8OJ2

Crystal structure of the DNA binding domain of M. polymorpha Auxin Response Factor 2 (MpARF2) in complex with protomor-like sequence IR7

• PDB DOI: https://doi.org/10.2210/pdb8OJ2/pdb
• NAKB: 8OJ2

• Classification: TRANSCRIPTION
• Organism(s): Marchantia polymorpha
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-03-23 Released: 2024-04-17 
• Deposition Author(s): Crespo, I., Weijers, D., Boer, D.R.
• Funding Organization(s): Ministry of Economy and Competitiveness (MINECO)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.56 Å
• R-Value Free: 0.266 
• R-Value Work: 0.220 
• R-Value Observed: 0.222 

Starting Model: experimental

Literature

Crystal structure of the DNA binding domain of M. polymorpha Auxin Response Factor 2 (MpARF2) in complex with protomor-like sequence IR7

Crespo, I., Weijers, D., Boer, D.R.

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: SAXS, gel filtration

Macromolecule Content

• Total Structure Weight: 47.38 kDa 
• Atom Count: 2,796 
• Modelled Residue Count: 313 
• Deposited Residue Count: 390 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Auxin response factor	A	366	Marchantia polymorpha	Mutation(s): 0  Gene Names: MARPO_0011s0167
UniProt
Find proteins for A0A176WDW1 (Marchantia polymorpha subsp. ruderalis) Explore A0A176WDW1  Go to UniProtKB:  A0A176WDW1

Entity ID: 2
Molecule	Chains	Length	Organism	Image
IR7	B	21	Marchantia polymorpha

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MES	C [auth A]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N
CL	D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.56 Å
• R-Value Free: 0.266 
• R-Value Work: 0.220 
• R-Value Observed: 0.222 
• Space Group: I 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.622	α = 90
b = 79.682	β = 90
c = 146.297	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MxCuBE	data collection
autoPROC	data processing
PHENIX	phasing
Coot	model building
autoPROC	data reduction
autoPROC	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-04-17 
Deposition Author(s): Crespo, I., Weijers, D., Boer, D.R.

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Funding Organization	Location	Grant Number
Ministry of Economy and Competitiveness (MINECO)	Spain	PID2020-117028 GB-I00
Ministry of Economy and Competitiveness (MINECO)	Spain	BIO2016-77883-C2-2-P
Ministry of Economy and Competitiveness (MINECO)	Spain	FIS2015-72574-EXP

Revision History  

• Version 1.0: 2024-04-17
  Type: Initial release