8ULK | pdb_00008ulk

Prefusion RSV F bound by neutralizing antibody 1G12

PDB DOI: https://doi.org/10.2210/pdb8ULK/pdb

Classification: VIRAL PROTEIN/IMMUNE SYSTEM
Organism(s): Human respiratory syncytial virus A2, Homo sapiens, Respiratory syncytial virus A2
Expression System: Cricetulus griseus, Homo sapiens
Mutation(s): No

Deposited: 2023-10-16 Released: 2024-11-06
Deposition Author(s): Harshbarger, W.D., Andreano, E., Malito, E.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 4.28 Å
R-Value Free:
0.279 (Depositor), 0.280 (DCC)
R-Value Work:
0.244 (Depositor), 0.245 (DCC)
R-Value Observed:
0.246 (Depositor)

Starting Model: experimental
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This is version 1.0 of the entry. See complete history.

Literature

Structural and functional properties of monoclonal and vaccine-induced antibodies targeting epitopes of emerging RSV variants

Xian, Y., Andreano, E., Tian, S., Phung, E., Garbinski, L., Biancucci, M., Lofano, G., Mallett, C.P., Balsaraf, A., Huang, Y., Buricchi, F., Finco, O., Rappuoli, R., Bottomley, M.J., Chandramouli, S., Warter, L., Williams, J., Malito, E., Harshbarger, W.D.

To be published.

Macromolecule Content

Total Structure Weight: 307.24 kDa
Atom Count: 20,187
Modeled Residue Count: 2,631
Deposited Residue Count: 2,805
Unique protein chains: 4

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fusion glycoprotein F2	A, B, C	72	Human respiratory syncytial virus A2	Mutation(s): 0
UniProt
Find proteins for P03420 (Human respiratory syncytial virus A (strain A2)) Explore P03420 Go to UniProtKB: P03420
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P03420
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
1G12 Fab heavy chain	D, F [auth H], H [auth F]	235	Homo sapiens	Mutation(s): 0

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
1G12 Fab light chain	E, G [auth L], I [auth G]	214	Homo sapiens	Mutation(s): 0

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Fusion glycoprotein F0,Fibritin	J [auth I], K [auth J], L [auth K]	414	Respiratory syncytial virus A2	Mutation(s): 0
UniProt
Find proteins for A0A088S9A7 (Human respiratory syncytial virus MinFLC) Explore A0A088S9A7 Go to UniProtKB: A0A088S9A7
Find proteins for P10104 (Enterobacteria phage T4) Explore P10104 Go to UniProtKB: P10104
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Groups	A0A088S9A7 P10104
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 4.28 Å
R-Value Free: 0.279 (Depositor), 0.280 (DCC)
R-Value Work: 0.244 (Depositor), 0.245 (DCC)
R-Value Observed: 0.246 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 143.982	α = 90
b = 174.605	β = 90
c = 226.286	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing
PHENIX	refinement
SERGUI	data collection
Coot	model building

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-11-06

Deposition Author(s):

Harshbarger, W.D.

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2024-11-06
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.