3V0W | pdb_00003v0w

Crystal structure of Fab WN1 222-5 in complex with LPS

PDB DOI: https://doi.org/10.2210/pdb3V0W/pdb

Classification: IMMUNE SYSTEM
Organism(s): Mus musculus
Mutation(s): No

Deposited: 2011-12-08 Released: 2012-12-05
Deposition Author(s): Gomery, K., Evans, S.V.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.73 Å
R-Value Free:
0.231 (Depositor), 0.242 (DCC)
R-Value Work:
0.182 (Depositor), 0.208 (DCC)
R-Value Observed:
0.184 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 2.1 of the entry. See complete history.

Literature

Antibody WN1 222-5 mimics Toll-like receptor 4 binding in the recognition of LPS.

Gomery, K., Muller-Loennies, S., Brooks, C.L., Brade, L., Kosma, P., Di Padova, F., Brade, H., Evans, S.V.

(2012) Proc Natl Acad Sci U S A 109: 20877-20882

PubMed: 23184990 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1073/pnas.1209253109
Primary Citation Related Structures:
3V0V, 3V0W

PubMed Abstract:
Escherichia coli infections, a leading cause of septic shock, remain a major threat to human health because of the fatal action to endotoxin (LPS). Therapeutic attempts to neutralize endotoxin currently focus on inhibiting the interaction of the toxic component lipid A with myeloid differentiating factor 2, which forms a trimeric complex together with Toll-like receptor 4 to induce immune cell activation. The 1.73-Å resolution structure of the unique endotoxin-neutralizing protective antibody WN1 222-5 in complex with the core region shows that it recognizes LPS of all E. coli serovars in a manner similar to Toll-like receptor 4, revealing that protection can be achieved by targeting the inner core of LPS and that recognition of lipid A is not required. Such interference with Toll-like receptor complex formation opens new paths for antibody sepsis therapy independent of lipid A antagonists.

Organizational Affiliation

Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada V8P 3P6.

Macromolecule Content

Total Structure Weight: 49.64 kDa
Atom Count: 3,953
Modeled Residue Count: 425
Deposited Residue Count: 431
Unique protein chains: 2

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
WN1 222-5 Fab (IgG2a) light chain	A [auth L]	212	Mus musculus	Mutation(s): 0

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
WN1 222-5 Fab (IgG2a) heavy chain	B [auth H]	219	Mus musculus	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-amino-2-deoxy-alpha-D-glucopyranose-(1-2)-alpha-D-glucopyranose-(1-2)-alpha-D-glucopyranose-(1-3)-[alpha-D-galactopyranose-(1-6)]alpha-D-glucopyranose-(1-3)-[L-glycero-alpha-D-manno-heptopyranose-(1-7)]4-O-phosphono-L-glycero-alpha-D-manno-heptopyranose-(1-3)-4-O-phosphono-L-glycero-alpha-D-manno-heptopyranose-(1-5)-[3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(2-4)]3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid	C [auth A]	10		N/A	Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
Glycosylation Resources
GlyTouCan: G52117HE GlyCosmos: G52117HE

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain D [auth L] SDF format, chain E [auth L] SDF format, chain F [auth L] SDF format, chain G [auth L] SDF format, chain H SDF format, chain K [auth H] SDF format, chain L [auth H] SDF format, chain M [auth H] SDF format, chain J [auth H] SDF format, chain I [auth H] MOL2 format, chain D [auth L] MOL2 format, chain E [auth L] MOL2 format, chain F [auth L] MOL2 format, chain G [auth L] MOL2 format, chain H MOL2 format, chain K [auth H] MOL2 format, chain L [auth H] MOL2 format, chain M [auth H] MOL2 format, chain J [auth H] MOL2 format, chain I [auth H] mmCIF format, chain D [auth L] mmCIF format, chain E [auth L] mmCIF format, chain F [auth L] mmCIF format, chain G [auth L] mmCIF format, chain H mmCIF format, chain K [auth H] mmCIF format, chain L [auth H] mmCIF format, chain M [auth H] mmCIF format, chain J [auth H] mmCIF format, chain I [auth H]	D [auth L] E [auth L] F [auth L] G [auth L] H D [auth L], E [auth L], F [auth L], G [auth L], H, I [auth H], J [auth H], K [auth H], L [auth H], M [auth H]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth L] Focus chain E [auth L] Focus chain F [auth L] Focus chain G [auth L] Focus chain H Focus chain I [auth H] Focus chain J [auth H] Focus chain K [auth H] Focus chain L [auth H] Focus chain M [auth H] Interactions & Density Focus chain D [auth L] Focus chain E [auth L] Focus chain F [auth L] Focus chain G [auth L] Focus chain H Focus chain I [auth H] Focus chain J [auth H] Focus chain K [auth H] Focus chain L [auth H] Focus chain M [auth H]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.73 Å
R-Value Free: 0.231 (Depositor), 0.242 (DCC)
R-Value Work: 0.182 (Depositor), 0.208 (DCC)
R-Value Observed: 0.184 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.852	α = 90
b = 101.852	β = 90
c = 118.532	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MxDC	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2012-12-05

Deposition Author(s):

Gomery, K.

Evans, S.V.

Revision History (Full details and data files)

Version 1.0: 2012-12-05
Type: Initial release
Version 1.1: 2013-01-02
Changes: Database references
Version 1.2: 2017-11-08
Changes: Refinement description
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2024-11-27
Changes: Data collection, Database references, Structure summary