4HJJ | pdb_00004hjj

Structure Reveals Function of the Dual Variable Domain Immunoglobulin (DVD-Ig) Molecule

PDB DOI: https://doi.org/10.2210/pdb4HJJ/pdb

Classification: IMMUNE SYSTEM
Organism(s): Homo sapiens
Expression System: Escherichia coli, Homo sapiens
Mutation(s): Yes

Deposited: 2012-10-12 Released: 2013-05-08
Deposition Author(s): Jakob, C.G., Edalji, R., Judge, R.A., DiGiammarino, E., Li, Y., Gu, J., Ghayur, T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.220 (Depositor), 0.225 (DCC)
R-Value Work:
0.184 (Depositor), 0.192 (DCC)
R-Value Observed:
0.186 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Structure reveals function of the dual variable domain immunoglobulin (DVD-Ig[TM]) molecule

Jakob, C.G., Edalji, R., Judge, R.A., Digiammarino, E., Li, Y., Gu, J., Ghayur, T.

(2013) MAbs 5: 358-363

PubMed: 23549062 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.4161/mabs.23977
Primary Citation Related Structures:
4HJJ

PubMed Abstract:
Several bispecific antibody-based formats have been developed over the past 25 years in an effort to produce a new generation of immunotherapeutics that target two or more disease mechanisms simultaneously. One such format, the dual-variable domain immunoglobulin (DVD-Ig™), combines the target binding domains of two monoclonal antibodies via flexible naturally occurring linkers, which yields a tetravalent IgG - like molecule. We report the structure of an interleukin (IL)12-IL18 DVD-Ig™ Fab (DFab) fragment with IL18 bound to the inner variable domain (VD) that reveals the remarkable flexibility of the DVD-Ig™ molecule and how the DVD-Ig™ format can function to bind four antigens simultaneously. An understanding of how the inner variable domain retains function is of critical importance for designing DVD-Ig™ molecules, and for better understanding of the flexibility of immunoglobulin variable domains and linkers, which may aid in the design of improved bi- and multi-specific biologics in general.

Organizational Affiliation

Department of Structural Biology; AbbVie Inc.; North Chicago, IL USA.

Macromolecule Content

Total Structure Weight: 91.91 kDa
Atom Count: 7,248
Modeled Residue Count: 825
Deposited Residue Count: 832
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Interleukin-18	A	157	Homo sapiens	Mutation(s): 4 Gene Names: IL18, IGIF, IL1F4
UniProt & NIH Common Fund Data Resources
Find proteins for Q14116 (Homo sapiens) Explore Q14116 Go to UniProtKB: Q14116
PHAROS: Q14116 GTEx: ENSG00000150782
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q14116
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Anti-IL12 Anti-IL18 DFab Heavy Chain	B [auth H]	348	Homo sapiens	Mutation(s): 0

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Anti-IL12 Anti-IL18 DFab Light Chain	C [auth L]	327	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain E [auth H] MOL2 format, chain E [auth H] mmCIF format, chain E [auth H]	E [auth H]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth H] Interactions & Density Focus chain E [auth H]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain F [auth L] SDF format, chain D [auth A] MOL2 format, chain F [auth L] MOL2 format, chain D [auth A] mmCIF format, chain F [auth L] mmCIF format, chain D [auth A]	D [auth A], F [auth L]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain F [auth L] Interactions & Density Focus chain D [auth A] Focus chain F [auth L]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain G [auth L] MOL2 format, chain G [auth L] mmCIF format, chain G [auth L]	G [auth L]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain G [auth L] Interactions & Density Focus chain G [auth L]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.220 (Depositor), 0.225 (DCC)
R-Value Work: 0.184 (Depositor), 0.192 (DCC)
R-Value Observed: 0.186 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 274.385	α = 90
b = 65.498	β = 95.2
c = 78.802	γ = 90

Software Package:

Software Name	Purpose
BUSTER-TNT	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing
MOLREP	phasing
BUSTER	refinement

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2013-05-08

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-05-08
Type: Initial release
Version 1.1: 2024-11-20
Changes: Data collection, Database references, Derived calculations, Structure summary