6IDD | pdb_00006idd

Crystal structure of H7 hemagglutinin mutant SH1-AVPL ( S138A, G186V, T221P, Q226L) from the influenza virus A/Shanghai/1/2013 (H7N9)

PDB DOI: https://doi.org/10.2210/pdb6IDD/pdb

Classification: VIRAL PROTEIN
Organism(s): Influenza A virus (A/Shanghai/MH01/2013(H7N9))
Expression System: Spodoptera frugiperda
Mutation(s): Yes

Deposited: 2018-09-09 Released: 2019-11-27
Deposition Author(s): Gao, G.F., Xu, Y., Qi, J.X.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.38 Å
R-Value Free:
0.282 (Depositor), 0.282 (DCC)
R-Value Work:
0.253 (Depositor), 0.254 (DCC)
R-Value Observed:
0.254 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Avian-to-Human Receptor-Binding Adaptation of Avian H7N9 Influenza Virus Hemagglutinin.

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.

(2019) Cell Rep 29: 2217

PubMed: 31747596 Search on PubMed
DOI: https://doi.org/10.1016/j.celrep.2019.10.047
Primary Citation Related Structures:
6ICW, 6ICX, 6ICY, 6ID2, 6ID3, 6ID5, 6ID8, 6ID9, 6IDA, 6IDB, 6IDD, 6IDZ

PubMed Abstract:
Since 2013, H7N9 avian influenza viruses (AIVs) have caused more than 1,600 human infections, posing a threat to public health. An emerging concern is whether H7N9 AIVs will cause pandemics among humans. Molecular analysis of hemagglutinin (HA), which is a critical determinant of interspecies transmission, shows that the current H7N9 AIVs are still dual-receptor tropic, indicating limited human-to-human transmission potency. Mutagenesis and structural studies reveal that a G186V substitution is sufficient for H7N9 AIVs to acquire human receptor-binding capacity, and a Q226L substitution would favor binding to both avian and human receptors only when paired with A138/V186/P221 hydrophobic residues. These data suggest a different evolutionary route of H7N9 viruses compared to other AIV-subtype HAs.

Organizational Affiliation

School of Life Sciences, University of Science and Technology of China, Hefei 230026, China; CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing 100101, China.

CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing 100101, China.

Research Network of Immunity and Health (RNIH), Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China.

CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing 100101, China; Laboratory of Animal Infectious Diseases, College of Animal Sciences and Veterinary Medicine, Guangxi University, Nanning 530004, China.

Laboratory of Protein Engineering and Vaccines, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China.

Center for Influenza Research and Early-Warning, Chinese Academy of Sciences (CASCIRE), Beijing 100101, China; Savaid Medical School, University of Chinese Academy of Sciences, Beijing 101408, China; Shenzhen Key Laboratory of Pathogen and Immunity, Shenzhen Third People's Hospital, Shenzhen 518112, China.

CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing 100101, China; Center for Influenza Research and Early-Warning, Chinese Academy of Sciences (CASCIRE), Beijing 100101, China; Savaid Medical School, University of Chinese Academy of Sciences, Beijing 101408, China; Shenzhen Key Laboratory of Pathogen and Immunity, Shenzhen Third People's Hospital, Shenzhen 518112, China.

School of Life Sciences, University of Science and Technology of China, Hefei 230026, China; CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing 100101, China; Research Network of Immunity and Health (RNIH), Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China; Laboratory of Animal Infectious Diseases, College of Animal Sciences and Veterinary Medicine, Guangxi University, Nanning 530004, China; Laboratory of Protein Engineering and Vaccines, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; Center for Influenza Research and Early-Warning, Chinese Academy of Sciences (CASCIRE), Beijing 100101, China; Savaid Medical School, University of Chinese Academy of Sciences, Beijing 101408, China; Shenzhen Key Laboratory of Pathogen and Immunity, Shenzhen Third People's Hospital, Shenzhen 518112, China. Electronic address: gaof@im.ac.cn.

Macromolecule Content

Total Structure Weight: 334.74 kDa
Atom Count: 23,265
Modeled Residue Count: 2,905
Deposited Residue Count: 2,988
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin	A B [auth C] C [auth E] D [auth G] E [auth I] A, B [auth C], C [auth E], D [auth G], E [auth I], F [auth K]	498	Influenza A virus (A/Shanghai/MH01/2013(H7N9))	Mutation(s): 4 Gene Names: HA
UniProt
Find proteins for A0A088BEK2 (Influenza A virus) Explore A0A088BEK2 Go to UniProtKB: A0A088BEK2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A088BEK2
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain A Focus chain B [auth C] Focus chain C [auth E] Focus chain D [auth G] Focus chain E [auth I] Focus chain F [auth K]
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG (Subject of Investigation/LOI) Query on NAG Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain K [auth E] SDF format, chain M [auth G] SDF format, chain N [auth I] SDF format, chain O [auth K] SDF format, chain L [auth G] SDF format, chain J [auth C] SDF format, chain I [auth C] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain K [auth E] MOL2 format, chain M [auth G] MOL2 format, chain N [auth I] MOL2 format, chain O [auth K] MOL2 format, chain L [auth G] MOL2 format, chain J [auth C] MOL2 format, chain I [auth C] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain K [auth E] mmCIF format, chain M [auth G] mmCIF format, chain N [auth I] mmCIF format, chain O [auth K] mmCIF format, chain L [auth G] mmCIF format, chain J [auth C] mmCIF format, chain I [auth C]	G [auth A] H [auth A] I [auth C] J [auth C] K [auth E] G [auth A], H [auth A], I [auth C], J [auth C], K [auth E], L [auth G], M [auth G], N [auth I], O [auth K]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth C] Focus chain J [auth C] Focus chain K [auth E] Focus chain L [auth G] Focus chain M [auth G] Focus chain N [auth I] Focus chain O [auth K] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth C] Focus chain J [auth C] Focus chain K [auth E] Focus chain L [auth G] Focus chain M [auth G] Focus chain N [auth I] Focus chain O [auth K]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.38 Å
R-Value Free: 0.282 (Depositor), 0.282 (DCC)
R-Value Work: 0.253 (Depositor), 0.254 (DCC)
R-Value Observed: 0.254 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.181	α = 90
b = 226.274	β = 96.65
c = 116.78	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2019-11-27

Deposition Author(s):

Gao, G.F.

Xu, Y.

Qi, J.X.

Revision History (Full details and data files)

Version 1.0: 2019-11-27
Type: Initial release
Version 1.1: 2019-12-04
Changes: Database references
Version 1.2: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary
Version 1.3: 2023-11-22
Changes: Data collection, Database references, Refinement description, Structure summary
Version 1.4: 2024-10-23
Changes: Structure summary