8UBD

Diversity-generating retroelement (DGR) ribonucleoprotein reverse transcriptase - Pre-active State 2

• PDB DOI: https://doi.org/10.2210/pdb8UBD/pdb
• EM Map EMD-42083: EMDB EMDataResource
• NAKB: 8UBD

• Classification: RNA BINDING PROTEIN/RNA
• Organism(s): Bordetella phage BPP-1, Methylorubrum extorquens AM1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-09-22 Released: 2024-10-23 
• Deposition Author(s): Biswas, T., Handa, S., Ghosh, P.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.05 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural Requirements for Reverse Transcription by a Diversity-generating Retroelement

Handa, S., Biswas, T., Ghosh, P.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 6-mer - A5B1 Local Symmetry: Cyclic - C5  (Explore in 3D)
Local Stoichiometry: Homo 5-mer - A5 

Local Symmetry: Cyclic - C5  (Explore in 3D)
Local Stoichiometry: Homo 5-mer - A5 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy, gel filtration

Macromolecule Content

• Total Structure Weight: 259.57 kDa 
• Atom Count: 10,368 
• Modelled Residue Count: 1,039 
• Deposited Residue Count: 1,973 
• Unique protein chains: 2
• Unique nucleic acid chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Reverse transcriptase	A	328	Bordetella phage BPP-1	Mutation(s): 0  Gene Names: brt
UniProt
Find proteins for Q775D8 (Bordetella phage BPP-1) Explore Q775D8  Go to UniProtKB:  Q775D8

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Avd	B, C, D, E, F	290	Bordetella phage BPP-1, Methylorubrum extorquens AM1 This entity is chimeric	Mutation(s): 0  Gene Names: bbp7, fae EC: 4.2.1.147
UniProt
Find proteins for Q9FA38 (Methylorubrum extorquens (strain ATCC 14718 / DSM 1338 / JCM 2805 / NCIMB 9133 / AM1)) Explore Q9FA38  Go to UniProtKB:  Q9FA38
Find proteins for Q775D7 (Bordetella phage BPP-1) Explore Q775D7  Go to UniProtKB:  Q775D7
UniProt Groups	Q9FA38Q775D7

Entity ID: 3
Molecule	Chains	Length	Organism	Image
Diversity-generating retroelement (DGR) RNA avd	G	19	Bordetella phage BPP-1

Entity ID: 4
Molecule	Chains	Length	Organism	Image
Diversity-generating retroelement (DGR) RNA TR	H	36	Bordetella phage BPP-1

Entity ID: 5
Molecule	Chains	Length	Organism	Image
Diversity-generating retroelement (DGR) RNA Sp	I	140	Bordetella phage BPP-1

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.05 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	3.1.1
MODEL REFINEMENT	CCP4 package

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-10-23 
Deposition Author(s): Biswas, T., Handa, S., Ghosh, P.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	5R01GM132720-03

Revision History  

• Version 1.0: 2024-10-23
  Type: Initial release