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- PDB-9y9c: Cryo-EM map of the in vitro reconstituted RAZR:GP77 complex with ... -

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Basic information

Entry
Database: PDB / ID: 9y9c
TitleCryo-EM map of the in vitro reconstituted RAZR:GP77 complex with AlphaFold-predicted models fitted into the density.
Components
  • DUF4145 domain-containing protein
  • Gp77
KeywordsRNA BINDING PROTEIN / Phage-bacterial defense complex / Abortive infection Ring-Activated Zinc-Finger RNase (RAZR)
Function / homologyDomain of unknown function DUF4145 / Domain of unknown function (DUF4145) / DUF4145 domain-containing protein / :
Function and homology information
Biological speciesEscherichia phage SECphi27 (virus)
Escherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsLyu, Y. / Zhang, T. / Laub, M. / Ghanbarpour, A.
Funding support United States, 2items
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, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 24, 2025Provider: repository / Type: Initial release
Revision 1.0Dec 24, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Dec 24, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 24, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 24, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Dec 24, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Dec 24, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
IA: Gp77
IB: Gp77
IC: Gp77
ID: Gp77
IE: Gp77
IF: Gp77
IG: Gp77
IH: Gp77
II: Gp77
IJ: Gp77
IK: Gp77
IL: Gp77
IM: Gp77
IN: Gp77
IO: Gp77
IP: Gp77
IQ: Gp77
IR: Gp77
IS: Gp77
IT: Gp77
IU: Gp77
IV: Gp77
IW: Gp77
IX: Gp77
OA: DUF4145 domain-containing protein
OB: DUF4145 domain-containing protein
OC: DUF4145 domain-containing protein
OD: DUF4145 domain-containing protein
OE: DUF4145 domain-containing protein
OF: DUF4145 domain-containing protein
OG: DUF4145 domain-containing protein
OH: DUF4145 domain-containing protein
OI: DUF4145 domain-containing protein
OJ: DUF4145 domain-containing protein
OK: DUF4145 domain-containing protein
OL: DUF4145 domain-containing protein
OM: DUF4145 domain-containing protein
ON: DUF4145 domain-containing protein
OO: DUF4145 domain-containing protein
OP: DUF4145 domain-containing protein
OQ: DUF4145 domain-containing protein
OR: DUF4145 domain-containing protein
OS: DUF4145 domain-containing protein
OT: DUF4145 domain-containing protein
OU: DUF4145 domain-containing protein
OV: DUF4145 domain-containing protein
OW: DUF4145 domain-containing protein
OX: DUF4145 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,205,95472
Polymers1,204,38448
Non-polymers1,57024
Water00
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

#1: Protein ...
Gp77


Mass: 25475.650 Da / Num. of mol.: 24
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia phage SECphi27 (virus) / Gene: JLBYU38_79 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0AAE8YXX1
#2: Protein ...
DUF4145 domain-containing protein


Mass: 24707.023 Da / Num. of mol.: 24
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: C9194_06935, DIV22_05270, DU321_12645, NY836_21110 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0F3V1L6
#3: Chemical...
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: Zn
Has ligand of interestN
Has protein modificationY

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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: RazR:GP77 complex / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Source (natural)Organism: Escherichia coli BL21(DE3) (bacteria)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 47.18 e/Å2 / Film or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Num. of real images: 11152

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Processing

EM software
IDNameVersionCategory
1cryoSPARCv.4.7.0particle selection
2Topazparticle selection
13cryoSPARC4.7.03D reconstruction
14PHENIX1.21.2_5419:model refinement
CTF correctionType: NONE
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 28191 / Symmetry type: POINT
Atomic model buildingSource name: AlphaFold / Type: in silico model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00357958
ELECTRON MICROSCOPYf_angle_d0.68478429
ELECTRON MICROSCOPYf_dihedral_angle_d4.0557896
ELECTRON MICROSCOPYf_chiral_restr0.0418567
ELECTRON MICROSCOPYf_plane_restr0.00410344

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