8TYC

Lassa GPC (strain Josiah) bound to rabbit polyclonal base-targeting antibody Base-1

PDB DOI: https://doi.org/10.2210/pdb8TYC/pdb
EM Map EMD-41713: EMDB EMDataResource

Classification: VIRAL PROTEIN/IMMUNE SYSTEM
Organism(s): Lassa virus Josiah, Oryctolagus cuniculus, Thermotoga maritima MSB8
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2023-08-24 Released: 2024-09-11
Deposition Author(s): Perrett, H.R., Brouwer, P.J.M., Ward, A.B.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), Netherlands Organisation for Scientific Research (NWO), Bill & Melinda Gates Foundation

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.30 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Mapping of vaccine-induced humoral responses to the Lassa virus glycoprotein reveals off-target and immunodominant responses

Brouwer, P.J.M., Perrett, H.R., Nijhuis, H., Lee, W.-H., Burger, J., Lloyd, N.M., Himansu, S., Beaumont, T., Carfi, A., Bukreyev, A., Sanders, R.W., van Gils, M.J., Ward, A.B.

To be published.

Macromolecule Content

Total Structure Weight: 255.62 kDa
Atom Count: 10,628
Modelled Residue Count: 1,273
Deposited Residue Count: 2,210
Unique protein chains: 4

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycoprotein G1	A, B, C	259	Lassa virus Josiah	Mutation(s): 0 Gene Names: GPC
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
Glycosylation
Glycosylation Sites: 7	Glycosylation Focus chain A Focus chain B Focus chain C
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Polyclonal antibody Base-1 heavy chain	D [auth H]	108	Oryctolagus cuniculus	Mutation(s): 0
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Polyclonal antibody Base-1 light chain	E [auth L]	107	Oryctolagus cuniculus	Mutation(s): 0
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycoprotein G2, 2-dehydro-3-deoxyphosphogluconate aldolase/4-hydroxy-2-oxoglutarate aldolase fusion protein	F [auth a], G [auth b], H [auth c]	406	Lassa virus Josiah, Thermotoga maritima MSB8 This entity is chimeric	Mutation(s): 0 Gene Names: GPC, GP-C, TM_0066
UniProt
Find proteins for P08669 (Lassa virus (strain Mouse/Sierra Leone/Josiah/1976)) Explore P08669 Go to UniProtKB: P08669
Find proteins for Q9WXS1 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9WXS1 Go to UniProtKB: Q9WXS1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Groups	Q9WXS1P08669
Glycosylation
Glycosylation Sites: 4	Glycosylation Focus chain F [auth a] Focus chain G [auth b] Focus chain H [auth c]
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	BA [auth Y], DA [auth d], GA [auth g], I [auth D], IA [auth i], BA [auth Y], DA [auth d], GA [auth g], I [auth D], IA [auth i], K [auth F], L [auth G], M [auth I], N [auth J], O [auth K], P [auth M], S [auth P], U [auth R], W [auth T], Y [auth V]	2		N-Glycosylation	Interactions Focus chain BA [auth Y] Focus chain DA [auth d] Focus chain GA [auth g] Focus chain I [auth D] Focus chain IA [auth i] Focus chain K [auth F] Focus chain L [auth G] Focus chain M [auth I] Focus chain N [auth J] Focus chain O [auth K] Focus chain P [auth M] Focus chain S [auth P] Focus chain U [auth R] Focus chain W [auth T] Focus chain Y [auth V] Interactions & Density Focus chain BA [auth Y] Focus chain DA [auth d] Focus chain GA [auth g] Focus chain I [auth D] Focus chain IA [auth i] Focus chain K [auth F] Focus chain L [auth G] Focus chain M [auth I] Focus chain N [auth J] Focus chain O [auth K] Focus chain P [auth M] Focus chain S [auth P] Focus chain U [auth R] Focus chain W [auth T] Focus chain Y [auth V]

Entity ID: 6
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	AA [auth X], EA [auth e], J [auth E], Q [auth N], R [auth O], AA [auth X], EA [auth e], J [auth E], Q [auth N], R [auth O], V [auth S], X [auth U]	3		N-Glycosylation	Interactions Focus chain AA [auth X] Focus chain EA [auth e] Focus chain J [auth E] Focus chain Q [auth N] Focus chain R [auth O] Focus chain V [auth S] Focus chain X [auth U] Interactions & Density Focus chain AA [auth X] Focus chain EA [auth e] Focus chain J [auth E] Focus chain Q [auth N] Focus chain R [auth O] Focus chain V [auth S] Focus chain X [auth U]

Entity ID: 7
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-L-fucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose	T [auth Q]	2		N-Glycosylation	Interactions Focus chain T [auth Q] Interactions & Density Focus chain T [auth Q]

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	Z [auth W]	3		N-Glycosylation	Interactions Focus chain Z [auth W] Interactions & Density Focus chain Z [auth W]

Entity ID: 9
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-2)-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	CA [auth Z], FA [auth f], HA [auth h]	6		N-Glycosylation	Interactions Focus chain CA [auth Z] Focus chain FA [auth f] Focus chain HA [auth h] Interactions & Density Focus chain CA [auth Z] Focus chain FA [auth f] Focus chain HA [auth h]

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 JA [auth C] SDF format, chain KA [auth a] SDF format, chain LA [auth a] SDF format, chain MA [auth b] SDF format, chain NA [auth c] SDF format, chain OA [auth c] MOL2 format, chain JA [auth C] MOL2 format, chain KA [auth a] MOL2 format, chain LA [auth a] MOL2 format, chain MA [auth b] MOL2 format, chain NA [auth c] MOL2 format, chain OA [auth c]	JA [auth C] KA [auth a] LA [auth a] MA [auth b] NA [auth c] JA [auth C], KA [auth a], LA [auth a], MA [auth b], NA [auth c], OA [auth c]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain JA [auth C] Focus chain KA [auth a] Focus chain LA [auth a] Focus chain MA [auth b] Focus chain NA [auth c] Focus chain OA [auth c] Interactions & Density Focus chain JA [auth C] Focus chain KA [auth a] Focus chain LA [auth a] Focus chain MA [auth b] Focus chain NA [auth c] Focus chain OA [auth c]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.30 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2024-09-11

Deposition Author(s):

Perrett, H.R.

Brouwer, P.J.M.

Ward, A.B.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	1F31Al172358
Netherlands Organisation for Scientific Research (NWO)	Netherlands	Rubicon Fellowship
Bill & Melinda Gates Foundation	United States	INV-004923
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI71438