Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 65.62 kDa 
• Atom Count: 4413 
• Modelled Residue Count: 428 
• Deposited Residue Count: 470 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

3AGV

Crystal structure of a human IgG-aptamer complex

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

• Classification: Immune System/RNA
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• 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 
• R-Value Observed: 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
• Primary Citation of Related Structures:  
  3AGV


• 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

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ig gamma-1 chain C region	A, B	211	Homo sapiens	Mutation(s): 0  Gene Names: IGHG1
UniProt & NIH Common Fund Data Resources
Find proteins for P01857 (Homo sapiens) Explore P01857  Go to UniProtKB:  P01857
PHAROS:  P01857 GTEx:  ENSG00000211896

Entity ID: 2
Molecule	Chains	Length	Organism	Image
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'	C [auth S], D [auth U]	24	N/A

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
alpha-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose	E [auth C]	4		N/A
Glycosylation Resources
GlyTouCan:  G43563SH GlyCosmos:  G43563SH

Entity ID: 4
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-alpha-D-glucopyranose	F [auth D]	8		N/A
Glycosylation Resources
GlyTouCan:  G11679NT GlyCosmos:  G11679NT GlyGen:  G11679NT

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	G [auth S], H [auth U]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

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

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.587	α = 90
b = 107.238	β = 90
c = 79.458	γ = 90

Software Package:

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

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
  Changes: Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary