5VK2

Structural basis for antibody-mediated neutralization of Lassa virus

PDB DOI: https://doi.org/10.2210/pdb5VK2/pdb

Classification: VIRAL PROTEIN/Immune system
Organism(s): Lassa virus Josiah, Homo sapiens
Expression System: Drosophila, Cricetulus griseus
Mutation(s): Yes

Deposited: 2017-04-20 Released: 2017-05-31
Deposition Author(s): Hastie, K.M., Zandonatti, M.A., Kleinfelter, L.M., Rowland, M.L., Rowland, M.M., Chandra, K., Branco, L.M., Robinson, J.E., Garry, R.F., Saphire, E.O.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.20 Å
R-Value Free: 0.231
R-Value Work: 0.189
R-Value Observed: 0.191

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 299.8 kDa
Atom Count: 18,672
Modelled Residue Count: 2,313
Deposited Residue Count: 2,607
Unique protein chains: 4

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pre-glycoprotein polyprotein GP complex	A, C [auth B], E [auth C]	259	Lassa virus Josiah	Mutation(s): 3 Gene Names: GPC, GP-C
UniProt
Find proteins for P08669 (Lassa virus (strain Mouse/Sierra Leone/Josiah/1976)) Explore P08669 Go to UniProtKB: P08669
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P08669
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Pre-glycoprotein polyprotein GP complex	B [auth a], D [auth b], F [auth c]	164	Lassa virus Josiah	Mutation(s): 3 Gene Names: GPC, GP-C
UniProt
Find proteins for P08669 (Lassa virus (strain Mouse/Sierra Leone/Josiah/1976)) Explore P08669 Go to UniProtKB: P08669
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P08669
Sequence Annotations Expand
Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab 37.7H heavy chain	G [auth D], I [auth F], K [auth H]	229	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab 37.7H light chain	H [auth E], J [auth G], L	217	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	CA [auth Z], M [auth I], Y [auth V]	3		N-Glycosylation	Interactions Focus chain CA [auth Z] Focus chain M [auth I] Focus chain Y [auth V] Interactions & Density Focus chain CA [auth Z] Focus chain M [auth I] Focus chain Y [auth V]
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	AA [auth X], BA [auth Y], EA [auth e], N [auth J], O [auth K], AA [auth X], BA [auth Y], EA [auth e], N [auth J], O [auth K], P [auth M], R [auth O], T [auth Q], U [auth R], V [auth S], Z [auth W]	2		N-Glycosylation	Interactions Focus chain AA [auth X] Focus chain BA [auth Y] Focus chain EA [auth e] Focus chain N [auth J] Focus chain O [auth K] Focus chain P [auth M] Focus chain R [auth O] Focus chain T [auth Q] Focus chain U [auth R] Focus chain V [auth S] Focus chain Z [auth W] Interactions & Density Focus chain AA [auth X] Focus chain BA [auth Y] Focus chain EA [auth e] Focus chain N [auth J] Focus chain O [auth K] Focus chain P [auth M] Focus chain R [auth O] Focus chain T [auth Q] Focus chain U [auth R] Focus chain V [auth S] Focus chain Z [auth W]
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 7
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	DA [auth d], Q [auth N], W [auth T]	4		N-Glycosylation	Interactions Focus chain DA [auth d] Focus chain Q [auth N] Focus chain W [auth T] Interactions & Density Focus chain DA [auth d] Focus chain Q [auth N] Focus chain W [auth T]
Glycosylation Resources
GlyTouCan: G81315DD GlyCosmos: G81315DD GlyGen: G81315DD

Entity ID: 8
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	FA [auth f], S [auth P], X [auth U]	3		N-Glycosylation	Interactions Focus chain FA [auth f] Focus chain S [auth P] Focus chain X [auth U] Interactions & Density Focus chain FA [auth f] Focus chain S [auth P] Focus chain X [auth U]
Glycosylation Resources
GlyTouCan: G21290RB GlyCosmos: G21290RB GlyGen: G21290RB

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain HA [auth A] SDF format, chain IA [auth A] SDF format, chain JA [auth a] SDF format, chain LA [auth B] SDF format, chain MA [auth B] SDF format, chain NA [auth b] SDF format, chain OA [auth C] SDF format, chain PA [auth C] SDF format, chain QA [auth c] SDF format, chain GA [auth A] SDF format, chain KA [auth B] MOL2 format, chain HA [auth A] MOL2 format, chain IA [auth A] MOL2 format, chain JA [auth a] MOL2 format, chain LA [auth B] MOL2 format, chain MA [auth B] MOL2 format, chain NA [auth b] MOL2 format, chain OA [auth C] MOL2 format, chain PA [auth C] MOL2 format, chain QA [auth c] MOL2 format, chain GA [auth A] MOL2 format, chain KA [auth B]	GA [auth A] HA [auth A] IA [auth A] JA [auth a] KA [auth B] GA [auth A], HA [auth A], IA [auth A], JA [auth a], KA [auth B], LA [auth B], MA [auth B], NA [auth b], OA [auth C], PA [auth C], QA [auth c]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain GA [auth A] Focus chain HA [auth A] Focus chain IA [auth A] Focus chain JA [auth a] Focus chain KA [auth B] Focus chain LA [auth B] Focus chain MA [auth B] Focus chain NA [auth b] Focus chain OA [auth C] Focus chain PA [auth C] Focus chain QA [auth c] Interactions & Density Focus chain GA [auth A] Focus chain HA [auth A] Focus chain IA [auth A] Focus chain JA [auth a] Focus chain KA [auth B] Focus chain LA [auth B] Focus chain MA [auth B] Focus chain NA [auth b] Focus chain OA [auth C] Focus chain PA [auth C] Focus chain QA [auth c]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.20 Å
R-Value Free: 0.231
R-Value Work: 0.189
R-Value Observed: 0.191
Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 152.697	α = 90
b = 152.697	β = 90
c = 456.738	γ = 120

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2017-05-31

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	1U19AI109762-01
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R21 AI116112
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	T32 GM007491

Revision History (Full details and data files)

Version 1.0: 2017-05-31
Type: Initial release
Version 1.1: 2017-06-14
Changes: Database references
Version 1.2: 2017-09-27
Changes: Author supporting evidence
Version 1.3: 2019-12-11
Changes: Author supporting evidence, Data collection
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2023-10-04
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary