6ICC

The NZ-1 Fab complexed with the PDZ tandem fragment of A. aeolicus S2P homolog with the PA12 tag inserted between the residues 181 and 186


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.215 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Application of the NZ-1 Fab as a crystallization chaperone for PA tag-inserted target proteins.

Tamura, R.Oi, R.Akashi, S.Kaneko, M.K.Kato, Y.Nogi, T.

(2019) Protein Sci 28: 823-836

  • DOI: 10.1002/pro.3580
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • An antibody fragment that recognizes the tertiary structure of a target protein with high affinity can be utilized as a crystallization chaperone. Difficulties in establishing conformation-specific antibodies, however, limit the applicability of antibody fragment-assisted crystallization ...

    An antibody fragment that recognizes the tertiary structure of a target protein with high affinity can be utilized as a crystallization chaperone. Difficulties in establishing conformation-specific antibodies, however, limit the applicability of antibody fragment-assisted crystallization. Here, we attempted to establish an alternative method to promote the crystallization of target proteins using an already established anti-tag antibody. The monoclonal antibody NZ-1 recognizes the PA tag with an extremely high affinity. It was also established that the PA tag is accommodated in the antigen-binding pocket in a bent conformation, compatible with an insertion into loop regions on the target. We, therefore, explored the application of NZ-1 Fab as a crystallization chaperone that complexes with a target protein displaying a PA tag. Specifically, we inserted the PA tag into the β-hairpins of the PDZ tandem fragment of a bacterial Site-2 protease. We crystallized the PA-inserted PDZ tandem mutants with the NZ-1 Fab and solved the co-crystal structure to analyze their interaction modes. Although the initial insertion designs produced only moderate-resolution structures, eliminating the solvent-accessible space between the NZ-1 Fab and target PDZ tandem improved the diffraction qualities remarkably. Our results demonstrate that the NZ-1-PA system efficiently promotes crystallization of the target protein. The present work also suggests that β-hairpins are suitable sites for the PA insertion because the PA tag contains a Pro-Gly sequence with a propensity for a β-turn conformation.


    Organizational Affiliation

    Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan.



Macromolecules

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Light chain of antigen binding fragment, Fab of NZ-1L214Rattus norvegicusMutation(s): 0 
Protein Feature View
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  • Reference Sequence

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PDZ tandem fragment with PA tagA188Aquifex aeolicus VF5Mutation(s): 0 
Gene Names: aq_1964
EC: 3.4.24
Find proteins for O67776 (Aquifex aeolicus (strain VF5))
Explore O67776 
Go to UniProtKB:  O67776
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Heavy chain of antigen binding fragment, Fab of NZ-1H219Rattus norvegicusMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Small Molecules
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
PCA
Query on PCA
LL-PEPTIDE LINKINGC5 H7 N O3GLN
SNN
Query on SNN
AL-PEPTIDE LINKINGC4 H6 N2 O2ASN
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.215 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.938α = 90
b = 84.293β = 90
c = 185.913γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of ScienceJapan26291016
Japan Agency for Medical Research and Development (AMED)JapanJP17am0101078
Japan Agency for Medical Research and Development (AMED)Japan16am0101020j0005

Revision History 

  • Version 1.0: 2019-02-13
    Type: Initial release
  • Version 1.1: 2019-04-03
    Changes: Data collection, Database references