5VQH | pdb_00005vqh

Crystal structure of the extended Tudor domain from BmPAPI in complex with sDMA

• PDB DOI: https://doi.org/10.2210/pdb5VQH/pdb

• Classification: RNA BINDING PROTEIN
• Organism(s): Bombyx mori
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-05-08 Released: 2017-06-14 
• Deposition Author(s): Hubbard, P.A., Pan, X., Ohtaki, A., McNally, R., Honda, S., Kirino, Y., Murali, R.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.262 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.195 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.198 (Depositor) 

Starting Model: experimental

Literature

Structural studies of the Tudor domain from the Bombyx homolog of Drosophila PAPI: Implication to piRNA biogenesis

Hubbard, P.A., Pan, X., Ohtaki, A., McNally, R., Honda, S., Kirino, Y., Murali, R.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 54.31 kDa 
• Atom Count: 3,404 
• Modeled Residue Count: 408 
• Deposited Residue Count: 474 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tudor and KH domain-containing protein homolog	A, B	237	Bombyx mori	Mutation(s): 0  Gene Names: PAPI
UniProt
Find proteins for H9JD76 (Bombyx mori) Explore H9JD76  Go to UniProtKB:  H9JD76

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
2MR	C [auth A], D [auth B]	N3, N4-DIMETHYLARGININE C8 H18 N4 O2 HVPFXCBJHIIJGS-LURJTMIESA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.262 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.195 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.198 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.03	α = 90
b = 66.03	β = 90
c = 224.48	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-06-14 
Deposition Author(s): Hubbard, P.A., Pan, X., Ohtaki, A., McNally, R., Honda, S., Kirino, Y., Murali, R.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM106047

Revision History  

• Version 1.0: 2017-06-14
  Type: Initial release
  
• Version 1.1: 2017-09-13
  Changes: Author supporting evidence
• Version 1.2: 2020-01-01
  Changes: Author supporting evidence, Derived calculations
• Version 1.3: 2021-03-10
  Changes: Derived calculations
• Version 1.4: 2023-10-04
  Changes: Data collection, Database references, Refinement description