PDB-6icw: Crystal structure of H7 hemagglutinin mutant AH-SGTQ (A138S, V186...

ID or keywords:

Entry

Database: PDB / ID: 6icw

Title

Crystal structure of H7 hemagglutinin mutant AH-SGTQ (A138S, V186G, P221T and L226Q) 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 / 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 / membrane
Similarity search - Function

Biological species

Influenza A virus

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.6 Å

Authors

Gao, G.F. / Xu, Y.

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 7, 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
Revision 1.4	Nov 6, 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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PDBx/mmCIF format	6icw.cif.gz	208.6 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	6icw_validation.pdf.gz	469.3 KB	Display	wwPDB validaton report
Full document	6icw_full_validation.pdf.gz	476.6 KB	Display
Data in XML	6icw_validation.xml.gz	20.2 KB	Display
Data in CIF	6icw_validation.cif.gz	26.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ic/6icw ftp://data.pdbj.org/pub/pdb/validation_reports/ic/6icw	HTTPS FTP

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Related structure data

Related structure data	6icxC 6icyC 6id2C 6id3C 6id5C 6id8C 6id9C 6idaC 6idbC 6iddC 6idzC 4lkgS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6icx-1 6d8b-d 4kol-1 4lki-1 4bsg-1 4lkh-1 4lkg-1 6idd-2 5vjl-1 4lkg-2 4lcx-d 4lkk-1 6id2-1 5vjk-1 3eyk-1 6idb-1 6twh-1 4ln4-5 4bsb-1 4ln8-5 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)	115.605, 115.605, 293.498
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-601- HOH
2	1	B-609- HOH

#1: Protein

Hemagglutinin HA1 chain

Mass: 34986.438 Da / Num. of mol.: 1 / Mutation: A138S,V186G,P221T,L226Q
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

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

Mass: 18.015 Da / Num. of mol.: 69 / Source method: isolated from a natural source / Formula: H₂O

Has protein modification

Y

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: 3.44 Å³/Da / Density % sol: 64.23 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 0.2M Sodium citrate tribasic dihydrate, 20% w/v Polyethylene glycol 3350

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / 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: 2.6→37.53 Å / Num. obs: 23594 / % possible obs: 99.8 % / Redundancy: 8.5 % / Net I/σ(I): 17.9
Reflection shell	Resolution: 2.6→2.69 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: 4LKG

4lkg

Resolution: 2.6→37.53 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.13

	R_factor	Num. reflection	% reflection
R_free	0.2835	1219	5.17 %
R_work	0.2575	-	-
obs	0.2588	23587	99.81 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.6→37.53 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3714	0	42	69	3825

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	3833
X-RAY DIFFRACTION	f_angle_d	0.93	5185
X-RAY DIFFRACTION	f_dihedral_angle_d	15.75	1428
X-RAY DIFFRACTION	f_chiral_restr	0.088	564
X-RAY DIFFRACTION	f_plane_restr	0.002	686

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 (%)
2.6004-2.7045	0.4106	145	0.3466	2433	X-RAY DIFFRACTION	100
2.7045-2.8275	0.3578	127	0.3226	2460	X-RAY DIFFRACTION	100
2.8275-2.9765	0.3443	114	0.3032	2476	X-RAY DIFFRACTION	100
2.9765-3.1629	0.3148	141	0.2896	2451	X-RAY DIFFRACTION	100
3.1629-3.407	0.3251	134	0.2825	2468	X-RAY DIFFRACTION	100
3.407-3.7496	0.2836	146	0.2457	2466	X-RAY DIFFRACTION	100
3.7496-4.2915	0.2401	125	0.2273	2505	X-RAY DIFFRACTION	100
4.2915-5.4042	0.2334	153	0.2239	2492	X-RAY DIFFRACTION	100
5.4042-37.5339	0.2783	134	0.2486	2617	X-RAY DIFFRACTION	99

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	1.3663	0.0274	0.0353	0.3901	0.3308	3.4507	0.1515	0.5103	-0.0855	-0.5405	-0.0148	0.1577	-0.7038	-0.0785	-0.0177	0.7354	0.1285	-0.0811	0.657	0.1071	0.484	42.2551	-24.789	-37.4671
2	1.4736	1.5345	-1.5053	1.6195	-1.2094	2.8225	-0.2061	0.185	0.6647	-0.1076	0.1707	0.0408	0.3506	-0.2368	-0.1249	0.1472	-0.0591	0.0245	0.3646	0.0555	0.5276	31.9547	-36.5339	-9.0849
3	2.0065	0.2605	-0.4246	1.6525	0.6907	2.9073	0.4154	-0.4095	0.0744	0.9456	-0.1946	0.0478	-0.2423	0.2831	-0.1114	0.562	-0.152	0.0484	0.3254	-0.031	0.4097	36.7632	-42.5545	17.1964
4	3.1995	-0.0667	-0.4917	4.3153	1.5063	2.238	0.4547	-0.4636	0.6158	1.4591	-0.1572	-0.0956	-0.724	0.3676	-0.2703	1.0325	-0.2781	0.185	0.6116	-0.0984	0.4057	31.4821	-40.9554	30.4578
5	1.0531	-0.4845	-0.2688	2.4174	1.5091	2.8556	0.3007	-0.7215	0.0707	1.3312	0.2308	-0.8298	-0.0337	0.7475	-0.4247	1.0434	-0.2878	-0.198	0.8869	-0.0914	0.6284	46.4134	-42.7013	31.3202
6	1.343	0.7547	-0.0087	1.0294	0.2606	0.9886	-0.0994	0.0526	0.0637	0.0798	0.1546	0.1282	-0.1181	0.0501	-0.027	0.3194	0.001	0.0063	0.2703	-0.0693	0.3879	36.6506	-38.8836	-3.0505
7	1.3899	-0.0489	1.0298	2.2995	-1.0761	4.4929	0.2675	0.682	0.3552	-0.4576	-0.7143	0.1031	-0.0707	0.2365	0.1878	0.3461	0.1171	-0.0023	0.5154	0.0999	0.3915	43.1607	-27.2094	-25.8354
8	0.667	-0.2729	0.6055	0.7329	-0.2647	0.4557	-0.1894	0.1227	0.1695	-0.9905	-0.0219	0.2482	0.4354	-0.8498	0.0889	1.1045	-0.0073	-0.3337	1.3377	0.0454	0.5972	36.9891	-29.8675	-53.7719
9	3.5856	0.3909	-0.7728	3.8066	1.089	1.117	-0.1806	1.0931	-0.4904	-1.0808	0.0657	-0.4789	0.99	-0.6325	0.1634	0.7115	-0.108	-0.0869	0.6128	-0.074	0.4527	42.7066	-40.792	-36.947
10	4.1206	-0.1993	1.2788	3.4513	0.5758	0.5191	-0.2723	0.9059	-0.9846	0.1723	0.7224	0.3585	0.7295	0.3703	-0.0069	0.581	-0.0931	0.0167	0.4988	-0.0057	0.6054	44.7271	-41.7035	-9.5815
11	2.0387	-0.9218	-0.2805	3.7882	0.2833	0.4766	-0.1462	-0.413	0.89	0.7709	0.2085	0.3255	-0.4894	0.3799	-0.0983	0.7265	-0.0339	0.1296	0.5865	-0.1023	0.4411	44.4623	-29.7571	8.1112
12	1.3768	-0.1915	0.6099	1.5607	0.0205	5.515	0.0677	0.2153	0.0065	-0.3787	-0.0828	0.0084	-0.2977	-0.336	-0.0588	0.2325	-0.0589	0.0163	0.3043	0.0395	0.3052	51.6275	-31.2829	-26.711
13	1.9567	0.6173	-0.3823	0.3471	-0.1796	1.0422	0.0203	1.8867	-0.201	-1.0594	0.0737	0.5366	-0.5515	-0.4716	-0.0843	1.5793	0.0567	-0.3143	1.6109	0.0137	0.6375	43.631	-37.0788	-65.7627
14	0.1054	-0.1701	0.1374	0.3442	-0.101	0.4737	-0.0756	0.498	-0.2438	-0.5916	-0.1384	0.1391	0.1947	-0.0383	-0.3532	1.6002	0.2694	-0.3623	2.5584	-0.3717	-0.023	49.1207	-36.4453	-76.5554

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 47 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 48 through 122 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 123 through 143 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 144 through 246 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 247 through 295 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 296 through 316 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 328 through 358 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 359 through 376 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 377 through 386 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 387 through 395 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 396 through 446 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 447 through 483 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 484 through 490 )

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