4LMQ | pdb_00004lmq

Development and Preclinical Characterization of a Humanized Antibody Targeting CXCL12


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.77 Å
  • R-Value Free: 
    0.301 (Depositor), 0.241 (DCC) 
  • R-Value Work: 
    0.253 (Depositor), 0.225 (DCC) 
  • R-Value Observed: 
    0.255 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 4LMQ

This is version 1.4 of the entry. See complete history

Literature

Development and Preclinical Characterization of a Humanized Antibody Targeting CXCL12.

Zhong, C.Wang, J.Li, B.Xiang, H.Ultsch, M.Coons, M.Wong, T.Chiang, N.Y.Clark, S.Clark, R.Quintana, L.Gribling, P.Suto, E.Barck, K.Corpuz, R.Yao, J.Takkar, R.Lee, W.P.Damico-Beyer, L.A.Carano, R.D.Adams, C.Kelley, R.F.Wang, W.Ferrara, N.

(2013) Clin Cancer Res 19: 4433-4445

  • DOI: https://doi.org/10.1158/1078-0432.CCR-13-0943
  • Primary Citation Related Structures: 
    4LMQ

  • PubMed Abstract: 

    Our goal was to develop a potent humanized antibody against mouse/human CXCL12. This report summarized its in vitro and in vivo activities. Cell surface binding and cell migration assays were used to select neutralizing hamster antibodies, followed by testing in several animal models. Monoclonal antibody (mAb) 30D8 was selected for humanization based on its in vitro and in vivo activities. 30D8, a hamster antibody against mouse and human CXCL12α, CXCL12β, and CXCL12γ, was shown to dose-dependently block CXCL12α binding to CXCR4 and CXCR7, and CXCL12α-induced Jurkat cell migration in vitro. Inhibition of primary tumor growth and/or metastasis was observed in several models. 30D8 alone significantly ameliorated arthritis in a mouse collagen-induced arthritis model (CIA). Combination with a TNF-α antagonist was additive. In addition, 30D8 inhibited 50% of laser-induced choroidal neovascularization (CNV) in mice. Humanized 30D8 (hu30D8) showed similar in vitro and in vivo activities as the parental hamster antibody. A crystal structure of the hu30D8 Fab/CXCL12α complex in combination with mutational analysis revealed a "hot spot" around residues Asn(44)/Asn(45) of CXCL12α and part of the RFFESH region required for CXCL12α binding to CXCR4 and CXCR7. Finally, hu30D8 exhibited fast clearance in cynomolgus monkeys but not in rats. CXCL12 is an attractive target for treatment of cancer and inflammation-related diseases; hu30D8 is suitable for testing this hypothesis in humans.


  • Organizational Affiliation
    • Genentech, Inc., South San Francisco, California, USA.

Macromolecule Content 

  • Total Structure Weight: 108.21 kDa 
  • Atom Count: 7,398 
  • Modeled Residue Count: 956 
  • Deposited Residue Count: 992 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Stromal cell-derived factor 1A [auth D],
C [auth F]
61Homo sapiensMutation(s): 0 
Gene Names: CXCL12SDF1SDF1ASDF1B
UniProt & NIH Common Fund Data Resources
Find proteins for P48061 (Homo sapiens)
Explore P48061 
Go to UniProtKB:  P48061
PHAROS:  P48061
GTEx:  ENSG00000107562 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP48061
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
hu30D8 Fab heavy chainB [auth E],
D [auth H]
221Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
hu30D8 Fab light chainE [auth I],
F [auth L]
214Homo sapiensMutation(s): 0 
Gene Names: CXCL12SDF1SDF1ASDF1B

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.77 Å
  • R-Value Free:  0.301 (Depositor), 0.241 (DCC) 
  • R-Value Work:  0.253 (Depositor), 0.225 (DCC) 
  • R-Value Observed: 0.255 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.949α = 90
b = 73.101β = 90.4
c = 106.626γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
PHASERphasing
PHENIXrefinement
XDSdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2013-08-14
    Type: Initial release
  • Version 1.1: 2013-08-28
    Changes: Database references
  • Version 1.2: 2018-01-24
    Changes: Structure summary
  • Version 1.3: 2021-10-27
    Changes: Database references, Structure summary
  • Version 1.4: 2024-11-20
    Changes: Data collection, Structure summary