5W1G | pdb_00005w1g

CR1-07 unliganded Fab

• PDB DOI: https://doi.org/10.2210/pdb5W1G/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• 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 General Medical Sciences (NIH/NIGMS), Other private

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.281 (Depositor), 0.282 (DCC) 
• R-Value Work: 
  0.231 (Depositor), 0.235 (DCC) 
• R-Value Observed: 
  0.233 (Depositor) 

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 
• 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.

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Organizational Affiliation: 
• Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, 02115, USA.
Laboratory of Molecular Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA.
Department of Pathology, University of Texas Medical Branch at Galveston, Galveston, TX, 77555, USA.
Instituto Nacional de Enfermedades Virales Humanas "Dr. Julio I. Maiztegui", Monteagudo 251 Pergamino, Buenos Aires, 2700, Argentina.
Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, 02115, USA.
Program in Immunology, Harvard Medical School, Boston, MA, 02115, USA.
Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, 02115, USA. [e-mail].
Laboratory of Molecular Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA. [e-mail].
Department of Medicine, Division of Infectious Diseases, Brigham and Women's Hospital, Boston, MA, 02115, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: homology

Macromolecule Content 

• Total Structure Weight: 48.41 kDa 
• Atom Count: 3,601 
• Modeled Residue Count: 441 
• Deposited Residue Count: 445 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CR1-07 Fab heavy chain	A [auth H]	223	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
CR1-07 Fab light chain	B [auth L]	222	Homo sapiens	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.281 (Depositor), 0.282 (DCC) 
• R-Value Work:  0.231 (Depositor), 0.235 (DCC) 
• R-Value Observed: 0.233 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.77	α = 90
b = 137.41	β = 148.66
c = 78.67	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data collection
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
BALBES	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-05-30 
Deposition Author(s): Raymond, D.D., Clark, L.E., Abraham, J.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	AI007061
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	AI109740
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	DP5OD023084
Other private	United States	--
Other private	United States	--

Revision History  

• Version 1.0: 2018-05-30
  Type: Initial release
  
• Version 1.1: 2020-01-01
  Changes: Author supporting evidence
• Version 1.2: 2024-10-30
  Changes: Data collection, Database references, Structure summary