38JD | pdb_000038jd

RNA polymerase ribozyme 85h34 replication complex, subclass 2 structure

PDB DOI: https://doi.org/10.2210/pdb38JD/pdb
EM Map EMD-78852: EMDB EMDataResource
NAKB: 38JD

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

This is version 1.1 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

PubMed: 42922616 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.64898/2026.08.30.748161
Primary Citation Related Structures:
38JC, 38JD, 38JE

PubMed Abstract:
Life began with the emergence of a molecule that could replicate its own genetic material, a task plausibly mediated by an RNA-dependent RNA polymerase ribozyme. Here, we present the structure of such a polymerase ribozyme, bound to RNA substrates comprising the template, primer, and nucleoside triphosphate (NTP) analog. The structure reveals how directed evolution shaped flanking elements around a highly conserved catalytic core derived from the ancestral class I ligase ribozyme. Each element serves as a functional module, positioning the primer-template duplex and incoming NTP within the active site of the enzyme. This emergent domain organization is remarkably similar to the "right hand" configuration of polymerase proteins, suggesting a common functional form for copying nucleic acids, regardless of biopolymer catalyst.

Organizational Affiliation

The Salk Institute; La Jolla, CA, USA.

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)

Molecule	Chains	Length	Organism
Entity ID: 1
RNA polymerase ribozyme 85h34	A	194	synthetic construct
Sequence Annotations Expand
Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 2
RNA primer	B	20	synthetic construct
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff)

Molecule	Chains	Length	Organism
Entity ID: 3
RNA template	C	42	synthetic construct
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
APC (Subject of Investigation/LOI) Query on APC Download:Ideal Coordinates CCD File SDF format, chain Q [auth A] MOL2 format, chain Q [auth A] mmCIF format, chain Q [auth A]	Q [auth A]	DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER C₁₁ H₁₈ N₅ O₁₂ P₃ CAWZRIXWFRFUQB-IOSLPCCCSA-N		Interactions Focus chain Q [auth A] Interactions & Density Focus chain Q [auth A]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain P [auth A] SDF format, chain O [auth A] SDF format, chain N [auth A] SDF format, chain M [auth A] SDF format, chain L [auth A] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain P [auth A] MOL2 format, chain O [auth A] MOL2 format, chain N [auth A] MOL2 format, chain M [auth A] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain P [auth A] mmCIF format, chain O [auth A] mmCIF format, chain N [auth A] mmCIF format, chain M [auth A] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	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		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A]

Experimental Data & Validation

Experimental Data

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

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	4.7.0
MODEL REFINEMENT	PHENIX	2.1_6048

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-09-09

Deposition Author(s):

Strutzenberg, T.S.

Lyumkis, D.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM148049
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM159035
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI136680
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI170855
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM151305
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI196844
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM146435