Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 65803.55 
• Atom Count: 4160 
• Residue Count: 470 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

3AGV

Crystal structure of a human IgG-aptamer complex

• DOI: 10.2210/pdb3AGV/pdb
• NDB: NA0496

• Classification: Immune System/RNA
• Expression System: Escherichia coli


• Deposited: 2010-04-08 Released: 2010-11-10 
• Deposition Author(s): Nomura, Y., Sugiyama, S., Sakamoto, T., Miyakawa, S., Adachi, H., Takano, K., Murakami, S., Inoue, T., Mori, Y., Nakamura, Y., Matsumura, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 0.277 
• R-Value Work: 0.237 

Literature

Conformational plasticity of RNA for target recognition as revealed by the 2.15 A crystal structure of a human IgG-aptamer complex

Nomura, Y., Sugiyama, S., Sakamoto, T., Miyakawa, S., Adachi, H., Takano, K., Murakami, S., Inoue, T., Mori, Y., Nakamura, Y., Matsumura, H.

(2010) Nucleic Acids Res. 38: 7822-7829

• PubMed: 20675355 
• DOI: 10.1093/nar/gkq615


• PubMed Abstract: 
  

Aptamers are short single-stranded nucleic acids with high affinity to target molecules and are applicable to therapeutics and diagnostics. Regardless of an increasing number of reported aptamers, the structural basis of the interaction of RNA aptamer with proteins is poorly understood. Here, we determined the 2.15 Å crystal structure of the Fc fragment of human IgG1 (hFc1) complexed with an anti-Fc RNA aptamer. The aptamer adopts a characteristic structure fit to hFc1 that is stabilized by a calcium ion, and the binding activity of the aptamer can be controlled many times by calcium chelation and addition. Importantly, the aptamer-hFc1 interaction involves mainly van der Waals contacts and hydrogen bonds rather than electrostatic forces, in contrast to other known aptamer-protein complexes. Moreover, the aptamer-hFc1 interaction involves human IgG-specific amino acids, rendering the aptamer specific to human IgGs, and not crossreactive to other species IgGs. Hence, the aptamer is a potent alternative for protein A affinity purification of Fc-fusion proteins and therapeutic antibodies. These results demonstrate, from a structural viewpoint, that conformational plasticity and selectivity of an RNA aptamer is achieved by multiple interactions other than electrostatic forces, which is applicable to many protein targets of low or no affinity to nucleic acids.

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Organizational Affiliation: 

Department of Life and Environmental Sciences, Faculty of Engineering, Chiba Institute of Technology, Narashino-shi, Chiba 275-0016, Japan.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Ig gamma-1 chain C region	A, B	211	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Entity ID: 2
Molecule	Chains	Length	Organism
5'-R(*GP*GP*AP*GP*GP*(UFT)P*GP*(CFZ)P*(UFT)P*(CFZ)P*(CFZ)P*GP*AP*AP*A*GP*GP*AP*AP*(CFZ)P*(UFT)P*(CFZ)P*(CFZ)P*A)-3'	S,U	24	N/A

Small Molecules

Ligands 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
CA	S, U	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MAN	A, B	ALPHA-D-MANNOSE C6 H12 O6 WQZGKKKJIJFFOK-PQMKYFCFSA-N
GAL	B	BETA-D-GALACTOSE C6 H12 O6 WQZGKKKJIJFFOK-FPRJBGLDSA-N
BMA	B	BETA-D-MANNOSE C6 H12 O6 WQZGKKKJIJFFOK-RWOPYEJCSA-N
NDG	A, B	2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE C8 H15 N O6 OVRNDRQMDRJTHS-PVFLNQBWSA-N
NAG	B	N-ACETYL-D-GLUCOSAMINE C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
FUL	B	BETA-L-FUCOSE 6-DEOXY-BETA-L-GALACTOSE C6 H12 O5 SHZGCJCMOBCMKK-KGJVWPDLSA-N
GLA	A	ALPHA D-GALACTOSE C6 H12 O6 WQZGKKKJIJFFOK-PHYPRBDBSA-N

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
UFT	S, U	DNA LINKING	C9 H12 F N2 O8 P		DU
CFZ	S, U	DNA LINKING	C9 H13 F N3 O7 P		DC

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 0.277 
• R-Value Work: 0.237 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length (Å)	Angle (°)
a = 83.587	α = 90.00
b = 107.238	β = 90.00
c = 79.458	γ = 90.00

Software Package:

Software Name	Purpose
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing
CNS	refinement
ADSC	data collection

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-04-08 
• Released Date: 2010-11-10 
• Deposition Author(s): Nomura, Y., Sugiyama, S., Sakamoto, T., Miyakawa, S., Adachi, H., Takano, K., Murakami, S., Inoue, T., Mori, Y., Nakamura, Y., Matsumura, H.

Revision History 

• Version 1.0: 2010-11-10
  Type: Initial release
• Version 1.1: 2011-07-13
  Type: Version format compliance