8Z39 | pdb_00008z39

Crystal structure of Sonic hedgehog in complex with antibody 5E1 mutant L-T56A with metals

• PDB DOI: https://doi.org/10.2210/pdb8Z39/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3), Homo sapiens
• Mutation(s): No 


• Deposited: 2024-04-14 Released: 2025-04-16 
• Deposition Author(s): Caaveiro, J.M.M., Kaneda, I., Tsumoto, K.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS), Japan Agency for Medical Research and Development (AMED)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.208 (Depositor), 0.214 (DCC) 
• R-Value Work: 
  0.180 (Depositor), 0.187 (DCC) 
• R-Value Observed: 
  0.181 (Depositor) 

Starting Model: experimental

Literature

Biophysical insights to improve affinity of antibodies to fluctuated epitope of antigen: A case of anti-Shh antibody 5E1 against Shh antigen.

Kaneda, I., Matsunaga, R., Nagatoishi, S., Senoo, A., Caaveiro, J.M.M., Kuroda, D., Tsumoto, K.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 71.75 kDa 
• Atom Count: 5,208 
• Modeled Residue Count: 578 
• Deposited Residue Count: 646 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sonic hedgehog protein N-product	A	169	Homo sapiens	Mutation(s): 0  Gene Names: SHH EC: 3.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q15465 (Homo sapiens) Explore Q15465  Go to UniProtKB:  Q15465
PHAROS:  Q15465 GTEx:  ENSG00000164690

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Heavy chain of antibody 5E1	B [auth H]	241	Homo sapiens	Mutation(s): 0  Gene Names: IgG

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Light chain of antibody 5E1	C [auth L]	236	Homo sapiens	Mutation(s): 0  Gene Names: IgG

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	H [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ZN (Subject of Investigation/LOI)	F [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA (Subject of Investigation/LOI)	D [auth A], E [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL	G [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.208 (Depositor), 0.214 (DCC) 
• R-Value Work:  0.180 (Depositor), 0.187 (DCC) 
• R-Value Observed: 0.181 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.519	α = 90
b = 70.005	β = 109.24
c = 119.974	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-04-16 
Deposition Author(s): Caaveiro, J.M.M., Kaneda, I., Tsumoto, K.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	JP18H02082, JP18H05425, 16H02420, JP19H05766, JP19H05760, JP20H02531
Japan Agency for Medical Research and Development (AMED)	Japan	JP23ama121033

Revision History  

• Version 1.0: 2025-04-16
  Type: Initial release