5HBA

Globular Domain of Zebrafish Complement 1qA protein

• PDB DOI: https://doi.org/10.2210/pdb5HBA/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Danio rerio
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-12-31 Released: 2016-07-27 
• Deposition Author(s): Xia, C., Yuan, H., Chen, R.
• Funding Organization(s): National Natural Science Foundation of China, the 973 Project of the China Ministry of Science and Technology, the open project of State Key Laboratory of Freshwater Ecology and Biotechnology

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 0.221 
• R-Value Work: 0.182 
• R-Value Observed: 0.184 

Literature

Crystal structure of zebrafish complement 1qA globular domain.

Yuan, H., Chen, R., Tariq, M., Liu, Y., Sun, Y., Xia, C.

(2016) Protein Sci 25: 1883-1889

• PubMed: 27391278 
• DOI: https://doi.org/10.1002/pro.2980
• Primary Citation of Related Structures:  
  5HBA


• PubMed Abstract: 
  

  C1q contains three globular domains (C1qgD) that are the key functional component of the classical complement system. C1qgD can interact with important immune molecules, including IgG and C-reactive protein (CRP) to form defense systems to protect animals. Here, the first non-mammalian structure, zebrafish C1qA globular domain (Dare-C1qAgD) was solved. Although the overall architecture of Dare-C1qAgD is similar to human C1qA, residues involved in C1qBgD, C1qCgD, and CRP binding are somewhat different while residues involved in IgG binding are not present in zebrafish. The structure gives insight into how human and fish C1qA evolved from an ancestral protein.

---

Organizational Affiliation: 

Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, People's Republic of China.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 44.67 kDa 
• Atom Count: 3,216 
• Modelled Residue Count: 386 
• Deposited Residue Count: 402 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein	A, B, C	134	Danio rerio	Mutation(s): 0  Gene Names: c1qa
UniProt
Find proteins for F1QFM5 (Danio rerio) Explore F1QFM5  Go to UniProtKB:  F1QFM5

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	D [auth A], E [auth B], F [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 0.221 
• R-Value Work: 0.182 
• R-Value Observed: 0.184 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.347	α = 90
b = 85.059	β = 90
c = 95.56	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
HKL-2000	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-07-27 
Deposition Author(s): Xia, C., Yuan, H., Chen, R.

---

Funding Organization	Location	Grant Number
National Natural Science Foundation of China	China	31230074
the 973 Project of the China Ministry of Science and Technology	China	2013CB835302
the open project of State Key Laboratory of Freshwater Ecology and Biotechnology	China	2015FB14

Revision History  

• Version 1.0: 2016-07-27
  Type: Initial release
  
• Version 1.1: 2017-12-13
  Changes: Database references, Derived calculations
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Refinement description