6C48

Crystal structure of B-Myb-LIN9-LIN52 complex

• PDB DOI: https://doi.org/10.2210/pdb6C48/pdb

• Classification: CELL CYCLE/DNA Binding
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-01-11 Released: 2018-09-19 
• Deposition Author(s): Guiley, K.Z., Tripathi, S.M., Rubin, S.M.
• Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.32 Å
• R-Value Free: 0.264 
• R-Value Work: 0.217 
• R-Value Observed: 0.219 

Literature

Structural mechanism of Myb-MuvB assembly.

Guiley, K.Z., Iness, A.N., Saini, S., Tripathi, S., Lipsick, J.S., Litovchick, L., Rubin, S.M.

(2018) Proc Natl Acad Sci U S A 115: 10016-10021

• PubMed: 30224471 
• DOI: https://doi.org/10.1073/pnas.1808136115
• Primary Citation of Related Structures:  
  6C48


• PubMed Abstract: 
  

  The MuvB transcriptional regulatory complex, which controls cell-cycle-dependent gene expression, cooperates with B-Myb to activate genes required for the G2 and M phases of the cell cycle. We have identified the domain in B-Myb that is essential for the assembly of the Myb-MuvB (MMB) complex. We determined a crystal structure that reveals how this B-Myb domain binds MuvB through the adaptor protein LIN52 and the scaffold protein LIN9. The structure and biochemical analysis provide an understanding of how oncogenic B-Myb is recruited to regulate genes required for cell-cycle progression, and the MMB interface presents a potential therapeutic target to inhibit cancer cell proliferation.

---

Organizational Affiliation: 

Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

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

Macromolecule Content

• Total Structure Weight: 51.14 kDa 
• Atom Count: 2,825 
• Modelled Residue Count: 335 
• Deposited Residue Count: 438 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein lin-9 homolog	A, B [auth D]	119	Homo sapiens	Mutation(s): 0  Gene Names: LIN9, BARA, TGS
UniProt & NIH Common Fund Data Resources
Find proteins for Q5TKA1 (Homo sapiens) Explore Q5TKA1  Go to UniProtKB:  Q5TKA1
PHAROS:  Q5TKA1 GTEx:  ENSG00000183814

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Myb-related protein B	C [auth F], D [auth C]	32	Homo sapiens	Mutation(s): 0  Gene Names: MYBL2, BMYB
UniProt & NIH Common Fund Data Resources
Find proteins for P10244 (Homo sapiens) Explore P10244  Go to UniProtKB:  P10244
PHAROS:  P10244 GTEx:  ENSG00000101057

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein lin-52 homolog	E [auth B], F [auth E]	68	Homo sapiens	Mutation(s): 0  Gene Names: LIN52, C14orf46
UniProt & NIH Common Fund Data Resources
Find proteins for Q52LA3 (Homo sapiens) Explore Q52LA3  Go to UniProtKB:  Q52LA3
PHAROS:  Q52LA3

Small Molecules

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

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	C [auth F], D [auth C]	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.32 Å
• R-Value Free: 0.264 
• R-Value Work: 0.217 
• R-Value Observed: 0.219 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.76	α = 90
b = 30.77	β = 99.89
c = 105.35	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
Aimless	data scaling
AutoSol	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-09-19 
Deposition Author(s): Guiley, K.Z., Tripathi, S.M., Rubin, S.M.

---

Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	F31CA206244
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	R01CA132685

Revision History  

• Version 1.0: 2018-09-19
  Type: Initial release
  
• Version 1.1: 2018-10-03
  Changes: Data collection, Database references
• Version 1.2: 2018-10-17
  Changes: Data collection, Database references
• Version 1.3: 2019-12-04
  Changes: Author supporting evidence