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- EMDB-67102: The neck structure of the Phage Phikz -

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Basic information

Entry
Database: EMDB / ID: EMD-67102
TitleThe neck structure of the Phage Phikz
Map data
Sample
  • Complex: Pseudomonas phage phiKZ
    • Protein or peptide: PHIKZ099
    • Protein or peptide: PHIKZ029
    • Protein or peptide: PHIKZ030
    • Protein or peptide: PHIKZ098
    • Protein or peptide: PHIKZ034
    • Protein or peptide: Endolysin gp144
Keywordsneck / VIRAL PROTEIN
Function / homology
Function and homology information


: / peptidoglycan lytic transglycosylase activity / viral release from host cell by cytolysis / defense response to bacterium
Similarity search - Function
: / : / Putative phage head-tail joining protein / Phage head to tail associated domain / : / Phage tail tube protein / : / Bacteriophage phiKZ, gp29PR / PGBD superfamily / Transglycosylase SLT domain 1 ...: / : / Putative phage head-tail joining protein / Phage head to tail associated domain / : / Phage tail tube protein / : / Bacteriophage phiKZ, gp29PR / PGBD superfamily / Transglycosylase SLT domain 1 / Transglycosylase SLT domain / Peptidoglycan binding-like / Putative peptidoglycan binding domain / PGBD-like superfamily / Lysozyme-like domain superfamily
Similarity search - Domain/homology
Endolysin gp144 / PHIKZ099 / PHIKZ098 / PHIKZ034 / PHIKZ030 / PHIKZ029
Similarity search - Component
Biological speciesPseudomonas phage phiKZ (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.52 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: Nat Commun / Year: 2026
Title: Structural atlas of the intact jumbo phage phiKZ.
Authors: Hao Xiao / Zeng Peng / Junquan Zhou / Yuan Chen / Yuning Peng / Yixiong Tang / Tao Li / Wenyuan Chen / Sheng-You Huang / Lingpeng Cheng / Hongrong Liu /
Abstract: Jumbo phage phiKZ, a key model for studying phage nucleus formation and bacterial defense mechanisms, possesses a highly complex tail machine that is essential for infection. Here, we present the ...Jumbo phage phiKZ, a key model for studying phage nucleus formation and bacterial defense mechanisms, possesses a highly complex tail machine that is essential for infection. Here, we present the structural atlas of the intact jumbo phage phiKZ by cryo-EM, thereby identifying 40 constituent proteins and unveiling its modular architecture. The virion, with a length of approximately 360 nm, is comprised of an icosahedral capsid of 2520 polypeptide chains from 11 proteins, and a massive tail machine of over 900 polypeptide chains from 29 proteins. The tail features a unique, multi-layered neck and a highly elaborate baseplate. The neck is reinforced by whisker-like proteins and anchors the contractile tail, which terminates in the baseplate. The baseplate is constituted by a central hub, an inner periphery of interlocking wedge heterotrimers and hexagonal rings, and an outer periphery with a striking hexagonal star configuration. This intricate peripheral region of the baseplate serves as an extended platform for twelve peripheral fibers, which mediate host cell adsorption. Our findings provide a structural framework for understanding jumbo phage assembly and infection, thus contributing to the foundation for future functional studies and rational engineering of these phages for potential therapeutic applications.
History
DepositionNov 17, 2025-
Header (metadata) releaseFeb 11, 2026-
Map releaseFeb 11, 2026-
UpdateApr 29, 2026-
Current statusApr 29, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_67102.png

Downloads & links

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Map

FileDownload / File: emd_67102.map.gz / Format: CCP4 / Size: 421.9 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 480 pix.
= 652.8 Å		1.36 Å/pix.
x 480 pix.
= 652.8 Å		1.36 Å/pix.
x 480 pix.
= 652.8 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: 0.3
Minimum - Maximum-0.7029782 - 1.308351
Average (Standard dev.)-0.0021001378 (±0.06254295)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 652.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_67102_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_67102_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: PHIKZ099
    • Protein or peptide: PHIKZ029
    • Protein or peptide: PHIKZ030
    • Protein or peptide: PHIKZ098
    • Protein or peptide: PHIKZ034
    • Protein or peptide: Endolysin gp144

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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: PHIKZ099

MacromoleculeName: PHIKZ099 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas phage phiKZ (virus)
Molecular weightTheoretical: 54.814367 KDa
SequenceString: MALLTIEDEE LPVNPEVKPV NPKECPDVFR GIAVDTKYVP RSDLMAWITG SNWRVDYFSQ ILREDQEPTA LDIHRRPDKQ QYIAIKGMD LKVTQALQYN QAENTTKFKV DGTGFTYPFL VPQKNDMFIA DVGDGRSGLF TITSVRRQTI LRDSTYAVTW K MIHYVTQQ ...String:
MALLTIEDEE LPVNPEVKPV NPKECPDVFR GIAVDTKYVP RSDLMAWITG SNWRVDYFSQ ILREDQEPTA LDIHRRPDKQ QYIAIKGMD LKVTQALQYN QAENTTKFKV DGTGFTYPFL VPQKNDMFIA DVGDGRSGLF TITSVRRQTI LRDSTYAVTW K MIHYVTQQ EYDDLITKSQ MSYYYSSTSL MNGCGPFVTE QEQEDNTNLT KLYKEIIRNY ITEFYSPQHQ TFLVPDQLTK TY DHFAVKA FLQMVDASAD PRMYKIKLLN VFSEPVMSQP TVWDAIVRQD VARMCYATEK AHLVTTKISR WKPVFQAIGF TGI ARMVFP IDAPIDVESR YDGETMCRPD GQPFREGRPM REAPGPYRTQ AERNLPWFKR IDPQYEDRVK PWQIPADIYP IVRD NYYVF TEAFYRGDKK LMSKLELCVW AMINGEAVNA DQLREVAKCS RSWDNLERYY YHIVLLSLIK YSLR

UniProtKB: PHIKZ099

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Macromolecule #2: PHIKZ029

MacromoleculeName: PHIKZ029 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas phage phiKZ (virus)
Molecular weightTheoretical: 77.712344 KDa
SequenceString: MAYYNAVPRV VFNGIRDRSR RPLIRPDITF AQHCPLLRLF TETGPTETTY VGDSDDGFAS IYGQASLDPR SKFFNTQSLL ALNLLGRGN GFYVKRLRPE DAANPSRLIV AIEIVEDEIP LTIRRLSGFN YPNSVRDIGN APVPTTDKVD GLKARIILIE D NTSEVGTQ ...String:
MAYYNAVPRV VFNGIRDRSR RPLIRPDITF AQHCPLLRLF TETGPTETTY VGDSDDGFAS IYGQASLDPR SKFFNTQSLL ALNLLGRGN GFYVKRLRPE DAANPSRLIV AIEIVEDEIP LTIRRLSGFN YPNSVRDIGN APVPTTDKVD GLKARIILIE D NTSEVGTQ RVLPGTLVSD KDGSQSLVYP LFEAPVSFFG KLGDSNGMRV WSTTTADIEE FDEAAMAKFK TRQFRIQLIE KP EVGTSPV IVKTADQQDY LNITFDKGVY SDMYNADLYV GDVLVDSYSD DGVVSGLSPL YSPFSQFYVY HENIDLVRQM IYD TEMRVN PAAAAHTTAP GEIDFLTFLA VDGDPYQGIQ VLGPLDGGIT LGKDGNIYAS GGTDGTTDLE EYAKLVDIEN INFG KLNDR YNNIAEYQFG VLYDTGLPME SKYRAMRVLS ARRDLQYFFT TFVETDSRLP DEATELSRVQ QIITRLKAFP ESTLY GTGV CRAMIVMQSG KLMDGTYRKY VPQLLDVAMS WARYAGAGTG NLVPGMEMDV SPNNRVTFVK DLNVKFFDDR VRAQAW ANG ATWSQSYDHR SSYYPCLRSV MLDDTSVLLS PITVNICCVL IRLIHKVHAQ FSGNATLTPE QLVERCDEYI LDLVRDM FG TRVNIIPRTE ITPIDANNGT SWTCNVTVEA NNPRTTLNFN LETVRIETPP AQQ

UniProtKB: PHIKZ029

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Macromolecule #3: PHIKZ030

MacromoleculeName: PHIKZ030 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas phage phiKZ (virus)
Molecular weightTheoretical: 32.686555 KDa
SequenceString: MARYNDPMAP ETGYGAGGAR NTVNLAQAGT NVFRPDLANL ATNTPYVARN LVPFLLDAPR FFKYASNTNW LVACLKAFVE THTRTIDGL QRTLTVDNAE APWGGSGEVI QTATNVTRAR SNPNFGCWEL QNRAIQRFLQ WWINYGIADE NTKVPRIVSD G IVPVEKYD ...String:
MARYNDPMAP ETGYGAGGAR NTVNLAQAGT NVFRPDLANL ATNTPYVARN LVPFLLDAPR FFKYASNTNW LVACLKAFVE THTRTIDGL QRTLTVDNAE APWGGSGEVI QTATNVTRAR SNPNFGCWEL QNRAIQRFLQ WWINYGIADE NTKVPRIVSD G IVPVEKYD ATFYGMTVLF VEPDPTFQDC VNAYLCTNMF PLTTGPWENR KDASQIGQNL DLNVEFSALT DVSEGVQEYA RQ MFRKLNI RGMNPNNQKL DWGGLSADVL RARNGIQDQI ERAVGNRVTY DGVGLS

UniProtKB: PHIKZ030

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Macromolecule #4: PHIKZ098

MacromoleculeName: PHIKZ098 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas phage phiKZ (virus)
Molecular weightTheoretical: 63.225426 KDa
SequenceString: MPNTTLVLPD VYESVTRRVA ADIIGQLAKM MGLPEDTLVQ FPGNVQTVPM NGGMFGNCCD SANVVKFDPE DHIIITYDEV ADERYTLST DVKNHQNFPW FVDETRGVRI TPVRRFVDVR FDIEYKSKNI TLAQRWLDEQ RLWFSNNGQE LVHTLTYHVD V PMPVQGIL ...String:
MPNTTLVLPD VYESVTRRVA ADIIGQLAKM MGLPEDTLVQ FPGNVQTVPM NGGMFGNCCD SANVVKFDPE DHIIITYDEV ADERYTLST DVKNHQNFPW FVDETRGVRI TPVRRFVDVR FDIEYKSKNI TLAQRWLDEQ RLWFSNNGQE LVHTLTYHVD V PMPVQGIL AAIYNTAQNS HWPMEETFPE YLNKYFTFPT TELADLSQKN KSLVIYERQV DVIGWYDYTS TPPTPEYDSE SD GSYNVRF SYFLTYARPT HVWIEYPLTV HQCLVPSVIR PKYIYENYQQ VDRKVSQFRG SLYHKFLLIR DKKIPYIQHP DID TWDTDN IPINQLTFFS GLLTLCPDEI ESGTLMSFDQ LGRYSFSPFF LEYFEGVGTK AIDQNGIFQV RLYENDNYTR AECY LDGLM LKTKWKLDPC KVYHVQISIH KNLLLVFDDR WRCLQRYPRV CWTIFNLFGV GIGRKPFEEV KLLGKGRDRL PSEEC PGEG TTCHTQCLNP TTEGVINWKD IVDAREEMNT RIGPDWDPTY LMGPLTVLYG NIITERKE

UniProtKB: PHIKZ098

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Macromolecule #5: PHIKZ034

MacromoleculeName: PHIKZ034 / type: protein_or_peptide / ID: 5 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas phage phiKZ (virus)
Molecular weightTheoretical: 29.899949 KDa
SequenceString: MSCCKAPVKP DTSIDIDHLG GGCQTYNHLQ DMFFYLKEER LNAKPCDLSR YSIQYSYVDS MTYLYVLTDE LTGETISWSV TKEFEKESP QAAFERDYIE RELIYNRGIK RALDDMLEGL ADADPSNVYK LERTDYGYRI LRRINDELGA VIFKLSYTIH R GPIITPFS ...String:
MSCCKAPVKP DTSIDIDHLG GGCQTYNHLQ DMFFYLKEER LNAKPCDLSR YSIQYSYVDS MTYLYVLTDE LTGETISWSV TKEFEKESP QAAFERDYIE RELIYNRGIK RALDDMLEGL ADADPSNVYK LERTDYGYRI LRRINDELGA VIFKLSYTIH R GPIITPFS DKCTVPENVP DIFPTETQRA LSRLVYRFHK LGVIFGDWVP DHVQKYNKME LTGYTRRTMD SYVILNMAIQ SI NLTDPEL VTYHKYYSI

UniProtKB: PHIKZ034

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Macromolecule #6: Endolysin gp144

MacromoleculeName: Endolysin gp144 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
EC number: Lyases; Carbon-oxygen lyases; Acting on polysaccharides
Source (natural)Organism: Pseudomonas phage phiKZ (virus)
Molecular weightTheoretical: 28.849973 KDa
SequenceString: MKVLRKGDRG DEVCQLQTLL NLCGYDVGKP DGIFGNNTFN QVVKFQKDNC LDSDGIVGKN TWAELFSKYS PPIPYKTIPM PTANKSRAA ATPVMNAVEN ATGVRSQLLL TFASIESAFD YEIKAKTSSA TGWFQFLTGT WKTMIENYGM KYGVLTDPTG A LRKDPRIS ...String:
MKVLRKGDRG DEVCQLQTLL NLCGYDVGKP DGIFGNNTFN QVVKFQKDNC LDSDGIVGKN TWAELFSKYS PPIPYKTIPM PTANKSRAA ATPVMNAVEN ATGVRSQLLL TFASIESAFD YEIKAKTSSA TGWFQFLTGT WKTMIENYGM KYGVLTDPTG A LRKDPRIS ALMGAELIKE NMNILRPVLK REPTDTDLYL AHFFGPGAAR RFLTTGQNEL AATHFPKEAQ ANPSIFYNKD GS PKTIQEV YNLMDGKVAA HRK

UniProtKB: Endolysin gp144

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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: 3.52 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 35244
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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