8IK5 | pdb_00008ik5

Transcription factor LMX1a homeobox domain in complex with Wnt1 promoter

• PDB DOI: https://doi.org/10.2210/pdb8IK5/pdb
• NAKB: 8IK5

• Classification: DNA BINDING PROTEIN/DNA
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-02-28 Released: 2024-03-06 
• Deposition Author(s): Lv, M.Q., Lin, L.Q.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.99 Å
• R-Value Free: 
  0.236 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.207 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.208 (Depositor) 

Starting Model: experimental

Literature

Structural insights into the recognition of the A/T-rich motif in target gene promoters by the LMX1a homeobox domain

Lv, M.Q., Lin, L.Q.

(2024) FEBS J 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 17.34 kDa 
• Atom Count: 1,224 
• Modeled Residue Count: 97 
• Deposited Residue Count: 97 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
LMX1A factor	C	67	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q8TE12 (Homo sapiens) Explore Q8TE12  Go to UniProtKB:  Q8TE12
PHAROS:  Q8TE12 GTEx:  ENSG00000162761

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*CP*AP*TP*AP*TP*TP*TP*AP*AP*TP*CP*TP*TP*C)-3')	A	15	Homo sapiens

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*GP*AP*AP*GP*AP*TP*TP*AP*AP*AP*TP*AP*TP*G)-3')	B	15	Homo sapiens

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	D [auth C], E [auth C]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.99 Å
• R-Value Free:  0.236 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.207 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.208 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.29	α = 90
b = 46.419	β = 90
c = 96.098	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
PHENIX	refinement
HKL-2000	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-03-06 
Deposition Author(s): Lv, M.Q., Lin, L.Q.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32293213, 32100958, 32090042, 31870760

Revision History  

• Version 1.0: 2024-03-06
  Type: Initial release