5VMF | pdb_00005vmf

Influenza hemagglutinin H1 mutant DH1D in complex with 6'SLN

• PDB DOI: https://doi.org/10.2210/pdb5VMF/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Influenza A virus (A/Brevig Mission/1/1918(H1N1))
• Expression System: unidentified baculovirus
• Mutation(s): Yes 


• Deposited: 2017-04-27 Released: 2017-11-08 
• Deposition Author(s): Ni, F., Kondrashkina, E., Wang, Q.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 
  0.232 (Depositor), 0.235 (DCC) 
• R-Value Work: 
  0.193 (Depositor), 0.199 (DCC) 
• R-Value Observed: 
  0.195 (Depositor) 

Starting Model: experimental

Literature

Determinant of receptor-preference switch in influenza hemagglutinin.

Ni, F., Kondrashkina, E., Wang, Q.

(2017) Virology 513: 98-107

• PubMed: 29055255 
• DOI: https://doi.org/10.1016/j.virol.2017.10.010
• Primary Citation Related Structures: 
  5VMC, 5VMF, 5VMG, 5VMJ


• PubMed Abstract: 
  

  Influenza pandemic occurs when a new strain from other animal species overcomes the inter-species barriers and supports rapid human-to-human transmission. A critical prerequisite to this process is that hemagglutinin (HA) acquires a few key mutations to switch from avian receptors to human receptors. Previous studies suggest that H1 and H2/H3 HAs use different sets of mutations for the switch. This report shows that HA from the 1918 H1N1 pandemic virus (1918H1 HA) adopts the set of mutations used by H2/H3 HAs in receptor-preference switch when its 130-loop is made similar to those of H2/H3 HAs. Thus, the 130-loop appears to be the key determinant for the different mutations employed by pandemic H1 or H2/H3 HA. The correlation of the mutational routes and the 130-loop as unraveled in this study opens the door for efficient investigation of mutations required by other HA subtypes for inter-human airborne transmission.

---

Organizational Affiliation: 
• Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA.
Life Sciences Collaborative Access Team (LS-CAT), Synchrotron Research Center, Northwestern University, Argonne, IL 60439, USA.
Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Hetero 6-mer - A3B3 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 176.87 kDa 
• Atom Count: 12,548 
• Modeled Residue Count: 1,455 
• Deposited Residue Count: 1,551 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin HA1	A, C, E	326	Influenza A virus (A/Brevig Mission/1/1918(H1N1))	Mutation(s): 2  Gene Names: HA
UniProt
Find proteins for Q9WFX3 (Influenza A virus (strain A/Brevig Mission/1/1918 H1N1)) Explore Q9WFX3  Go to UniProtKB:  Q9WFX3
Glycosylation
Glycosylation Sites: 1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin HA2	B, D, F	191	Influenza A virus (A/Brevig Mission/1/1918(H1N1))	Mutation(s): 0  Gene Names: HA
UniProt
Find proteins for Q9WFX3 (Influenza A virus (strain A/Brevig Mission/1/1918 H1N1)) Explore Q9WFX3  Go to UniProtKB:  Q9WFX3

Oligosaccharides

Help  

Entity ID: 3
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	G	3		N-Glycosylation
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	H, I, K	3		N/A
Glycosylation Resources
GlyTouCan: G73578JC GlyCosmos: G73578JC GlyGen: G73578JC

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	J	2		N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	L [auth A], M [auth C], N [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 4
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900046	H, I, K	6'-sialyl-N-acetyllactosamine	Oligosaccharide / Glycan component

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free:  0.232 (Depositor), 0.235 (DCC) 
• R-Value Work:  0.193 (Depositor), 0.199 (DCC) 
• R-Value Observed: 0.195 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.75	α = 90
b = 80.26	β = 91.35
c = 121.23	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2017-11-08 
Deposition Author(s): Ni, F., Kondrashkina, E., Wang, Q.

---

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01-AI067839
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01-GM116280

Revision History  

• Version 1.0: 2017-11-08
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2022-03-23
  Changes: Author supporting evidence, Database references, Derived calculations, Structure summary
• Version 2.2: 2023-10-04
  Changes: Data collection, Refinement description
• Version 2.3: 2024-10-23
  Changes: Structure summary