5NUZ
Junin virus GP1 glycoprotein in complex with an antibody Fab fragment
- PDB DOI: https://doi.org/10.2210/pdb5NUZ/pdb
- Classification: IMMUNE SYSTEM
- Organism(s): Mus musculus, Mammarenavirus juninense
- Expression System: Homo sapiens
- Mutation(s): No 
- Deposited: 2017-05-03 Released: 2017-06-28 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.85 Å
- R-Value Free: 0.210 
- R-Value Work: 0.184 
- R-Value Observed: 0.186 
This is version 2.0 of the entry. See complete history. 
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
eOD01 heavy chain | A, B [auth H] | 231 | Mus musculus | Mutation(s): 0  | |
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
eOD01 light chain | C [auth B], E [auth L] | 221 | Mus musculus | Mutation(s): 0  | |
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 3 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Pre-glycoprotein polyprotein GP complex | D [auth C], F [auth D] | 156 | Mammarenavirus juninense | Mutation(s): 0  Gene Names: GPC | |
UniProt | |||||
Find proteins for C1K9J9 (Junin mammarenavirus) Explore C1K9J9  Go to UniProtKB:  C1K9J9 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | C1K9J9 | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
Entity ID: 4 | |||||
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Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[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] | 6 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G09724ZC GlyCosmos:  G09724ZC GlyGen:  G09724ZC |
Entity ID: 5 | |||||
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Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-2)-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 | H [auth F] | 9 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G83161QT GlyCosmos:  G83161QT GlyGen:  G83161QT |
Small Molecules
Ligands 3 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
NAG Query on NAG | AA [auth D], BA [auth D], V [auth C] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N | |||
GOL Query on GOL | I [auth A] J [auth A] K [auth A] N [auth H] O [auth H] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N | |||
IPA Query on IPA | L [auth A] M [auth A] P [auth H] Q [auth H] R [auth H] | ISOPROPYL ALCOHOL C3 H8 O KFZMGEQAYNKOFK-UHFFFAOYSA-N |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.85 Å
- R-Value Free: 0.210 
- R-Value Work: 0.184 
- R-Value Observed: 0.186 
- Space Group: P 21 21 21
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 97.09 | α = 90 |
b = 101.91 | β = 90 |
c = 147.76 | γ = 90 |
Software Name | Purpose |
---|---|
xia2 | data reduction |
PHASER | phasing |
Coot | model building |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
XDS | data reduction |
xia2 | data scaling |
Entry History 
Deposition Data
- Released Date: 2017-06-28  Deposition Author(s): Zeltina, A., Krumm, S.A., Sahin, M., Struwe, W.B., Harlos, K., Nunberg, J.H., Crispin, M., Pinschewer, D.D., Doores, K.J., Bowden, T.A.
Revision History (Full details and data files)
- Version 1.0: 2017-06-28
Type: Initial release - Version 1.1: 2017-07-12
Changes: Database references - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary