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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free:
0.212 (Depositor), 0.230 (DCC)
R-Value Work:
0.187 (Depositor)
R-Value Observed:
0.188 (Depositor)

Starting Model: in silico
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 8UP2

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

Literature

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

Beernink, P.T., Beernink, B.P.

To be published.

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

Find similar proteins by:

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

Find similar proteins by:

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

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9JXV4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain G [auth C] SDF format, chain I [auth F] MOL2 format, chain G [auth C] MOL2 format, chain I [auth F] mmCIF format, chain G [auth C] mmCIF format, chain I [auth F]	G [auth C], I [auth F]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth C] Focus chain I [auth F] Interactions & Density Focus chain G [auth C] Focus chain I [auth F]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain H [auth D] MOL2 format, chain H [auth D] mmCIF format, chain H [auth D]	H [auth D]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain H [auth D] Interactions & Density Focus chain H [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.212 (Depositor), 0.230 (DCC)
R-Value Work: 0.187 (Depositor)
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

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2024-10-16

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

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

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.