5W1M | pdb_00005w1m

MACV GP1 CR1-07 Fab complex

PDB DOI: https://doi.org/10.2210/pdb5W1M/pdb

Classification: VIRAL PROTEIN/IMMUNE SYSTEM
Organism(s): Homo sapiens, Mammarenavirus machupoense
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2017-06-03 Released: 2018-05-30
Deposition Author(s): Raymond, D.D., Clark, L.E., Abraham, J.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), Other private

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.91 Å
R-Value Free:
0.264 (Depositor), 0.284 (DCC)
R-Value Work:
0.248 (Depositor)
R-Value Observed:
0.249 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.2 of the entry. See complete history.

Literature

Vaccine-elicited receptor-binding site antibodies neutralize two New World hemorrhagic fever arenaviruses.

Clark, L.E., Mahmutovic, S., Raymond, D.D., Dilanyan, T., Koma, T., Manning, J.T., Shankar, S., Levis, S.C., Briggiler, A.M., Enria, D.A., Wucherpfennig, K.W., Paessler, S., Abraham, J.

(2018) Nat Commun 9: 1884-1884

PubMed: 29760382 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41467-018-04271-z
Primary Citation Related Structures:
5W1G, 5W1K, 5W1M

PubMed Abstract:
While five arenaviruses cause human hemorrhagic fevers in the Western Hemisphere, only Junin virus (JUNV) has a vaccine. The GP1 subunit of their envelope glycoprotein binds transferrin receptor 1 (TfR1) using a surface that substantially varies in sequence among the viruses. As such, receptor-mimicking antibodies described to date are type-specific and lack the usual breadth associated with this mode of neutralization. Here we isolate, from the blood of a recipient of the live attenuated JUNV vaccine, two antibodies that cross-neutralize Machupo virus with varying efficiency. Structures of GP1-Fab complexes explain the basis for efficient cross-neutralization, which involves avoiding receptor mimicry and targeting a conserved epitope within the receptor-binding site (RBS). The viral RBS, despite its extensive sequence diversity, is therefore a target for cross-reactive antibodies with activity against New World arenaviruses of public health concern.

Organizational Affiliation

Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, 02115, USA.

Macromolecule Content

Total Structure Weight: 265.98 kDa
Atom Count: 18,425
Modeled Residue Count: 2,360
Deposited Residue Count: 2,396
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CR1-07 Fab light chain	A, C, E, G	221	Homo sapiens	Mutation(s): 0
UniProt
Find proteins for Q0KKI6 (Homo sapiens) Explore Q0KKI6 Go to UniProtKB: Q0KKI6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q0KKI6
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
CR1-07 Fab heavy chain	B, D, F, H	226	Homo sapiens	Mutation(s): 0
UniProt
Find proteins for Q6N089 (Homo sapiens) Explore Q6N089 Go to UniProtKB: Q6N089
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6N089
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Pre-glycoprotein polyprotein GP complex	I [auth Q], J [auth R], K [auth S], L [auth T]	152	Mammarenavirus machupoense	Mutation(s): 0 Gene Names: GPC
UniProt
Find proteins for Q8AZ57 (Machupo virus) Explore Q8AZ57 Go to UniProtKB: Q8AZ57
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8AZ57
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain I [auth Q] Focus chain J [auth R] Focus chain K [auth S] Focus chain L [auth T]
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	M [auth I], N [auth J]	2		N-Glycosylation	Interactions Focus chain M [auth I] Focus chain N [auth J] Interactions & Density Focus chain M [auth I] Focus chain N [auth J]
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain Q [auth T] MOL2 format, chain Q [auth T] mmCIF format, chain Q [auth T]	Q [auth T]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain Q [auth T] Interactions & Density Focus chain Q [auth T]
BMA Query on BMA Download:Ideal Coordinates CCD File SDF format, chain P [auth Q] MOL2 format, chain P [auth Q] mmCIF format, chain P [auth Q]	P [auth Q]	beta-D-mannopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-RWOPYEJCSA-N		Interactions Focus chain P [auth Q] Interactions & Density Focus chain P [auth Q]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.91 Å
R-Value Free: 0.264 (Depositor), 0.284 (DCC)
R-Value Work: 0.248 (Depositor)
R-Value Observed: 0.249 (Depositor)

Space Group: P 4₂ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 206.97	α = 90
b = 206.97	β = 90
c = 238.23	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2018-05-30

Deposition Author(s):

Raymond, D.D.

Clark, L.E.

Abraham, J.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI007061
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI109740
Other private	United States	Burroughs Wellcome
Other private	United States	William Randolph Hearst Foundation and Brigham and Womens Hospital
Other private	United States	Harvard Medical School DICP

Revision History (Full details and data files)

Version 1.0: 2018-05-30
Type: Initial release
Version 1.1: 2019-12-11
Changes: Author supporting evidence
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2023-10-04
Changes: Data collection, Database references, Refinement description, Structure summary
Version 2.2: 2024-11-20
Changes: Structure summary