38JD | pdb_000038jd

RNA polymerase ribozyme 85h34 replication complex, subclass 2 structure

  • Classification: RNA
  • Organism(s): synthetic construct
  • Mutation(s): No 

  • Deposited: 2026-08-29 Released: 2026-09-09 
  • Deposition Author(s): Strutzenberg, T.S., Lyumkis, D.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.92 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 38JD

This is version 1.0 of the entry. See complete history. 

Literature

Structure of an RNA polymerase ribozyme replication complex

Strutzenberg, T.S., Horning, D.P., Cochrane, W.G., Andrade, L., Han, X., Joyce, G.F., Lyumkis, D.

(2026) bioRxiv 

Macromolecule Content 

  • Total Structure Weight: 83.35 kDa 
  • Atom Count: 4,796 
  • Modeled Residue Count: 215 
  • Deposited Residue Count: 256 
  • Unique nucleic acid chains: 3

Macromolecules

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(by identity cutoff) 
Entity ID: 1
MoleculeChains LengthOrganismImage
RNA polymerase ribozyme 85h34194synthetic construct
Sequence Annotations
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Reference Sequence
Find similar nucleic acids by:  Sequence
Entity ID: 2
MoleculeChains LengthOrganismImage
RNA primer20synthetic construct
Sequence Annotations
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Reference Sequence
Find similar nucleic acids by: 
(by identity cutoff) 
Entity ID: 3
MoleculeChains LengthOrganismImage
RNA template42synthetic construct
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
APC
(Subject of Investigation/LOI)

Query on APC


Download:Ideal Coordinates CCD File
Q [auth A]DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER
C11 H18 N5 O12 P3
CAWZRIXWFRFUQB-IOSLPCCCSA-N
MG

Query on MG


Download:Ideal Coordinates CCD File
D [auth A]
E [auth A]
F [auth A]
G [auth A]
H [auth A]
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.92 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC4.7.0
MODEL REFINEMENTPHENIX2.1_6048

Structure Validation

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View more in-depth experimental data

Entry History 

& Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM148049
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM159035
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI136680
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI170855
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM151305
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI196844
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM146435

Revision History  (Full details and data files)

  • Version 1.0: 2026-09-09
    Type: Initial release