7E9M | pdb_00007e9m

Crystal Structure of Spindlin1 bound to SPINDOC Docpep3

• PDB DOI: https://doi.org/10.2210/pdb7E9M/pdb

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3), Escherichia coli
• Mutation(s): No 


• Deposited: 2021-03-04 Released: 2022-06-15 
• Deposition Author(s): Zhao, F., Li, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.253 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.204 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.206 (Depositor) 

Starting Model: experimental

Literature

Molecular basis for SPINDOC-Spindlin1 engagement and its role in transcriptional inhibition

Zhao, F., Li, H.

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)

Biological Assembly Evidence: gel filtration

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: 65.2 kDa 
• Atom Count: 3,686 
• Modeled Residue Count: 448 
• Deposited Residue Count: 578 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spindlin-1	A, C	262	Homo sapiens	Mutation(s): 0  Gene Names: SPIN1, OCR, SPIN
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y657 (Homo sapiens) Explore Q9Y657  Go to UniProtKB:  Q9Y657
PHAROS:  Q9Y657 GTEx:  ENSG00000106723

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptide from Spindlin interactor and repressor of chromatin-binding protein	B, D	27	Homo sapiens	Mutation(s): 0  Gene Names: SPINDOC, C11orf84
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BUA3 (Homo sapiens) Explore Q9BUA3  Go to UniProtKB:  Q9BUA3
PHAROS:  Q9BUA3 GTEx:  ENSG00000168005

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.253 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.204 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.206 (Depositor) 

Space Group: P 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.612	α = 90
b = 45.541	β = 93.09
c = 85.984	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2022-06-15 
Deposition Author(s): Zhao, F., Li, H.

Revision History  

• Version 1.0: 2022-06-15
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description