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 
- 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 
This is version 2.2 of the entry. See complete history. 
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
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 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Groups | M1E1E4Q6W8S4 | ||||
Sequence AnnotationsExpand | |||||
|
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
458 Fab heavy chain | B [auth H] | 219 | Homo sapiens | Mutation(s): 0  | |
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
|
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 3 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
458 Fab light chain | C [auth L] | 214 | Homo sapiens | Mutation(s): 0  | |
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
|
Oligosaccharides
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 | 3D Interactions | |
NAG Query on 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 Name | Purpose |
---|---|
PHENIX | refinement |
XDS | data reduction |
Aimless | data scaling |
PHASER | phasing |
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 (Full details and data files)
- 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