Download MendeleyCrystal structure of Nipah Virus attachment (G) glycoprotein in complex with neutralizing antibody 14F8
Li, Y.H., Huang, X.Y., Li, R.H., Xu, J.J., Chen, W.To be published.
8JA5
Crystal structure of Nipah Virus attachment (G) glycoprotein in complex with neutralizing antibody 14F8
- PDB DOI: https://doi.org/10.2210/pdb8JA5/pdb
- Classification: VIRAL PROTEIN/IMMUNE SYSTEM
- Organism(s): Mus musculus, Henipavirus nipahense
- Expression System: Homo sapiens
- Mutation(s): No
- Deposited: 2023-05-05 Released: 2024-05-08
- Funding Organization(s): National Natural Science Foundation of China (NSFC)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.79 Å
- R-Value Free: 0.245
- R-Value Work: 0.217
- R-Value Observed: 0.218
This is version 1.0 of the entry. See complete history.
Literature
To be published.
Macromolecules
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(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| 14F8 antibody heavy chain | A [auth H], D [auth B] | 233 | Mus musculus | Mutation(s): 0 |  |
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
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(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| 14F8 antibody light chain | B [auth L] | 216 | Mus musculus | Mutation(s): 0 |  |
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
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(by identity cutoff) | 3D Structure
Entity ID: 3 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Glycoprotein G | C [auth A], F [auth D] | 423 | Henipavirus nipahense | Mutation(s): 0 |  |
UniProt | |||||
Find proteins for Q9IH62 (Nipah virus) Explore Q9IH62 Go to UniProtKB: Q9IH62 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q9IH62 | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 4 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| 14F8 antibody light chain | E [auth C] | 219 | Mus musculus | Mutation(s): 0 |  |
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
Entity ID: 5 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D 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 | G [auth E] | 4 |  | N-Glycosylation | |
Glycosylation Resources | |||||
GlyTouCan: G81315DD GlyCosmos: G81315DD GlyGen: G81315DD | |||||
Entity ID: 6 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
| alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose | H [auth F] | 6 |  | N-Glycosylation | |
Entity ID: 7 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
| 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | I [auth G], J [auth I], L [auth K] | 2 |  | N-Glycosylation | |
Glycosylation Resources | |||||
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT | |||||
Entity ID: 8 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
| alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose | K [auth J] | 5 |  | N-Glycosylation | |
Glycosylation Resources | |||||
GlyTouCan: G00395TQ GlyCosmos: G00395TQ GlyGen: G00395TQ | |||||
Small Molecules
| Ligands 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| NAG Query on NAG | M [auth A], N [auth D] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.79 Å
- R-Value Free: 0.245
- R-Value Work: 0.217
- R-Value Observed: 0.218
- Space Group: P 41 21 2
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 125.957 | α = 90 |
| b = 125.957 | β = 90 |
| c = 317.264 | γ = 90 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| HKL-2000 | data reduction |
| SCALEPACK | data scaling |
| PHASER | phasing |
| PDB_EXTRACT | data extraction |
Entry History & Funding Information
Deposition Data
- Released Date: 2024-05-08 Deposition Author(s): Li, Y.H., Huang, X.Y., Xu, J.J., Chen, W.
| Funding Organization | Location | Grant Number |
|---|---|---|
| National Natural Science Foundation of China (NSFC) | China | 32200762 |
Revision History (Full details and data files)
- Version 1.0: 2024-05-08
Type: Initial release
