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
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.

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

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.0 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 139.49 kDa
Atom Count: 10,177
Modelled Residue Count: 1,151
Deposited Residue Count: 1,216
Unique protein chains: 3

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
eOD01 heavy chain	A, B [auth H]	231	Mus musculus	Mutation(s): 0
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Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
eOD01 light chain	C [auth B], E [auth L]	221	Mus musculus	Mutation(s): 0
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Reference Sequence

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Entity ID: 3
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
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Reference Sequence

Oligosaccharides

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Entity ID: 4
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	Interactions Focus chain G [auth E] Interactions & Density Focus chain G [auth E]
Glycosylation Resources
GlyTouCan: G09724ZC GlyCosmos: G09724ZC GlyGen: G09724ZC

Entity ID: 5
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	Interactions Focus chain H [auth F] Interactions & Density Focus chain H [auth F]
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 Download Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain BA [auth D] SDF format, chain V [auth C] MOL2 format, chain AA [auth D] MOL2 format, chain BA [auth D] MOL2 format, chain V [auth C]	AA [auth D], BA [auth D], V [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth D] Focus chain BA [auth D] Focus chain V [auth C] Interactions & Density Focus chain AA [auth D] Focus chain BA [auth D] Focus chain V [auth C]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain N [auth H] SDF format, chain O [auth H] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain U [auth B] SDF format, chain W [auth C] SDF format, chain X [auth L] SDF format, chain Y [auth L] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain N [auth H] MOL2 format, chain O [auth H] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] MOL2 format, chain W [auth C] MOL2 format, chain X [auth L] MOL2 format, chain Y [auth L]	I [auth A] J [auth A] K [auth A] N [auth H] O [auth H] I [auth A], J [auth A], K [auth A], N [auth H], O [auth H], S [auth B], T [auth B], U [auth B], W [auth C], X [auth L], Y [auth L]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain N [auth H] Focus chain O [auth H] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain W [auth C] Focus chain X [auth L] Focus chain Y [auth L] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain N [auth H] Focus chain O [auth H] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain W [auth C] Focus chain X [auth L] Focus chain Y [auth L]
IPA Query on IPA Download Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain P [auth H] SDF format, chain Q [auth H] SDF format, chain R [auth H] SDF format, chain Z [auth L] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain P [auth H] MOL2 format, chain Q [auth H] MOL2 format, chain R [auth H] MOL2 format, chain Z [auth L]	L [auth A] M [auth A] P [auth H] Q [auth H] R [auth H] L [auth A], M [auth A], P [auth H], Q [auth H], R [auth H], Z [auth L]	ISOPROPYL ALCOHOL C₃ H₈ O KFZMGEQAYNKOFK-UHFFFAOYSA-N		Interactions Focus chain L [auth A] Focus chain M [auth A] Focus chain P [auth H] Focus chain Q [auth H] Focus chain R [auth H] Focus chain Z [auth L] Interactions & Density Focus chain L [auth A] Focus chain M [auth A] Focus chain P [auth H] Focus chain Q [auth H] Focus chain R [auth H] Focus chain Z [auth L]

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 Package:

Software Name	Purpose
xia2	data reduction
PHASER	phasing
Coot	model building
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
xia2	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2017-06-28

Deposition Author(s):

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

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Help and Resources

5NUZ

Junin virus GP1 glycoprotein in complex with an antibody Fab fragment

Entity ID: 1

Entity Groups

Sequence Annotations

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Entity ID: 2

Entity Groups

Sequence Annotations

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Entity ID: 3

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 4

Glycosylation Resources

Entity ID: 5

Glycosylation Resources

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)