PDB-6id9: Crystal structure of H7 hemagglutinin mutant H7-SGTL ( A138S, V18...

ID or keywords:

Entry

Database: PDB / ID: 6id9

Title

Crystal structure of H7 hemagglutinin mutant H7-SGTL ( A138S, V186G, P221T) from the influenza virus A/Anhui/1/2013 (H7N9)

Components

Hemagglutinin HA1 chain
Hemagglutinin HA2 chain

Keywords

VIRAL PROTEIN /

influenza virus /

H7N9 /

Hemagglutinin

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 /

metal ion binding
Similarity search - Function

Biological species

Influenza A virus

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.7 Å

Authors

Gao, G.F. / Xu, Y. / Qi, J.X.

Citation

Journal: Cell Rep / Year: 2019
Title: Avian-to-Human Receptor-Binding Adaptation of Avian H7N9 Influenza Virus Hemagglutinin.
Authors: Xu, Y. / Peng, R. / Zhang, W. / Qi, J. / Song, H. / Liu, S. / Wang, H. / Wang, M. / Xiao, H. / Fu, L. / Fan, Z. / Bi, Y. / Yan, J. / Shi, Y. / Gao, G.F.

History

Deposition	Sep 9, 2018	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Nov 27, 2019	Provider: repository / Type: Initial release
Revision 1.1	Dec 4, 2019	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2	Jul 29, 2020	Group: Data collection / Derived calculations / Structure summary Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / 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_entity_nonpoly.name / _struct_conn.pdbx_role Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3	Nov 22, 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

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6id9.cif.gz	208.4 KB	Display	PDBx/mmCIF format
PDB format	pdb6id9.ent.gz	167.4 KB	Display	PDB format
PDBx/mmJSON format	6id9.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/id/6id9 ftp://data.pdbj.org/pub/pdb/validation_reports/id/6id9	HTTPS FTP

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Related structure data

Related structure data	6icwC 6icxC 6icyC 6id2C 6id3C 6id5C 6id8C 6idaC 6idbC 6iddC 6idzC 4kolS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5vjk-1 6d7c-1 4kom-1 4lkk-1 4n5j-2 4lkg-2 4dj6-d 4lki-1 6id8-1 6icw-1 6icx-1 5xl1-1 5xl1-2 4ln4-1 4bsf-1 4lcx-d 4bsg-1 5t6s-2 6id2-2 6id3-1 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

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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 HA1 chain

B: Hemagglutinin HA2 chain

hetero molecules

56.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Hemagglutinin HA1 chain

B: Hemagglutinin HA2 chain

hetero molecules

A: Hemagglutinin HA1 chain

B: Hemagglutinin HA2 chain

hetero molecules

A: Hemagglutinin HA1 chain

B: Hemagglutinin HA2 chain

hetero molecules

defined by author&software
Evidence: homology, gel filtration
168 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	116.268, 116.268, 293.839
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	155
Space group name H-M	H32

Components on special symmetry positions

ID	Model	Components
1	1	B-602- HOH
2	1	B-605- HOH
3	1	B-607- HOH

#1: Protein

Hemagglutinin HA1 chain

Mass: 34971.469 Da / Num. of mol.: 1 / Mutation: A138S,V186G,P221T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Influenza A virus / Gene: HA / Production host:

Spodoptera frugiperda (fall armyworm) / References: UniProt: R4NN21

#2: Protein

Hemagglutinin HA2 chain

Mass: 20442.463 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Influenza A virus / Gene: HA / Production host:

Spodoptera frugiperda (fall armyworm) / References: UniProt: R4NN21

#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.: 3
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: Water

ChemComp-HOH / water /

Water

Mass: 18.015 Da / Num. of mol.: 25 / Source method: isolated from a natural source / Formula: H₂O

Sequence details

Sequence reference R4NN21_9INFA was used according to author's suggestion. Author stated ...

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.45 Å³/Da / Density % sol: 64.34 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 2.0M Ammonium sulfate, 0.1M Sodium HEPES pH 7.5, 5% v/v PEG 400

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97923 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 11, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97923 Å / Relative weight: 1
Reflection	Resolution: 2.7→50 Å / Num. obs: 20977 / % possible obs: 97.5 % / Redundancy: 4.7 % / Net I/σ(I): 13.24
Reflection shell	Resolution: 2.7→2.79 Å

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Processing

Software

Name	Version	Classification
PHENIX	(1.11.1_2575: ???)	refinement
HKL-3000		data reduction
HKL-3000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4KOL

4kol

Resolution: 2.7→41.528 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.81

	R_factor	Num. reflection	% reflection
R_free	0.2869	1102	5.26 %
R_work	0.2449	-	-
obs	0.2471	20968	97.39 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 2.7→41.528 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3713	0	42	25	3780

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	3832
X-RAY DIFFRACTION	f_angle_d	0.6	5184
X-RAY DIFFRACTION	f_dihedral_angle_d	16.632	1427
X-RAY DIFFRACTION	f_chiral_restr	0.043	565
X-RAY DIFFRACTION	f_plane_restr	0.002	685

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 (%)
2.6948-2.8174	0.3295	134	0.305	2505	X-RAY DIFFRACTION	99
2.8174-2.9659	0.3402	137	0.3091	2512	X-RAY DIFFRACTION	100
2.9659-3.1517	0.3464	145	0.2894	2487	X-RAY DIFFRACTION	100
3.1517-3.3949	0.3311	126	0.2726	2526	X-RAY DIFFRACTION	99
3.3949-3.7364	0.2909	158	0.2409	2478	X-RAY DIFFRACTION	99
3.7364-4.2766	0.2619	145	0.2219	2479	X-RAY DIFFRACTION	98
4.2766-5.3862	0.2444	137	0.2114	2445	X-RAY DIFFRACTION	95
5.3862-41.5334	0.2902	120	0.2451	2434	X-RAY DIFFRACTION	90

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	0.6004	0.2184	0.2457	0.2879	0.2267	0.2305	0.1434	-0.6187	-0.3082	0.6068	-0.2353	-0.2521	0.1776	0.7065	0.0002	0.7706	0.0274	-0.1419	0.9239	0.0805	0.5394	-42.6789	24.6465	37.1573
2	1.0419	0.6083	-0.1634	3.0672	0.2954	0.8813	-0.2075	0.252	0.0078	-0.6062	0.1183	-0.1835	0.0381	0.0386	-0.0031	0.3669	0.0234	0.0081	0.2006	-0.0425	0.4276	-54.3514	10.2891	-12.3967
3	0.0141	-0.0891	-0.0318	0.1215	0.1131	0.0293	-0.8302	0.2133	0.2794	-0.6287	0.5981	-0.5056	-0.5566	-0.3066	0.0002	1.0633	-0.0748	0.0611	0.6694	0.0231	0.5519	-51.8922	6.5524	-30.435
4	0.8572	0.2296	0.0215	1.4119	0.462	1.8639	0.1823	1.5547	-0.0703	-1.8042	0.5085	1.0393	0.039	-1.6046	1.0732	1.2193	-0.1432	-0.3853	0.8199	0.0272	0.6383	-64.7726	14.6049	-31.7957
5	0.2649	0.0872	0.1146	0.1583	-0.1268	0.3461	0.6855	1.2194	0.4677	-1.6865	-0.4331	0.2447	-0.7237	0.0494	0.0015	1.7841	0.1613	-0.0448	1.0582	0.2462	0.97	-59.7998	23.0045	-35.1999
6	0.2923	-0.2483	0.4218	0.395	-0.0039	0.9474	0.2311	0.333	1.015	-0.7792	0.1767	-0.5602	-0.1381	0.7775	0.0439	1.0512	0.0213	0.0429	0.7191	0.0896	0.9458	-51.5069	20.5397	-27.9334
7	0.5201	-0.4897	-0.3843	0.5686	0.1806	0.6134	-0.1171	-0.2129	-0.5738	-0.8562	-0.254	1.5394	0.4043	-1.2082	-0.0739	1.355	0.1557	-0.2449	0.8559	0.0181	0.7858	-68.2092	16.6082	-28.8324
8	0.3193	-0.5257	0.3509	1.6939	0.0924	0.2448	-0.1315	-0.1055	-0.3058	0.1401	-0.0852	-0.0923	-0.0036	-0.3227	-0.0002	0.2501	-0.0048	0.0239	0.3096	-0.0233	0.4353	-54.3589	8.8201	-1.8394
9	0.1974	-0.4693	-0.1121	1.107	0.4045	0.1409	-0.4293	0.4253	-0.266	0.0322	0.3474	-0.6222	0.3115	0.1497	0.0289	0.2897	-0.0903	0.0614	0.299	0.0119	0.3697	-49.3255	17.7575	10.2809
10	0.2425	-0.2932	0.3766	0.0902	-0.1521	0.2846	-0.3006	-0.6956	-0.119	0.3241	0.2495	-0.2082	0.2657	-0.5146	-0.0739	0.4745	0.1371	-0.0914	0.7283	0.0188	0.4184	-45.3247	24.1519	25.5526
11	0.1188	-0.159	0.0105	0.3194	-0.0001	0.0195	-0.1593	-0.927	-0.5628	0.7723	-0.5265	-0.9041	0.4914	0.1899	-0.058	1.3873	0.0854	-0.3515	1.3585	0.3383	0.6262	-44.1467	19.4161	50.8694
12	0.1015	0.0465	-0.1921	0.7257	-0.2754	0.3723	0.3261	-0.6893	-0.2251	0.4474	-0.2789	-0.2449	0.8766	0.5105	0.0015	0.9775	-0.013	-0.1084	1.0169	0.2394	0.4465	-52.9855	15.4643	44.2
13	1.4364	0.2494	-0.3119	0.8887	0.2213	0.1748	-0.1522	0.9066	-0.1479	0.6266	-0.0551	0.7566	-0.664	0.1246	-0.0409	0.4626	0.0176	0.094	0.3795	0.0514	0.5169	-58.9255	17.7383	9.7114
14	0.162	-0.19	-0.1082	1.8395	0.2	0.0684	0.0663	0.329	0.7024	-0.9233	0.1012	-1.4705	-0.6651	0.2176	-0.0206	0.4125	-0.0195	0.1068	0.5047	-0.0229	0.4347	-48.34	23.696	-8.3826
15	1.1049	-0.0587	0.8977	1.1507	0.1872	0.6738	-0.0113	-0.4416	-0.0362	0.3439	-0.2186	-0.1388	0.3719	-0.028	-0.0055	0.348	-0.0445	-0.051	0.2855	-0.0128	0.2893	-53.1518	29.3226	26.3878
16	0.3309	0.2694	-0.5436	0.4181	-0.4072	1.0618	0.1785	-0.7075	-0.0375	1.5961	0.3965	-0.4936	0.1582	0.2358	0.9079	2.4609	-0.1538	-0.2878	1.7112	0.1197	0.5162	-52.4811	27.2138	63.7353
17	1.0829	1.2222	-0.1928	2.2281	0.2551	0.2092	0.2003	-1.3343	-0.8398	1.2316	0.7045	-0.6445	-0.3838	-0.7295	0.1289	1.8027	0.1248	-0.1669	2.0453	0.3785	0.9958	-54.4754	16.4464	66.3585
18	1.6837	-0.1798	-1.6372	3.0737	1.914	2.5494	-0.3291	-0.2023	0.022	0.0826	0.0225	0.5768	0.2475	-0.4698	-1.2229	2.3467	0.7344	0.083	2.1953	0.3329	0.3638	-56.1528	24.7751	76.2888

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 3 through 31 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 32 through 122 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 123 through 143 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 144 through 175 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 176 through 204 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 205 through 228 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 229 through 246 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 247 through 275 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 276 through 295 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 296 through 316 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 328 through 348 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 349 through 376 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 377 through 386 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 387 through 395 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 396 through 446 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 447 through 458 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 459 through 483 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 484 through 490 )

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