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- PDB-38jd: RNA polymerase ribozyme 85h34 replication complex, subclass 2 str... -

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Basic information

Entry
Database: PDB / ID: 38jd
TitleRNA polymerase ribozyme 85h34 replication complex, subclass 2 structure
Components
  • RNA polymerase ribozyme 85h34
  • RNA primer
  • RNA template
KeywordsRNA / RNA polymerase / replication complex / ribozyme
Function / homologyDIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / RNA / RNA (> 10) / RNA (> 100)
Function and homology information
Biological speciessynthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.92 Å
AuthorsStrutzenberg, T.S. / Lyumkis, D.
Funding support United States, 7items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM148049 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM159035 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI136680 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI170855 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM151305 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI196844 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM146435 United States
CitationJournal: Biorxiv / Year: 2026
Title: Structure of an RNA polymerase ribozyme replication complex
Authors: Strutzenberg, T.S. / Horning, D.P. / Cochrane, W.G. / Andrade, L. / Han, X. / Joyce, G.F. / Lyumkis, D.
History
DepositionAug 29, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 9, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 9, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA polymerase ribozyme 85h34
B: RNA primer
C: RNA template
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,35417
Polymers82,5323
Non-polymers82114
Water2,792155
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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RNA chain , 3 types, 3 molecules ABC

#1: RNA chain RNA polymerase ribozyme 85h34


Mass: 62584.438 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: RNA chain RNA primer


Mass: 6487.912 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: RNA chain RNA template


Mass: 13460.117 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 3 types, 169 molecules

#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-APC / DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / ALPHA,BETA-METHYLENEADENOSINE-5'-TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-CPP, energy-carrying molecule analogue*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 155 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: RNA polymerase 85h34 replication complex / Type: COMPLEX / Entity ID: #1-#3 / Source: NATURAL
Molecular weightValue: 0.0826 MDa / Experimental value: NO
Source (natural)Organism: synthetic construct (others)
Buffer solutionpH: 8.3 / Details: 10 mM Tris, 75 mM MgCl2, 1 mM EDTA, 0.05% DM
SpecimenConc.: 0.826 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 400 divisions/in. / Grid type: UltrAuFoil R0./1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 298 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 700 nm
Image recordingAverage exposure time: 2.7 sec. / Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Num. of grids imaged: 2 / Num. of real images: 34997

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.7.0particle selection
4cryoSPARC4.7.0CTF correction
7Coot1.2model fitting
9cryoSPARC4.7.0initial Euler assignment
10RELION5final Euler assignment
12cryoSPARC4.7.03D reconstruction
13PHENIX2.1_6048model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1155053
3D reconstructionResolution: 2.92 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 98137 / Symmetry type: POINT
RefinementStereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0295394
ELECTRON MICROSCOPYf_angle_d0.5648461
ELECTRON MICROSCOPYf_dihedral_angle_d24.013412
ELECTRON MICROSCOPYf_chiral_restr0.0331103
ELECTRON MICROSCOPYf_plane_restr0.004222

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