8UP2 | pdb_00008up2

Murine Fab JAR 4 bound to meningococcal Factor H binding protein

• PDB DOI: https://doi.org/10.2210/pdb8UP2/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus, Neisseria meningitidis
• Expression System: Cricetulus griseus, Escherichia coli
• Mutation(s): No 


• Deposited: 2023-10-20 Released: 2024-10-16 
• Deposition Author(s): Beernink, P.T., Beernink, B.P.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.212 (Depositor), 0.215 (DCC) 
• R-Value Work: 
  0.187 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.188 (Depositor) 

Starting Model: in silico

Literature

Structure of murine Fab JAR 4 bound to FHbp at 1.60-Angstroms resolution

Beernink, P.T., Beernink, B.P.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 2 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 151.88 kDa 
• Atom Count: 11,203 
• Modeled Residue Count: 1,333 
• Deposited Residue Count: 1,400 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Human-mouse chimeric immunoglobulin heavy chain, Fd fragment	A, D	223	Mus musculus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Human-mouse chimeric immunoglobulin, kappa light chain	B, E	220	Mus musculus	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Factor H binding protein, sequence variant ID 1	C, F	257	Neisseria meningitidis	Mutation(s): 0  Gene Names: fhbp
UniProt
Find proteins for Q9JXV4 (Neisseria meningitidis serogroup B (strain ATCC BAA-335 / MC58)) Explore Q9JXV4  Go to UniProtKB:  Q9JXV4

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	G [auth C], I [auth F]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT	H [auth D]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.212 (Depositor), 0.215 (DCC) 
• R-Value Work:  0.187 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.188 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.43	α = 90
b = 67.44	β = 90
c = 168.47	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-10-16 
Deposition Author(s): Beernink, P.T., Beernink, B.P.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-10-16
  Type: Initial release