9IGJ | pdb_00009igj

structure of two human ELF2 transcription factors in complex with a nucleosome

• PDB DOI: https://doi.org/10.2210/pdb9IGJ/pdb
• NAKB: 9IGJ
• EM Map EMD-52852: EMDB EMDataResource

• Classification: DNA BINDING PROTEIN
• Organism(s): Xenopus laevis, synthetic construct, Homo sapiens
• Expression System: Escherichia coli BL21(DE3), Escherichia coli
• Mutation(s): No 


• Deposited: 2025-02-19 Released: 2026-03-04 
• Deposition Author(s): Xiao, T., Crowe-McAuliffe, C., Dienemann, C., Taipale, J.
• Funding Organization(s): Biotechnology and Biological Sciences Research Council (BBSRC), Cancer Research UK, Medical Research Council (MRC, United Kingdom), Max Planck Society

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.40 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental, in silico

Literature

The pioneer transcription factor ELF2 remodels the nucleosome near transcription start sites

Xiao, T., Crowe-McAuliffe, C., Ochmann, M., Du, Y., Hou, T., Chen, Y., Zhu, F., Seyednasrollah, F., Osmala, M., Vanharanta, S., Morgunova, E., Cramer, P., Rogerson, C., Dienemann, C., Taipale, J.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 10-mer - A2B2C2D2E2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 10-mer - A6B2C2 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Hetero 8-mer - A2B2C2D2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Hetero 8-mer - A2B2C2D2 

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

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 232.53 kDa 
• Atom Count: 12,529 
• Modeled Residue Count: 1,170 
• Deposited Residue Count: 1,560 
• Unique protein chains: 5
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3	A, E	135	Xenopus laevis	Mutation(s): 0  Gene Names: LOC121398065, LOC108703785, LOC121398067
UniProt
Find proteins for A0A310TTQ1 (Xenopus laevis) Explore A0A310TTQ1  Go to UniProtKB:  A0A310TTQ1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H4	B, F	102	Xenopus laevis	Mutation(s): 0
UniProt
Find proteins for P62799 (Xenopus laevis) Explore P62799  Go to UniProtKB:  P62799

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2A	C, G	129	Xenopus laevis	Mutation(s): 0  Gene Names: hist1h2aj, LOC494591
UniProt
Find proteins for Q6AZJ8 (Xenopus laevis) Explore Q6AZJ8  Go to UniProtKB:  Q6AZJ8

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2B	D, H	122	Xenopus laevis	Mutation(s): 0  Gene Names: LOC108704303
UniProt
Find proteins for A0A8J0U496 (Xenopus laevis) Explore A0A8J0U496  Go to UniProtKB:  A0A8J0U496

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
ETS-related transcription factor Elf-2	K, L	145	Homo sapiens	Mutation(s): 0  Gene Names: ELF2, NERF
UniProt & NIH Common Fund Data Resources
Find proteins for Q15723 (Homo sapiens) Explore Q15723  Go to UniProtKB:  Q15723
GTEx:  ENSG00000109381

Entity ID: 5
Molecule	Chains	Length	Organism	Image
DNA (147-MER)	I [auth J]	147	synthetic construct

Entity ID: 6
Molecule	Chains	Length	Organism	Image
DNA (147-MER)	J [auth I]	147	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.40 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21.2_5419
RECONSTRUCTION	RELION

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-03-04 
Deposition Author(s): Xiao, T., Crowe-McAuliffe, C., Dienemann, C., Taipale, J.

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Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	G107673
Cancer Research UK	United Kingdom	RG99643
Medical Research Council (MRC, United Kingdom)	United Kingdom	G105296
Max Planck Society	Germany	--

Revision History  

• Version 1.0: 2026-03-04
  Type: Initial release
  
• Version 2.0: 2026-07-29
  Type: Coordinate replacement
  Reason: Model completeness
  Changes: Advisory, Atomic model, Data collection, Data processing, Database references, Derived calculations, Polymer sequence, Refinement description, Source and taxonomy, Structure summary