6W16

Crystal structure of a human metapneumovirus monomeric fusion protein complexed with 458 Fab

• PDB DOI: https://doi.org/10.2210/pdb6W16/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): human metapneumovirus, Human immunodeficiency virus 1, Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2020-03-03 Released: 2020-06-03 
• Deposition Author(s): Huang, J., Mousa, J.J.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 0.234 
• R-Value Work: 0.190 
• R-Value Observed: 0.193 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 107.13 kDa 
• Atom Count: 6,265 
• Modelled Residue Count: 818 
• Deposited Residue Count: 972 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fusion glycoprotein F0,Envelope glycoprotein fusion	A [auth F]	539	human metapneumovirus, Human immunodeficiency virus 1	Mutation(s): 0
UniProt
Find proteins for M1E1E4 (Human immunodeficiency virus 1) Explore M1E1E4  Go to UniProtKB:  M1E1E4
Find proteins for Q6W8S4 (Human metapneumovirus) Explore Q6W8S4  Go to UniProtKB:  Q6W8S4
UniProt Groups	M1E1E4Q6W8S4

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
458 Fab heavy chain	B [auth H]	219	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
458 Fab light chain	C [auth L]	214	Homo sapiens	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
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	D [auth A]	5		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G22768VO GlyCosmos:  G22768VO GlyGen:  G22768VO

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 0.234 
• R-Value Work: 0.190 
• R-Value Observed: 0.193 
• Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 128.489	α = 90
b = 128.489	β = 90
c = 188.352	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-06-03 
Deposition Author(s): Huang, J., Mousa, J.J.

---

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01AI14386

Revision History  

• Version 1.0: 2020-06-03
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2021-02-10
  Changes: Database references, Structure summary
• Version 2.2: 2023-10-18
  Changes: Data collection, Database references, Refinement description