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- EMDB-78852: RNA polymerase ribozyme 85h34 replication complex, subclass 2 str... -

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Basic information

Entry
Database: EMDB / ID: EMD-78852
TitleRNA polymerase ribozyme 85h34 replication complex, subclass 2 structure.
Map dataProduct of processing pipeline.
Sample
  • Complex: RNA polymerase 85h34 replication complex
    • RNA: RNA polymerase ribozyme 85h34
    • RNA: RNA primer
    • RNA: RNA template
  • Ligand: MAGNESIUM ION
  • Ligand: DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER
  • Ligand: water
KeywordsRNA polymerase / replication complex / ribozyme / RNA
Biological speciessynthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.92 Å
AuthorsStrutzenberg TS / Lyumkis D
Funding support United States, 7 items
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 TS / Horning DP / Cochrane WG / Andrade L / Han X / Joyce GF / Lyumkis D
History
DepositionAug 29, 2026-
Header (metadata) releaseSep 9, 2026-
Map releaseSep 9, 2026-
UpdateSep 9, 2026-
Current statusSep 9, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_78852.png

Downloads & links

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Map

FileDownload / File: emd_78852.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationProduct of processing pipeline.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 256 pix.
= 265.6 Å		1.04 Å/pix.
x 256 pix.
= 265.6 Å		1.04 Å/pix.
x 256 pix.
= 265.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0375 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05
Minimum - Maximum-0.14635341 - 0.39873344
Average (Standard dev.)0.000016555696 (±0.006774364)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 265.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_78852_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: MRC with local resolution data.

Fileemd_78852_additional_1.map
AnnotationMRC with local resolution data.
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Additional map: B-factor sharpened map used for atomic modeling.

Fileemd_78852_additional_2.map
AnnotationB-factor sharpened map used for atomic modeling.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2 for FSC calculation.

Fileemd_78852_half_map_1.map
AnnotationHalf map 2 for FSC calculation.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 1 for FSC calculation.

Fileemd_78852_half_map_2.map
AnnotationHalf map 1 for FSC calculation.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : RNA polymerase 85h34 replication complex

EntireName: RNA polymerase 85h34 replication complex
Components
  • Complex: RNA polymerase 85h34 replication complex
    • RNA: RNA polymerase ribozyme 85h34
    • RNA: RNA primer
    • RNA: RNA template
  • Ligand: MAGNESIUM ION
  • Ligand: DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER
  • Ligand: water

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Supramolecule #1: RNA polymerase 85h34 replication complex

SupramoleculeName: RNA polymerase 85h34 replication complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 82.6 KDa

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Macromolecule #1: RNA polymerase ribozyme 85h34

MacromoleculeName: RNA polymerase ribozyme 85h34 / type: rna / ID: 1 / Number of copies: 1
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 62.584438 KDa
SequenceString: AGAGGGAAAC CUCUGCCGCC GCCGCACCAA GACAAAUCUC CCCUCAGAGC CUCAGAACAU CGAAAGAUGC AGAGCAGGGA GGCUUCGGU GGAUAAUGGU GCACCACCGU UCUGAGCACG UACCCGAACG UAAAUUGACC UGACAGAAAG GCGUAGUUAG A AUCGCACA ...String:
AGAGGGAAAC CUCUGCCGCC GCCGCACCAA GACAAAUCUC CCCUCAGAGC CUCAGAACAU CGAAAGAUGC AGAGCAGGGA GGCUUCGGU GGAUAAUGGU GCACCACCGU UCUGAGCACG UACCCGAACG UAAAUUGACC UGACAGAAAG GCGUAGUUAG A AUCGCACA GGUACCAUGC CCAACACAUG GCUGAC

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Macromolecule #2: RNA primer

MacromoleculeName: RNA primer / type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 6.487912 KDa
SequenceString:
GGAGCGAGAA AGUUGUUAUC

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Macromolecule #3: RNA template

MacromoleculeName: RNA template / type: rna / ID: 3 / Number of copies: 1
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 13.460117 KDa
SequenceString:
GACGGCGGCA AAAAACACAA GUGAUAACAA CUUUCUCGCU CC

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Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 13 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #5: DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER

MacromoleculeName: DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / type: ligand / ID: 5 / Number of copies: 1 / Formula: APC
Molecular weightTheoretical: 505.208 Da
Chemical component information

ChemComp-APC:
DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / AMP-CPP, energy-carrying molecule analogue*YM

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Macromolecule #6: water

MacromoleculeName: water / type: ligand / ID: 6 / Number of copies: 155 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.826 mg/mL
BufferpH: 8.3 / Details: 10 mM Tris, 75 mM MgCl2, 1 mM EDTA, 0.05% DM
GridModel: UltrAuFoil R0./1 / Material: GOLD / Mesh: 400 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 40 sec. / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Number grids imaged: 2 / Number real images: 34997 / Average exposure time: 2.7 sec. / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.7000000000000001 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1155053
CTF correctionSoftware - Name: cryoSPARC (ver. 4.7.0) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.92 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7.0) / Number images used: 98137
Initial angle assignmentType: COMMON LINE / Software - Name: cryoSPARC (ver. 4.7.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 5.0)
Final 3D classificationNumber classes: 10 / Avg.num./class: 100000
FSC plot (resolution estimation)

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