFFRACTION	r_angle_other_deg	0.764	3.003	25357
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.37	5	1449
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.649	25.147	614
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.083	15	2016
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	11.846	15	56
X-RAY DIFFRACTION	r_chiral_restr	0.061	0.2	1742
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.021	13817
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	2843
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	1.315	3.824	5814
X-RAY DIFFRACTION	r_mcbond_other	1.315	3.823	5813
X-RAY DIFFRACTION	r_mcangle_it	2.256	5.733	7257
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	1.714	4.035	6225
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

LS refinement shell

Resolution: 2.86→2.934 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.398	168	-
R_work	0.332	3222	-
obs	-	-	98.18 %

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	2.3268	-1.3679	2.2082	1.232	-0.5903	3.5664	-0.5469	-0.1759	0.5558	0.4317	0.2027	-0.4202	-0.5848	-0.0478	0.3443	0.3916	0.0795	-0.176	0.2631	-0.1462	0.2828	-20.6797	-18.1586	14.7323
2	1.4333	0.8393	0.9019	2.139	0.1574	2.6649	-0.238	-0.1078	0.1034	-0.6467	0.0147	0.0782	0.0195	-0.1227	0.2232	0.6504	-0.0175	-0.0669	0.0302	0.0343	0.1595	-51.3317	-15.8448	-40.4088
3	1.2605	-0.8564	2.7104	2.4427	-3.3101	9.0526	0.0091	-0.1669	0.1466	-0.0702	0.1517	-0.1208	-0.0871	0.2659	-0.1608	0.4459	-0.0015	0.0093	0.2738	-0.0947	0.3162	-34.5022	-13.429	-15.4438
4	15.5066	1.5675	16.631	1.0259	1.7613	21.9513	0.4258	-0.8566	-0.4784	-0.0763	0.0591	-0.3857	0.3885	-0.6597	-0.4848	0.2772	0.0928	-0.0444	0.2709	-0.0168	0.3433	-25.3314	-20.9181	9.4059
5	8.1786	-2.6893	4.6181	1.1149	-0.8633	8.7712	-1.1668	-0.6752	1.3995	0.5822	0.4017	-0.4192	-1.0802	0.1185	0.765	0.6549	0.129	-0.3145	0.3504	-0.2802	0.6991	-7.1467	-17.6105	24.3573
6	22.9173	6.4119	12.5925	10.1656	3.4033	10.6262	-0.3215	0.4691	0.5871	-0.2898	-0.3216	-0.502	-1.0151	0.1743	0.643	0.2516	-0.0567	0.0631	0.5052	-0.0425	0.4436	-11.0458	-21.8276	3.9127
7	15.4136	9.0239	12.7209	9.8574	3.9325	13.2869	-0.6083	0.1159	0.1861	0.0497	0.327	0.0122	-0.9745	-0.1249	0.2813	0.3448	0.023	0.0575	0.2031	-0.0431	0.2288	-42.7599	-29.8567	-18.8396
8	8.108	1.9106	7.9183	2.6271	2.2934	9.4123	-0.3053	0.0071	0.2867	0.6134	0.2126	-0.8127	-0.3053	0.4466	0.0927	0.2659	0.0541	-0.2285	0.3967	-0.1354	0.5372	-7.1935	-25.7048	18.1239
9	3.878	-0.3579	3.8946	1.5977	-0.3899	3.9194	0.4747	-0.651	-0.4251	0.0001	-0.0271	0.2347	0.4963	-0.6006	-0.4476	0.1192	-0.0426	0.055	0.5217	0.1384	0.278	-48.4026	-49.6696	-2.0392
10	2.5545	-0.2688	0.6597	3.1371	-0.7216	5.0794	0.1134	-0.3575	-0.0297	-0.9273	0.1614	0.839	0.4062	-0.4735	-0.2748	0.2986	-0.0888	-0.2771	0.2873	0.107	0.4992	-72.0705	-41.9211	-30.622
11	8.2919	-3.0151	6.3357	2.3721	-1.592	5.2479	-0.0331	-0.6276	-0.0145	0.2865	0.0233	0.0671	0.0944	-0.64	0.0098	0.1371	-0.0963	0.0834	0.5233	0.1487	0.2387	-51.4395	-47.872	-1.8748
12	6.2145	-0.7362	9.5266	2.532	0.2084	15.3376	0.0538	0.2771	-0.1667	0.2499	0.3033	-0.108	0.227	0.597	-0.3571	0.0817	-0.0806	0.0095	0.4109	0.0916	0.341	-31.3698	-47.927	8.9879
13	2.6445	0.1687	2.0496	3.0658	-0.3624	5.5913	0.1084	-0.3002	-0.0963	0.6397	-0.0374	-0.068	0.7063	0.1369	-0.0711	0.3937	0.0872	-0.1608	0.2376	0.038	0.2166	-17.0549	-46.6203	31.9911
14	1.7171	-1.8313	2.6553	6.9366	-6.3273	10.911	-0.0434	-0.1619	0.4496	-0.0519	-0.185	0.2513	0.1769	-0.6013	0.2284	0.1128	0.0522	0.0609	0.4452	-0.0565	0.4281	-29.1621	-37.7639	20.8399
15	4.3705	-0.6449	7.9272	0.3132	-1.0154	14.6005	-0.0887	-0.0403	-0.0021	-0.0261	0.044	-0.083	-0.2247	0.0236	0.0447	0.0816	-0.019	0.0931	0.4283	0.0333	0.3044	-29.9306	-41.325	0.2244
16	4.0778	1.4423	1.6883	6.5069	-1.7661	7.564	-0.1222	-0.5265	0.2545	0.5933	0.0794	-0.2212	-0.3914	0.6181	0.0427	0.5235	0.0258	-0.3002	0.478	-0.0986	0.193	-9.8193	-37.7729	43.3377
17	2.2045	1.3184	3.6981	1.6463	2.3167	7.4167	0.0072	0.3345	-0.1714	-0.4854	0.308	-0.66	0.1416	1.1395	-0.3152	0.3248	0.0657	0.2843	0.4644	-0.1837	0.4821	-13.7669	-45.4635	-22.23
18	2.8526	-1.2184	0.4545	1.7734	0.4366	0.4952	0.1006	-0.2191	0.0836	-0.3679	0.0961	-0.2955	-0.0354	0.1055	-0.1966	0.8867	-0.0015	0.1774	0.1856	-0.0996	0.1766	-38.1149	-50.9585	-43.3224
19	2.9024	-0.6402	1.07	2.357	0.4748	1.9086	0.1981	0.0949	0.0026	-0.667	-0.1574	0.3265	-0.228	0.1633	-0.0407	0.8987	0.0263	0.0277	0.0753	-0.0816	0.1231	-45.8686	-49.2207	-50.5617
20	2.7639	1.741	4.6283	2.3929	3.0027	7.9986	0.1544	0.0738	-0.1047	-0.366	0.1864	-0.7457	0.2512	0.4772	-0.3409	0.1928	0.0107	0.2469	0.5417	-0.2063	0.4668	-13.5499	-44.202	-18.6064
21	2.8351	0.8551	1.4348	3.3918	-0.0808	7.364	0.175	0.2574	-0.1159	0.3291	-0.0533	-0.4105	0.9097	1.4327	-0.1218	0.2134	0.2863	-0.1694	0.6364	-0.1731	0.5495	1.6784	-45.9786	9.9444
22	8.5286	-6.0987	8.5797	9.0218	-4.8829	12.1444	0.1144	0.2001	-0.0017	-0.2894	-0.0241	-0.4736	0.0255	0.5996	-0.0903	0.1793	-0.062	0.1929	0.222	0.0058	0.2783	-33.2761	-37.3087	-23.2011
23	15.3654	-3.2204	15.4382	1.2071	-2.8055	16.5194	-0.2285	-0.5297	0.3756	0.1269	0.0823	-0.4887	0.029	-0.1273	0.1462	0.092	0.0612	0.005	0.5321	-0.0796	0.4432	-8.4687	-39.3884	8.4363
24	2.5813	0.94	-6.8808	0.6184	-1.4875	22.1809	-0.1116	-0.8499	-0.4708	0.515	0.0378	-0.5659	2.5073	3.3682	0.0738	1.2677	0.6309	-0.9673	1.432	-0.0582	1.2293	11.1378	-50.4713	27.9721

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	-1 - 39
2	X-RAY DIFFRACTION	2	A	40 - 254
3	X-RAY DIFFRACTION	3	A	255 - 304
4	X-RAY DIFFRACTION	4	A	305 - 320
5	X-RAY DIFFRACTION	5	B	1 - 37
6	X-RAY DIFFRACTION	6	B	38 - 59
7	X-RAY DIFFRACTION	7	B	60 - 82
8	X-RAY DIFFRACTION	8	B	83 - 166
9	X-RAY DIFFRACTION	9	C	-1 - 103
10	X-RAY DIFFRACTION	10	C	104 - 256
11	X-RAY DIFFRACTION	11	C	257 - 299
12	X-RAY DIFFRACTION	12	C	300 - 320
13	X-RAY DIFFRACTION	13	D	1 - 31
14	X-RAY DIFFRACTION	14	D	32 - 61
15	X-RAY DIFFRACTION	15	D	62 - 124
16	X-RAY DIFFRACTION	16	D	125 - 166
17	X-RAY DIFFRACTION	17	E	-1 - 84
18	X-RAY DIFFRACTION	18	E	85 - 122
19	X-RAY DIFFRACTION	19	E	123 - 266
20	X-RAY DIFFRACTION	20	E	267 - 320
21	X-RAY DIFFRACTION	21	F	1 - 57
22	X-RAY DIFFRACTION	22	F	58 - 83
23	X-RAY DIFFRACTION	23	F	84 - 136
24	X-RAY DIFFRACTION	24	F	137 - 166

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