5Y1U

Crystal structure of RBBP4 bound to AEBP2 RRK motif

• PDB DOI: https://doi.org/10.2210/pdb5Y1U/pdb

• Classification: GENE REGULATION
• Organism(s): Homo sapiens
• Expression System: Trichoplusia ni
• Mutation(s): No 


• Deposited: 2017-07-21 Released: 2018-04-18 
• Deposition Author(s): Sun, A., Li, F., Wu, J., Shi, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.14 Å
• R-Value Free: 0.219 
• R-Value Work: 0.169 
• R-Value Observed: 0.171 

Starting Model: experimental

Literature

Structural and biochemical insights into human zinc finger protein AEBP2 reveals interactions with RBBP4

Sun, A., Li, F., Liu, Z., Jiang, Y., Zhang, J., Wu, J., Shi, Y.

(2017) Protein Cell 

• PubMed: 29134516 
• DOI: https://doi.org/10.1007/s13238-017-0483-6
• Primary Citation of Related Structures:  
  5Y0U, 5Y1U

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Organizational Affiliation: 

Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, 230027, China.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content

• Total Structure Weight: 106.23 kDa 
• Atom Count: 6,586 
• Modelled Residue Count: 777 
• Deposited Residue Count: 936 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone-binding protein RBBP4	A, B	456	Homo sapiens	Mutation(s): 0  Gene Names: RBBP4, RBAP48
UniProt & NIH Common Fund Data Resources
Find proteins for Q09028 (Homo sapiens) Explore Q09028  Go to UniProtKB:  Q09028
PHAROS:  Q09028 GTEx:  ENSG00000162521

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Zinc finger protein AEBP2	C, D	12	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q6ZN18 (Homo sapiens) Explore Q6ZN18  Go to UniProtKB:  Q6ZN18
PHAROS:  Q6ZN18 GTEx:  ENSG00000139154

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	E [auth B], F [auth D]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.14 Å
• R-Value Free: 0.219 
• R-Value Work: 0.169 
• R-Value Observed: 0.171 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.761	α = 90
b = 59.452	β = 94.33
c = 102.438	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-04-18 
Deposition Author(s): Sun, A., Li, F., Wu, J., Shi, Y.

Revision History  

• Version 1.0: 2018-04-18
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description