6LKS | pdb_00006lks

Effects of zinc ion on oligomerization and pH stability of influenza virus hemagglutinin

PDB DOI: https://doi.org/10.2210/pdb6LKS/pdb

Classification: VIRAL PROTEIN
Organism(s): Influenza A virus (A/Thailand/CU44/2006(H1N1))
Expression System: Baculovirus expression vector pFastBac1-HM
Mutation(s): No

Deposited: 2019-12-20 Released: 2020-10-21
Deposition Author(s): Seok, J., Kim, K.
Funding Organization(s): National Research Foundation (NRF, Korea)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.24 Å
R-Value Free:
0.295 (Depositor), 0.295 (DCC)
R-Value Work:
0.265 (Depositor), 0.265 (DCC)
R-Value Observed:
0.266 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Divalent cation-induced conformational changes of influenza virus hemagglutinin.

Seok, J.H., Kim, H., Lee, D.B., An, J.S., Kim, E.J., Lee, J.H., Chung, M.S., Kim, K.H.

(2020) Sci Rep 10: 15457-15457

PubMed: 32963316 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41598-020-72368-x
Primary Citation Related Structures:
6LKS

PubMed Abstract:
Divalent cations Cu ²⁺ and Zn ²⁺ can prevent the viral growth in mammalian cells during influenza infection, and viral titers decrease significantly on a copper surface. The underlying mechanisms include DNA damage by radicals, modulation of viral protease, M1 or neuraminidase, and morphological changes in viral particles. However, the molecular mechanisms underlying divalent cation-mediated antiviral activities are unclear. An unexpected observation of this study was that a Zn ²⁺ ion is bound by Glu68 and His137 residues at the head regions of two neighboring trimers in the crystal structure of hemagglutinin (HA) derived from A/Thailand/CU44/2006. The binding of Zn ²⁺ at high concentrations induced multimerization of HA and decreased its acid stability. The acid-induced conformational change of HA occurred even at neutral pH in the presence of Zn ²⁺. The fusion of viral and host endosomal membranes requires substantial conformational changes in HA upon exposure to acidic pH. Therefore, our results suggest that binding of Zn ²⁺ may facilitate the conformational changes of HA, analogous to that induced by acidic pH.

Organizational Affiliation

Department of Biotechnology and Bioinformatics, Korea University, Sejong, 30019, Korea.

Macromolecule Content

Total Structure Weight: 359.73 kDa
Atom Count: 24,413
Modeled Residue Count: 2,914
Deposited Residue Count: 3,078
Unique protein chains: 2

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin HA1 chain	A [auth K] C [auth A] E [auth C] G [auth E] I [auth G] A [auth K], C [auth A], E [auth C], G [auth E], I [auth G], K [auth I]	330	Influenza A virus (A/Thailand/CU44/2006(H1N1))	Mutation(s): 0 Gene Names: HA
UniProt
Find proteins for A7LI25 (Influenza A virus) Explore A7LI25 Go to UniProtKB: A7LI25
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A7LI25
Glycosylation
Glycosylation Sites: 5	Glycosylation Focus chain A [auth K] Focus chain C [auth A] Focus chain E [auth C] Focus chain G [auth E] Focus chain I [auth G] Focus chain K [auth I]
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin HA2 chain	B [auth L] D [auth B] F [auth D] H [auth F] J [auth H] B [auth L], D [auth B], F [auth D], H [auth F], J [auth H], L [auth J]	183	Influenza A virus (A/Thailand/CU44/2006(H1N1))	Mutation(s): 0 Gene Names: HA
UniProt
Find proteins for A7LI25 (Influenza A virus) Explore A7LI25 Go to UniProtKB: A7LI25
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A7LI25
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	M, S, V	6		N-Glycosylation	Interactions Focus chain M Focus chain S Focus chain V Interactions & Density Focus chain M Focus chain S Focus chain V
Glycosylation Resources
GlyTouCan: G61751GZ GlyCosmos: G61751GZ GlyGen: G61751GZ

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	N, P	5		N-Glycosylation	Interactions Focus chain N Focus chain P Interactions & Density Focus chain N Focus chain P
Glycosylation Resources
GlyTouCan: G10133VD GlyCosmos: G10133VD GlyGen: G10133VD

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	O, Q, R, T, U O, Q, R, T, U, X	4		N-Glycosylation	Interactions Focus chain O Focus chain Q Focus chain R Focus chain T Focus chain U Focus chain X Interactions & Density Focus chain O Focus chain Q Focus chain R Focus chain T Focus chain U Focus chain X
Glycosylation Resources
GlyTouCan: G81315DD GlyCosmos: G81315DD GlyGen: G81315DD

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	W	3		N-Glycosylation	Interactions Focus chain W Interactions & Density Focus chain W
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Small Molecules

Ligands 2 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 AA [auth K] SDF format, chain CA [auth A] SDF format, chain DA [auth A] SDF format, chain EA [auth A] SDF format, chain FA [auth A] SDF format, chain GA [auth A] SDF format, chain IA [auth E] SDF format, chain JA [auth E] SDF format, chain MA [auth G] SDF format, chain NA [auth G] SDF format, chain OA [auth G] SDF format, chain QA [auth I] SDF format, chain RA [auth I] SDF format, chain SA [auth I] SDF format, chain Y [auth K] SDF format, chain Z [auth K] SDF format, chain LA [auth E] SDF format, chain KA [auth E] SDF format, chain HA [auth C] MOL2 format, chain AA [auth K] MOL2 format, chain CA [auth A] MOL2 format, chain DA [auth A] MOL2 format, chain EA [auth A] MOL2 format, chain FA [auth A] MOL2 format, chain GA [auth A] MOL2 format, chain IA [auth E] MOL2 format, chain JA [auth E] MOL2 format, chain MA [auth G] MOL2 format, chain NA [auth G] MOL2 format, chain OA [auth G] MOL2 format, chain QA [auth I] MOL2 format, chain RA [auth I] MOL2 format, chain SA [auth I] MOL2 format, chain Y [auth K] MOL2 format, chain Z [auth K] MOL2 format, chain LA [auth E] MOL2 format, chain KA [auth E] MOL2 format, chain HA [auth C] mmCIF format, chain AA [auth K] mmCIF format, chain CA [auth A] mmCIF format, chain DA [auth A] mmCIF format, chain EA [auth A] mmCIF format, chain FA [auth A] mmCIF format, chain GA [auth A] mmCIF format, chain IA [auth E] mmCIF format, chain JA [auth E] mmCIF format, chain MA [auth G] mmCIF format, chain NA [auth G] mmCIF format, chain OA [auth G] mmCIF format, chain QA [auth I] mmCIF format, chain RA [auth I] mmCIF format, chain SA [auth I] mmCIF format, chain Y [auth K] mmCIF format, chain Z [auth K] mmCIF format, chain LA [auth E] mmCIF format, chain KA [auth E] mmCIF format, chain HA [auth C]	AA [auth K] CA [auth A] DA [auth A] EA [auth A] FA [auth A] AA [auth K], CA [auth A], DA [auth A], EA [auth A], FA [auth A], GA [auth A], HA [auth C], IA [auth E], JA [auth E], KA [auth E], LA [auth E], MA [auth G], NA [auth G], OA [auth G], QA [auth I], RA [auth I], SA [auth I], Y [auth K], Z [auth K]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth K] Focus chain CA [auth A] Focus chain DA [auth A] Focus chain EA [auth A] Focus chain FA [auth A] Focus chain GA [auth A] Focus chain HA [auth C] Focus chain IA [auth E] Focus chain JA [auth E] Focus chain KA [auth E] Focus chain LA [auth E] Focus chain MA [auth G] Focus chain NA [auth G] Focus chain OA [auth G] Focus chain QA [auth I] Focus chain RA [auth I] Focus chain SA [auth I] Focus chain Y [auth K] Focus chain Z [auth K] Interactions & Density Focus chain AA [auth K] Focus chain CA [auth A] Focus chain DA [auth A] Focus chain EA [auth A] Focus chain FA [auth A] Focus chain GA [auth A] Focus chain HA [auth C] Focus chain IA [auth E] Focus chain JA [auth E] Focus chain KA [auth E] Focus chain LA [auth E] Focus chain MA [auth G] Focus chain NA [auth G] Focus chain OA [auth G] Focus chain QA [auth I] Focus chain RA [auth I] Focus chain SA [auth I] Focus chain Y [auth K] Focus chain Z [auth K]
ZN (Subject of Investigation/LOI) Query on ZN Download:Ideal Coordinates CCD File SDF format, chain BA [auth K] SDF format, chain PA [auth G] SDF format, chain TA [auth I] MOL2 format, chain BA [auth K] MOL2 format, chain PA [auth G] MOL2 format, chain TA [auth I] mmCIF format, chain BA [auth K] mmCIF format, chain PA [auth G] mmCIF format, chain TA [auth I]	BA [auth K], PA [auth G], TA [auth I]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain BA [auth K] Focus chain PA [auth G] Focus chain TA [auth I] Interactions & Density Focus chain BA [auth K] Focus chain PA [auth G] Focus chain TA [auth I]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.24 Å
R-Value Free: 0.295 (Depositor), 0.295 (DCC)
R-Value Work: 0.265 (Depositor), 0.265 (DCC)
R-Value Observed: 0.266 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 215.71	α = 90
b = 124.27	β = 102.909
c = 214.53	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHENIX	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2020-10-21

Deposition Author(s):

Seok, J.

Kim, K.

Funding Organization	Location	Grant Number
National Research Foundation (NRF, Korea)	Korea, Republic Of	2010-0029242

Revision History (Full details and data files)

Version 1.0: 2020-10-21
Type: Initial release
Version 1.1: 2020-10-28
Changes: Database references
Version 1.2: 2023-11-22
Changes: Data collection, Database references, Refinement description
Version 1.3: 2024-10-23
Changes: Structure summary