Biological Assembly 1  

 3D View: Structure | Electron Density

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

 3D View: Structure | Electron Density

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 108.21 kDa 
• Atom Count: 7398 
• Residue Count: 956 
• Unique protein chains: 3

4LMQ

Development and Preclinical Characterization of a Humanized Antibody Targeting CXCL12

• DOI: 10.2210/pdb4LMQ/pdb

• Classification: cell adhesion/immune system
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-07-10 Released: 2013-08-14 
• Deposition Author(s): Zhong, Z., 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.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.77 Å
• R-Value Free: 0.301 
• R-Value Work: 0.253 
• R-Value Observed: 0.255 

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

• PubMed: 23812669 
• DOI: 10.1158/1078-0432.CCR-13-0943
• Primary Citation of 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.

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Organizational Affiliation: 

Genentech, Inc., South San Francisco, California, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Stromal cell-derived factor 1	D, F	61	Homo sapiens	Mutation(s): 0  Gene Names: CXCL12, SDF1, SDF1A, SDF1B
Find proteins for P48061 (Homo sapiens) Explore P48061  Go to UniProtKB:  P48061
NIH Common Fund Data Resources
PHAROS:  P48061 GTEx:  ENSG00000107562

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
immunoglobulin G1 heavy chain	E, H	221	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Stromal cell-derived factor 1	I, L	214	Homo sapiens	Mutation(s): 0  Gene Names: CXCL12, SDF1, SDF1A, SDF1B

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.77 Å
• R-Value Free: 0.301 
• R-Value Work: 0.253 
• R-Value Observed: 0.255 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.949	α = 90
b = 73.101	β = 90.4
c = 106.626	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
PHENIX	refinement
XDS	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-07-10 
• Released Date: 2013-08-14 
Deposition Author(s): Zhong, Z., 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.

Revision History 

• 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