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- EMDB-72631: Cryo-EM Structure of Gp77 within the In Vitro Reconstituted RAZR:... -

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Basic information

Entry
Database: EMDB / ID: EMD-72631
TitleCryo-EM Structure of Gp77 within the In Vitro Reconstituted RAZR:GP77 Complex
Map data
Sample
  • Complex: GP77 within RAZR:GP77 complex
    • Protein or peptide: Gp77
KeywordsPhage-bacterial defense complex / Abortive infection Ring-Activated Zinc-Finger RNase (RAZR) / RNA BINDING PROTEIN
Function / homology:
Function and homology information
Biological speciesBL21 DE3 (bacteria) / Escherichia phage SECphi27 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsYifei L / Zhang T / Laub M / Ghanbarpour A
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35-GM141517 United States
National Science Foundation (NSF, United States)2046778 United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: To Be Published
Title: Cryo-EM Structure of Gp77 within the In Vitro Reconstituted RAZR:GP77 Complex
Authors: Yifei L / Zhang T / Laub M / Ghanbarpour A
History
DepositionSep 9, 2025-
Header (metadata) releaseDec 24, 2025-
Map releaseDec 24, 2025-
UpdateDec 24, 2025-
Current statusDec 24, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_72631.png

Downloads & links

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Map

FileDownload / File: emd_72631.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.49 Å/pix.
x 440 pix.
= 653.972 Å		1.49 Å/pix.
x 440 pix.
= 653.972 Å		1.49 Å/pix.
x 440 pix.
= 653.972 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.4863 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.167
Minimum - Maximum-0.46091393 - 1.1276315
Average (Standard dev.)0.00018978484 (±0.015377137)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 653.972 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_72631_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_72631_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_72631_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : GP77 within RAZR:GP77 complex

EntireName: GP77 within RAZR:GP77 complex
Components
  • Complex: GP77 within RAZR:GP77 complex
    • Protein or peptide: Gp77

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Supramolecule #1: GP77 within RAZR:GP77 complex

SupramoleculeName: GP77 within RAZR:GP77 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: BL21 DE3 (bacteria)

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Macromolecule #1: Gp77

MacromoleculeName: Gp77 / type: protein_or_peptide / ID: 1 / Number of copies: 24 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage SECphi27 (virus)
Molecular weightTheoretical: 25.47565 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MKLSDQFDKV LPALHKARSL FVKVKKDRQN SHLKNRYATL DSVLDAITPA LMDNELMIMQ DGERIDVSTL RVETTVMHVS GQWVKFYFD IPIVKNDPQG VGSAFTYGRR YSAAAAFGLS QADDDAQIAV KTVNDWKRDI EKCESVGELQ EVLKNAWKSS D AASKQVIR ...String:
MKLSDQFDKV LPALHKARSL FVKVKKDRQN SHLKNRYATL DSVLDAITPA LMDNELMIMQ DGERIDVSTL RVETTVMHVS GQWVKFYFD IPIVKNDPQG VGSAFTYGRR YSAAAAFGLS QADDDAQIAV KTVNDWKRDI EKCESVGELQ EVLKNAWKSS D AASKQVIR DHYEKRKAEI EIGGARGFNP AKPKENLASD AVDTPNSEKV KSQSITDFEG SSGHHHHHH

UniProtKB: UNIPROTKB: A0AAE8YXX1

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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

BufferpH: 8
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Average electron dose: 47.18 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. 4.7.0) / Type: NONE
Startup modelType of model: INSILICO MODEL / In silico model: Ab-initio
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7.0) / Number images used: 28191
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: cryoSPARC (ver. 4.7.0)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: cryoSPARC (ver. 4.7.0)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
Output model

PDB-9y6u:
Cryo-EM Structure of Gp77 within the In Vitro Reconstituted RAZR:GP77 Complex

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