3IVB

Structures of SPOP-Substrate Complexes: Insights into Architectures of BTB-Cul3 Ubiquitin Ligases: SPOPMATH-MacroH2ASBCpep1

• PDB DOI: https://doi.org/10.2210/pdb3IVB/pdb

• Classification: protein binding, ligase
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-08-31 Released: 2009-10-20 
• Deposition Author(s): Schulman, B.A., Miller, D.J., Calabrese, M.F., Seyedin, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.247 
• R-Value Work: 0.218 
• R-Value Observed: 0.220 

Literature

Structure 9

Zhuang, M., Calabrese, M.F., Liu, J., Waddell, M.B., Nourse, A., Hammel, M., Miller, D.J., Walden, H., Duda, D.M., Steven, S., Hoggard, T., Harper, J.W., White, K.P., Schulman, B.A.

To be published.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 18.33 kDa 
• Atom Count: 1,307 
• Modelled Residue Count: 148 
• Deposited Residue Count: 160 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Speckle-type POZ protein	A	145	Homo sapiens	Mutation(s): 0  Gene Names: SPOP
UniProt & NIH Common Fund Data Resources
Find proteins for O43791 (Homo sapiens) Explore O43791  Go to UniProtKB:  O43791
PHAROS:  O43791 GTEx:  ENSG00000121067

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Core histone macro-H2A.1	B [auth M]	15	Homo sapiens	Mutation(s): 0  Gene Names: MACROH2A1
UniProt & NIH Common Fund Data Resources
Find proteins for O75367 (Homo sapiens) Explore O75367  Go to UniProtKB:  O75367
PHAROS:  O75367 GTEx:  ENSG00000113648

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL	H [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.247 
• R-Value Work: 0.218 
• R-Value Observed: 0.220 
• Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.021	α = 90
b = 44.021	β = 90
c = 266.84	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-10-20 
Deposition Author(s): Schulman, B.A., Miller, D.J., Calabrese, M.F., Seyedin, S.

Revision History  

• Version 1.0: 2009-10-20
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-02-21
  Changes: Data collection, Database references, Derived calculations