8R38 | pdb_00008r38

BIIG2 anti-integrin Fab

• PDB DOI: https://doi.org/10.2210/pdb8R38/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Rattus norvegicus
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2023-11-08 Released: 2024-09-25 
• Deposition Author(s): Cordara, G., Heim, J.B., Johannesen, H., Krengel, U.
• Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI), Norwegian Research Council

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.38 Å
• R-Value Free: 
  0.217 (Depositor), 0.222 (DCC) 
• R-Value Work: 
  0.195 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.197 (Depositor) 

Starting Model: experimental

Literature

Shared ligand-blocking mechanism but distinct conformational modulation by alpha 5-targeting antibodies BIIG2 and MINT1526A.

Nguyen, A., Heim, J.B., Cordara, G., Chan, M.C., Johannesen, H., Charlesworth, C., Li, M., Azumaya, C.M., Madden, B., Krengel, U., Meves, A., Campbell, M.G.

(2025) bioRxiv 

• PubMed: 39829743 
• DOI: https://doi.org/10.1101/2025.01.08.631572
• Primary Citation Related Structures: 
  8R38, 9B9J, 9B9K


• PubMed Abstract: 
  

  Integrins are heterodimeric receptors important for cell adhesion and signaling. Integrin α5β1 is a key mediator of angiogenesis and its dysregulation is associated with tumor progression and metastasis. Despite numerous efforts, α5β1-targeting therapeutics have been unsuccessful due to poor efficacy and off-target effects. A contributing factor is our limited understanding of how integrin conformation influences interactions with therapeutics. Using cell-based functional assays, patient derived xenografts, biophysics, and electron microscopy, we shed light on these relationships by characterizing two anti-α5β1 antibodies, BIIG2 and MINT1526A. We show that both antibodies bind α5β1 with nanomolar affinity, reduce angiogenesis in vitro , and bind overlapping epitopes that block fibronectin binding. However, using cryoEM, we reveal that while BIIG2 binding doesn't alter the conformational states, MINT1526A restricts α5β1's range of flexibility. These insights can guide which aspects to prioritize and improve the design of future integrin-targeted therapeutics.

---

Organizational Affiliation: 
• Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington 98109, USA.
Biological Physics Structure and Design Program, University of Washington, Seattle, Washington 98195, USA.
Department of Dermatology, Mayo Clinic, Rochester, Minnesota 55905, USA.
Department of Chemistry, University of Oslo, NO-0315 Oslo, Norway.
Current Address: Nykode Therapeutics, Oslo Science Park, 0349 Oslo, Norway.
Medical Genome Facility, Proteomics Core, Mayo Clinic, Rochester, Minnesota 55905, USA.
Current Address: Genentech, South San Francisco, California 94080, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 48.46 kDa 
• Atom Count: 4,185 
• Modeled Residue Count: 431 
• Deposited Residue Count: 434 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BIIG2 Fab, heavy chain	A [auth H]	220	Rattus norvegicus	Mutation(s): 0
Glycosylation
Glycosylation Sites: 1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
BIIG2 Fab, light chain	B [auth L]	214	Rattus norvegicus	Mutation(s): 0

Oligosaccharides

Help  

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C [auth S]	4		N-Glycosylation
Glycosylation Resources
GlyTouCan: G22573RC GlyCosmos: G22573RC GlyGen: G22573RC

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	D [auth H], E [auth L], F [auth L], G [auth L], H [auth L]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	I [auth L]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  3 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PCA	A [auth H]	L-PEPTIDE LINKING	C5 H7 N O3		GLN
XRE	A [auth H]	L-PEPTIDE LINKING	C5 H9 N O3		PRO
MLZ	B [auth L]	L-PEPTIDE LINKING	C7 H16 N2 O2		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.38 Å
• R-Value Free:  0.217 (Depositor), 0.222 (DCC) 
• R-Value Work:  0.195 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.197 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.93	α = 90
b = 80.882	β = 90
c = 87.469	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-09-25 
Deposition Author(s): Cordara, G., Heim, J.B., Johannesen, H., Krengel, U.

---

Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	P30 CA015704-40
Norwegian Research Council	Norway	245828

Revision History  

• Version 1.0: 2024-09-25
  Type: Initial release
  
• Version 1.1: 2025-02-05
  Changes: Database references, Structure summary
• Version 1.2: 2025-10-22
  Changes: Database references