7VP1 | pdb_00007vp1

Structure of a transcription factor and DNA complex

• PDB DOI: https://doi.org/10.2210/pdb7VP1/pdb
• NAKB: 7VP1

• Classification: DNA BINDING PROTEIN
• Organism(s): Arabidopsis thaliana, synthetic construct
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• 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)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 
  0.238 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.178 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.184 (Depositor) 

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 31.42 kDa 
• Atom Count: 1,442 
• Modeled Residue Count: 143 
• Deposited Residue Count: 238 
• 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	107	Arabidopsis thaliana	Mutation(s): 1  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*CP*C)-3')	C	12	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*TP*GP*GP*GP*GP*GP*AP*CP*CP*AP*CP*A)-3')	D	12	synthetic construct

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free:  0.238 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.178 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.184 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.123	α = 90
b = 68.123	β = 90
c = 210.819	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data scaling
SHELXCD	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.

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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: 2024-10-16
  Changes: Data collection, Structure summary