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- EMDB-67098: The structure of baseplate central region of phage phikz -

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Basic information

Entry
Database: EMDB / ID: EMD-67098
TitleThe structure of baseplate central region of phage phikz
Map data
Sample
  • Complex: Pseudomonas phage phiKZ
    • Protein or peptide: PHIKZ101
    • Protein or peptide: PHIKZ174
    • Protein or peptide: PHIKZ164
    • Protein or peptide: PHIKZ163.1
Keywordsspike / VIRAL PROTEIN
Function / homologymetal ion binding / PHIKZ163.1 / PHIKZ174 / PHIKZ164 / PHIKZ101
Function and homology information
Biological speciesPseudomonas phage phiKZ (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.02 Å
AuthorsXiao H / Peng Z / Zhou J / Liu H
Funding support China, 3 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)12034006 China
National Natural Science Foundation of China (NSFC)32430020 China
National Natural Science Foundation of China (NSFC)32200994 China
CitationJournal: To Be Published
Title: Structural atlas of the intact jumbo phage phiKZ
Authors: Xiao H / Peng Z / Zhou J / Liu H
History
DepositionNov 16, 2025-
Header (metadata) releaseFeb 11, 2026-
Map releaseFeb 11, 2026-
UpdateFeb 11, 2026-
Current statusFeb 11, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_67098.png

Downloads & links

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Map

FileDownload / File: emd_67098.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.36 Å/pix.
x 300 pix.
= 408. Å		1.36 Å/pix.
x 300 pix.
= 408. Å		1.36 Å/pix.
x 300 pix.
= 408. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.36 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.42429847 - 0.8199702
Average (Standard dev.)0.006142746 (±0.0716721)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 408.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_67098_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_67098_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_67098_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 : Pseudomonas phage phiKZ

EntireName: Pseudomonas phage phiKZ (virus)
Components
  • Complex: Pseudomonas phage phiKZ
    • Protein or peptide: PHIKZ101
    • Protein or peptide: PHIKZ174
    • Protein or peptide: PHIKZ164
    • Protein or peptide: PHIKZ163.1

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Supramolecule #1: Pseudomonas phage phiKZ

SupramoleculeName: Pseudomonas phage phiKZ / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Pseudomonas phage phiKZ (virus)

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Macromolecule #1: PHIKZ101

MacromoleculeName: PHIKZ101 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas phage phiKZ (virus)
Molecular weightTheoretical: 52.013387 KDa
SequenceString: MAVDASSLMR EVDTIINSAN NYSAYKIEAK ILVGDFDWVV PLRVDYFDTF RNYADGSYGD LILTELLIGT GDFQFDILPR RDELRCDVK FIPLLPNSSL LDTSRKASVK RYRCFVVLSP EDDITLTNKQ SQLTSKEAMN QISYKPYRFQ LVEESVYQSL M ITIGKNFT ...String:
MAVDASSLMR EVDTIINSAN NYSAYKIEAK ILVGDFDWVV PLRVDYFDTF RNYADGSYGD LILTELLIGT GDFQFDILPR RDELRCDVK FIPLLPNSSL LDTSRKASVK RYRCFVVLSP EDDITLTNKQ SQLTSKEAMN QISYKPYRFQ LVEESVYQSL M ITIGKNFT NVTTADVLRA FLKQSISQLT EADDNRVIDI NMEPGWNTEV RPVIPIPDGT PLKDLPNILQ NKEGGVYATG LG RYIQGSY LYVYSLYDTK KYQKGAKTLN IINVPNDRLY GVEKTYVNGD TYTTILATGD ASSLDKALYE MVDNGSGYRF ADA NKLLDD FTISKDNKML VDAASNLYEV RGDGLKTGFQ NIQWTKQRST SNPFKHYTEL AKRQGQFLKI QWNHGDADIL TPGM PVKFQ TVDNNVVKTY YGVLLGVDEQ FAAGDNNPNP HRYVCVVTLA IFLNRSDQNE IEPST

UniProtKB: PHIKZ101

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Macromolecule #2: PHIKZ174

MacromoleculeName: PHIKZ174 / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas phage phiKZ (virus)
Molecular weightTheoretical: 39.125891 KDa
SequenceString: MVDFALPSFI GTGKDEVAKI DAYTEVSSDV RNSLVSGISN FEQGFSGILN RTLKAVRGIG DLIPSDGINL ADASRRIQGA LKGSRSDLQ NIAQSLENII FGELTGSNGG PGYVQQATRM ANEVKMIING VDVYKQNSNY QNMSSILSFL EDMSGSNAII K FFDLGAEA ...String:
MVDFALPSFI GTGKDEVAKI DAYTEVSSDV RNSLVSGISN FEQGFSGILN RTLKAVRGIG DLIPSDGINL ADASRRIQGA LKGSRSDLQ NIAQSLENII FGELTGSNGG PGYVQQATRM ANEVKMIING VDVYKQNSNY QNMSSILSFL EDMSGSNAII K FFDLGAEA AVLRGVLQEV AQWGIPDLID DTFGATKRYD GSGNWVGYDY KYNDDFRFTL TKRTADSLGN NIDLDVIDRI IT HSGAEAL TADVPDYPNR IIANYVFPEG TKPEDYPTIL SKLVSIMDKL KPDWFWTLRN TQKVFNFGVL QTASDDATTL FLS NDTYRT PMLVAPFYKP AQALELFRDM YPMIAIPT

UniProtKB: PHIKZ174

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Macromolecule #3: PHIKZ164

MacromoleculeName: PHIKZ164 / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas phage phiKZ (virus)
Molecular weightTheoretical: 32.434172 KDa
SequenceString: MDEAVSLLSN MQDSEIQTSE FRLWSIGRAT ENKPRNSFTL MVLPIESATA TDGETTFNPV EEVVDGVDAD GRAYTTKVSV SRDIPCIWL PNEDNRATPP DVMRGEKIAI YRLGDTSQFY WRSMGLSNDL RTLESVVYTF NASLSPGGAG KNFDTCYFMQ F SAHDKHVT ...String:
MDEAVSLLSN MQDSEIQTSE FRLWSIGRAT ENKPRNSFTL MVLPIESATA TDGETTFNPV EEVVDGVDAD GRAYTTKVSV SRDIPCIWL PNEDNRATPP DVMRGEKIAI YRLGDTSQFY WRSMGLSNDL RTLESVVYTF NASLSPGGAG KNFDTCYFMQ F SAHDKHVT IGTSKANGEP YRYSVQINTG TGAVYILDDI GNRFELVSKD KRLMLMNADN SFVKVEKKAI DLNADQYIKL TS GGSTLEL NPTEFKVNTT NTTIKSSGTH IQEAGGTMTH KAGGNMLFTA PRYDFT

UniProtKB: PHIKZ164

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Macromolecule #4: PHIKZ163.1

MacromoleculeName: PHIKZ163.1 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas phage phiKZ (virus)
Molecular weightTheoretical: 8.809327 KDa
SequenceString:
MPGIAVCNMD SAGGVILPGP NVKCFYKGQP FAVIGCAVAG HGRTPHDSAR MIQGSVKMAI AGIPVCLQGS MASCGHTATG RPNLTCGS

UniProtKB: PHIKZ163.1

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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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 30.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.02 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 27796
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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