4WEF | pdb_00004wef

Structure of the Hemagglutinin-neuraminidase from Human parainfluenza virus type III: complex with difluorosialic acid

PDB DOI: https://doi.org/10.2210/pdb4WEF/pdb

Classification: VIRAL PROTEIN
Organism(s): Human respirovirus 3
Expression System: Trichoplusia ni
Mutation(s): Yes

Deposited: 2014-09-10 Released: 2015-09-16
Deposition Author(s): Streltsov, V.A., Pilling, P., Barrett, S., McKimm-Breschkin, J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.258 (Depositor), 0.259 (DCC)
R-Value Work:
0.189 (Depositor), 0.196 (DCC)
R-Value Observed:
0.193 (Depositor)

Starting Model: experimental
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Literature

Catalytic mechanism and novel receptor binding sites of human parainfluenza virus type 3 hemagglutinin-neuraminidase (hPIV3 HN)

Streltsov, V.A., Pilling, P., Barrett, S., McKimm-Breschkin, J.L.

(2015) Antiviral Res 123: 216-223

PubMed: 26364554 Search on PubMed
DOI: https://doi.org/10.1016/j.antiviral.2015.08.014
Primary Citation Related Structures:
4WEF, 4WEG

PubMed Abstract:
The human parainfluenza virus type 3 (hPIV3) hemagglutinin-neuraminidase (HN) has opposing functions of binding sialic acid receptors and cleaving them, facilitating virus release. The crystal structure of hPIV3 HN complexed with the substrate analogue difluorosialic acid (DFSA) revealed that catalysis by HN involves the formation of a covalently linked sialosyl-enzyme intermediate which was trapped along with a transition-state analogue resembling an oxocarbenium ion. This mechanism of enzyme catalysis was also confirmed in the crystal structure of the influenza N9 neuraminidase complexed with DFSA. Additionally, novel secondary receptor binding sites were identified in the hPIV3 HN-DFSA complex including one near the catalytic cavity which upon binding DFSA imposes subtle changes and may help the HN balance the opposing functions. Multiple receptor binding sites may increase avidity to facilitate cell binding and fusion promotion. The secondary receptor binding sites in the paramyxoviruses are so far unique to each virus type.

Organizational Affiliation

CSIRO Manufacturing, 343 Royal Parade, Parkville, Victoria 3052, Australia. Electronic address: victor.streltsov@csiro.au.

Macromolecule Content

Total Structure Weight: 102.83 kDa
Atom Count: 7,765
Modeled Residue Count: 862
Deposited Residue Count: 862
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin-neuraminidase glycoprotein	A, B	431	Human respirovirus 3	Mutation(s): 1 Gene Names: HN
UniProt
Find proteins for Q6WJ03 (Human respirovirus 3) Explore Q6WJ03 Go to UniProtKB: Q6WJ03
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6WJ03
Glycosylation
Glycosylation Sites: 3	Glycosylation Focus chain A Focus chain B
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-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	C, E	4		N-Glycosylation	Interactions Focus chain C Focus chain E Interactions & Density Focus chain C Focus chain E
Glycosylation Resources
GlyTouCan: G31886NL GlyCosmos: G31886NL GlyGen: G31886NL

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	D, F	3		N-Glycosylation	Interactions Focus chain D Focus chain F Interactions & Density Focus chain D Focus chain F
Glycosylation Resources
GlyTouCan: G21290RB GlyCosmos: G21290RB GlyGen: G21290RB

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SFJ Query on SFJ Download:Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain W [auth B] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain W [auth B] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain W [auth B]	J [auth A], K [auth A], W [auth B]	(2R,3R,4R,5R,6R)-5-acetamido-2,3-difluoro-4-hydroxy-6-[(1R,2R)-1,2,3-trihydroxypropyl]tetrahydro-2H-pyran-2-carboxylic acid C₁₁ H₁₇ F₂ N O₈ HMALKZAXODOYOP-DAXAGCIGSA-N		Interactions Focus chain J [auth A] Focus chain K [auth A] Focus chain W [auth B] Interactions & Density Focus chain J [auth A] Focus chain K [auth A] Focus chain W [auth B]
FSI Query on FSI Download:Ideal Coordinates CCD File SDF format, chain U [auth B] SDF format, chain H [auth A] MOL2 format, chain U [auth B] MOL2 format, chain H [auth A] mmCIF format, chain U [auth B] mmCIF format, chain H [auth A]	H [auth A], U [auth B]	5-acetamido-3,5-dideoxy-3-fluoro-D-erythro-alpha-L-manno-non-2-ulopyranosonic acid C₁₁ H₁₈ F N O₉ ALJLGESFXXDPKH-RISWTRDCSA-N		Interactions Focus chain H [auth A] Focus chain U [auth B] Interactions & Density Focus chain H [auth A] Focus chain U [auth B]
DF4 Query on DF4 Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain V [auth B] MOL2 format, chain I [auth A] MOL2 format, chain V [auth B] mmCIF format, chain I [auth A] mmCIF format, chain V [auth B]	I [auth A], V [auth B]	(3R,4R,5R,6R)-5-(acetylamino)-3-fluoro-4-hydroxy-6-[(1R,2R)-1,2,3-trihydroxypropyl]-3,4,5,6-tetrahydropyranium-2-carboxylate C₁₁ H₁₆ F N O₈ OXSMZBYWMIZHJQ-LNSOWFDVSA-N		Interactions Focus chain I [auth A] Focus chain V [auth B] Interactions & Density Focus chain I [auth A] Focus chain V [auth B]
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain T [auth B] MOL2 format, chain G [auth A] MOL2 format, chain T [auth B] mmCIF format, chain G [auth A] mmCIF format, chain T [auth B]	G [auth A], T [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain G [auth A] Focus chain T [auth B] Interactions & Density Focus chain G [auth A] Focus chain T [auth B]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain BA [auth B] SDF format, chain CA [auth B] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain Q [auth A] SDF format, chain S [auth B] SDF format, chain X [auth B] SDF format, chain Y [auth B] SDF format, chain Z [auth B] SDF format, chain AA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain CA [auth B] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain S [auth B] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth B] MOL2 format, chain AA [auth B] mmCIF format, chain BA [auth B] mmCIF format, chain CA [auth B] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain S [auth B] mmCIF format, chain X [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain Z [auth B] mmCIF format, chain AA [auth B]	AA [auth B] BA [auth B] CA [auth B] L [auth A] M [auth A] AA [auth B], BA [auth B], CA [auth B], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], S [auth B], X [auth B], Y [auth B], Z [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain S [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain S [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain DA [auth B] SDF format, chain R [auth A] MOL2 format, chain DA [auth B] MOL2 format, chain R [auth A] mmCIF format, chain DA [auth B] mmCIF format, chain R [auth A]	DA [auth B], R [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain DA [auth B] Focus chain R [auth A] Interactions & Density Focus chain DA [auth B] Focus chain R [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.258 (Depositor), 0.259 (DCC)
R-Value Work: 0.189 (Depositor), 0.196 (DCC)
R-Value Observed: 0.193 (Depositor)

Space Group: P 6₂ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 218.668	α = 90
b = 218.668	β = 90
c = 109.769	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data processing
PHASER	phasing
PDB_EXTRACT	data extraction
SCALEPACK	data scaling
SCALEPACK	data reduction
HKL	data reduction

Structure Validation

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Entry History

Deposition Data

Released Date: 2015-09-16

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2015-09-16
Type: Initial release
Version 1.1: 2015-10-07
Changes: Database references
Version 1.2: 2015-11-18
Changes: Database references, Experimental preparation
Version 1.3: 2020-01-29
Changes: Data collection, Derived calculations
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2023-11-08
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
Version 2.2: 2024-11-20
Changes: Structure summary