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- EMDB-72693: Cryo-EM map of the in vitro reconstituted RAZR:GP77 complex with ... -

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Basic information

Entry
Database: EMDB / ID: EMD-72693
TitleCryo-EM map of the in vitro reconstituted RAZR:GP77 complex with AlphaFold-predicted models fitted into the density.
Map data
Sample
  • Complex: RazR:GP77 complex
    • Protein or peptide: Gp77
    • Protein or peptide: DUF4145 domain-containing protein
  • Ligand: ZINC ION
KeywordsPhage-bacterial defense complex / Abortive infection Ring-Activated Zinc-Finger RNase (RAZR) / RNA BINDING PROTEIN
Function / homologyDomain of unknown function DUF4145 / Domain of unknown function (DUF4145) / DUF4145 domain-containing protein / :
Function and homology information
Biological speciesEscherichia coli BL21(DE3) (bacteria) / Escherichia phage SECphi27 (virus) / Escherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsLyu Y / Zhang T / Laub M / Ghanbarpour A
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/John E. Fogarty International Center (NIH/FIC)R35-GM141517 United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: To Be Published
Title: Cryo-EM map of the in vitro reconstituted RAZR:GP77 complex with AlphaFold-predicted models fitted into the density.
Authors: Lyu Y / Zhang T / Laub M / Ghanbarpour A
History
DepositionSep 14, 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_72693.png

Downloads & links

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Map

FileDownload / File: emd_72693.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: 0.0777
Minimum - Maximum-0.35850126 - 0.8280184
Average (Standard dev.)0.0005773878 (±0.016053865)
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_72693_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_72693_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_72693_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 : RazR:GP77 complex

EntireName: RazR:GP77 complex
Components
  • Complex: RazR:GP77 complex
    • Protein or peptide: Gp77
    • Protein or peptide: DUF4145 domain-containing protein
  • Ligand: ZINC ION

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Supramolecule #1: RazR:GP77 complex

SupramoleculeName: RazR:GP77 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Escherichia coli 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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Macromolecule #2: DUF4145 domain-containing protein

MacromoleculeName: DUF4145 domain-containing protein / type: protein_or_peptide / ID: 2 / Number of copies: 24 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 24.707023 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MAEYYPAVFE AEAFNCPHCG VYARQFWRRM YGSARELAQR TTEFRMSTCS HCGDDAYWYD GNMIIPAAGN VELPNPDMPD NCKSDYMEA RSIINLSPKG AAALLRLCLQ KLMVHLGEPG ENINKDIRSL VQKGLPVRIQ QAADICRIVG NQAVHPGEIS L DDDPQLAH ...String:
MAEYYPAVFE AEAFNCPHCG VYARQFWRRM YGSARELAQR TTEFRMSTCS HCGDDAYWYD GNMIIPAAGN VELPNPDMPD NCKSDYMEA RSIINLSPKG AAALLRLCLQ KLMVHLGEPG ENINKDIRSL VQKGLPVRIQ QAADICRIVG NQAVHPGEIS L DDDPQLAH GLFKLLNIIV DDRITRPKEI EAMFQSMPEG PRQGIENQDR QAREQQQAAN E

UniProtKB: DUF4145 domain-containing protein

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Macromolecule #3: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 3 / Number of copies: 24 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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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

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Number real images: 11152 / 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 correctionType: NONE
Startup modelType of model: OTHER / Details: Ab-initio
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7.0) / Number images used: 28191
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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Atomic model buiding 1

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

PDB-9y9c:
Cryo-EM map of the in vitro reconstituted RAZR:GP77 complex with AlphaFold-predicted models fitted into the density.

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