7VP5

Structure of a transcription factor and DNA complex

• PDB DOI: https://doi.org/10.2210/pdb7VP5/pdb
• NAKB: 7VP5

• Classification: DNA BINDING PROTEIN
• Organism(s): Arabidopsis thaliana, synthetic construct
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2021-10-15 Released: 2022-10-19 
• Deposition Author(s): Zhang, Y., Xu, Y.P., Wang, B., Su, X.D.
• Funding Organization(s): National Science Foundation (NSF, China)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.99 Å
• R-Value Free: 0.267 
• R-Value Work: 0.209 

Literature

Structural basis for DNA recognition by TCP transcription factors

Zhang, Y., Xu, Y.P., Wang, B., Su, X.D.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 97 kDa 
• Atom Count: 4,487 
• Modelled Residue Count: 454 
• Deposited Residue Count: 726 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcription factor TCP10	A, B, E, F, I, J	107	Arabidopsis thaliana	Mutation(s): 0  Gene Names: TCP10, At2g31070, T16B12.12
UniProt
Find proteins for O82277 (Arabidopsis thaliana) Explore O82277  Go to UniProtKB:  O82277

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*AP*TP*GP*TP*GP*GP*TP*CP*CP*CP*GP*TP*GP*T)-3')	C, G, K	14	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*AP*TP*GP*TP*GP*GP*TP*CP*CP*CP*GP*TP*GP*T)-3')	D, H, L	14	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.99 Å
• R-Value Free: 0.267 
• R-Value Work: 0.209 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.766	α = 90
b = 76.896	β = 113.85
c = 83.078	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
PHENIX	model building
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-10-19 
Deposition Author(s): Zhang, Y., Xu, Y.P., Wang, B., Su, X.D.

---

Funding Organization	Location	Grant Number
National Science Foundation (NSF, China)	China	31670740
National Science Foundation (NSF, China)	China	31270803

Revision History  

• Version 1.0: 2022-10-19
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description