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- EMDB-67121: Structure of the inner peripheral region in the phage phiKZ basep... -

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Basic information

Entry
Database: EMDB / ID: EMD-67121
TitleStructure of the inner peripheral region in the phage phiKZ baseplate complex
Map data
Sample
  • Virus: Pseudomonas phage phiKZ (virus)
    • Protein or peptide: PHIKZ087
    • Protein or peptide: PHIKZ128
    • Protein or peptide: PHIKZ161
    • Protein or peptide: PHIKZ088
    • Protein or peptide: PHIKZ182
    • Protein or peptide: PHIKZ049
    • Protein or peptide: PHIKZ029
    • Protein or peptide: PHIKZ062
Keywordsbaseplate / inner peripheral / VIRAL PROTEIN
Function / homology
Function and homology information


SH3 fold domain associated with phage DNA polymerases / : / : / SH3 fold domain associated with phage DNA polymerases / Family of unknown function (DUF7194) / Putative phage tail tube protein / : / Bacteriophage phiKZ, gp29PR
Similarity search - Domain/homology
PHIKZ182 / PHIKZ161 / PHIKZ128 / PHIKZ088 / PHIKZ087 / PHIKZ062 / PHIKZ049 / PHIKZ029
Similarity search - Component
Biological speciesPseudomonas phage phiKZ (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.65 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 18, 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_67121.png

Downloads & links

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Map

FileDownload / File: emd_67121.map.gz / Format: CCP4 / Size: 244.1 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 400 pix.
= 544. Å		1.36 Å/pix.
x 400 pix.
= 544. Å		1.36 Å/pix.
x 400 pix.
= 544. 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: 0.23
Minimum - Maximum-0.65071684 - 1.2083207
Average (Standard dev.)0.0016155066 (±0.08148335)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 544.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_67121_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_67121_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_67121_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
  • Virus: Pseudomonas phage phiKZ (virus)
    • Protein or peptide: PHIKZ087
    • Protein or peptide: PHIKZ128
    • Protein or peptide: PHIKZ161
    • Protein or peptide: PHIKZ088
    • Protein or peptide: PHIKZ182
    • Protein or peptide: PHIKZ049
    • Protein or peptide: PHIKZ029
    • Protein or peptide: PHIKZ062

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Supramolecule #1: Pseudomonas phage phiKZ

SupramoleculeName: Pseudomonas phage phiKZ / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 2905945 / Sci species name: Pseudomonas phage phiKZ / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No

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Macromolecule #1: PHIKZ087

MacromoleculeName: PHIKZ087 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas phage phiKZ (virus)
Molecular weightTheoretical: 110.486031 KDa
SequenceString: MASEFKNQLL NLRRNPVLMQ SLMLSELDKQ LNGETGERYD IPDSANPFVS LMEMGVIGVS AAFTEMEALS RRLYPRLAIT SDELYLHMS DEDYIGRFAI PAQNYFNFIL DYDEVIKYAV PYGDQGQRKL VIPRLTKFTG AGISYTMQYP LELRVMRHGG V VAEYNTDS ...String:
MASEFKNQLL NLRRNPVLMQ SLMLSELDKQ LNGETGERYD IPDSANPFVS LMEMGVIGVS AAFTEMEALS RRLYPRLAIT SDELYLHMS DEDYIGRFAI PAQNYFNFIL DYDEVIKYAV PYGDQGQRKL VIPRLTKFTG AGISYTMQYP LELRVMRHGG V VAEYNTDS LSPIETLSTN IAQMTMINDG RGHRLMNLII PVKQFDITRY QETLNPSNLF EKEYVFSDQF YYARAYIKRT VD AQEWEEV ITTHTDQVYD PLNLTVVLKV INNRLQVSIP AIYNTTGLAT GVIRIDIYST RGKIEIDYGS YQPDQFTYSL NDI DDDPKY TEPLKKLARI SALSTYYVSG GSNSMDFDTL RNQVIDNTTG PQQLPITNVQ LSADLARRGY TLVTNIDNIT KKQY LASRR LGAPRTLDII SGAGVAMSQL QVSMNELVKS KHVKDNGDRI TILPSMLYRF SNGRVSVVPD AQLDSILSSS AESIA RQIN DSRTVYCPFH GVLDATEDNF DYRPYYLDNP VINEKTFVGE NDTAQLQASI DVFEIDRVTE GYRIKIRLDE GEQFKK LAD EQIAVQIGYQ PKGETKYASI NGKFLGIEEE KRVYEFIIET NYDIDSSGAI YTTNMSMYDQ FQKVFSTPLN TDFDVSI IV VNTITPGYIP NELDSLVQRH LLPSEFMVIN RERLITTLGY DMTKIWHRNR TVFSQESYQT WPADVPAYYQ KDVFETDS T GHIVITIGPD GKPVYKVKHK KGDPVLDANG KPVMQYRKGD TKLDANGKPI LLEPRKILRE MMVLMVDGLF YFATEQEAV AYRKEIPMEF VKWIQNDIDY IDQRLLETCE LYLYPTTTFG DTIVSVREGQ KSTVQVDQNF FTMLYLKPSA FANSTIRPSL IKTVKTIVN DMLGRKTIAL SEIIAALEAA IGEDVLQIDA GGLGGSNNYS IITVDDDAVR LTLRKKLTVM ANQELTIEDD M SITFLRHE QIQ

UniProtKB: PHIKZ087

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Macromolecule #2: PHIKZ128

MacromoleculeName: PHIKZ128 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas phage phiKZ (virus)
Molecular weightTheoretical: 84.297812 KDa
SequenceString: MNNSNSVYFK VYLDDVIRLA RSIVIKFDDI ADQINTELYR DYLFKADPDK PWTWKYYLNL AGEYHETDTM MYVTSADTLE RIEFTKENL RLHRATAREF TPGSQSYNNL VLKYPTQAGL INGILYPIDI NFAIDSDNGD ILYFDNKYVE GNEDNFIPEL Q SWIKAFYN ...String:
MNNSNSVYFK VYLDDVIRLA RSIVIKFDDI ADQINTELYR DYLFKADPDK PWTWKYYLNL AGEYHETDTM MYVTSADTLE RIEFTKENL RLHRATAREF TPGSQSYNNL VLKYPTQAGL INGILYPIDI NFAIDSDNGD ILYFDNKYVE GNEDNFIPEL Q SWIKAFYN SNYNSQYLIT DDLYLTAFLG ELTVLLPLEI MNIRLGNARS RRVHSFHIRE YLASANRLDE FMPYLNKSQQ LW LYRNIQF LRRNSGKQAI FDQLVEKILT ERGIPVISYT LEQNTANMPP NLKPDVEMVK HDMNIPVVQP GQDKNTVLEI LTR EDPIAR DNPLVKYDAE KEITEQVSTS AFSNLPTRVL DSEVIDRSNS SVRNLMNVLL NNWLHLSTSG RYRAYVSIPN PRTG EYMLM TVKDAFIVML YSYGRTKDFK FDKIPSVPAY EVLRNPFPTY EELQVQVDKK LVGPNLLGAV RDNFTPMGDY ISTEL FYTD SSRFHKEYLK GWELYSFNDH KDIRCYLEQS VKTFYINRMC KLVNEDISFE QYFKDSAFAI ADLTTSEYEQ LVVDCI NIA TGSDLNRVIT LGEIQRELLR LVSKLSSYPL QFLRNVSFTD FHVLGIVMPR LGDYGAAGNA NHIVPINNIN VLTYRTS AE MTYYINDVDI IPFNDWSYWA EDRWWINPFV GIKELSLSEY TYQIPSMVNV WQYTEEVSEH TPPDGGLGQY NNSTDPNW P NLP

UniProtKB: PHIKZ128

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Macromolecule #3: PHIKZ161

MacromoleculeName: PHIKZ161 / type: protein_or_peptide / ID: 3 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas phage phiKZ (virus)
Molecular weightTheoretical: 22.584465 KDa
SequenceString: MIPPIGTKGR YELISPFDKL IKPNTLYVNS AVRAFIDIEN NGRNVYDTYY KPLNIDISEY NKDRENGEYI VTLTTEQYNP VYVPSSYIA RYPDLNGVPY QQTVLSASLG ALPVTLDLTN LQAKVAGVIS DVIGVEPVIN LGSMPLMSDV TPQQHEAAEN A REAKIKDR ...String:
MIPPIGTKGR YELISPFDKL IKPNTLYVNS AVRAFIDIEN NGRNVYDTYY KPLNIDISEY NKDRENGEYI VTLTTEQYNP VYVPSSYIA RYPDLNGVPY QQTVLSASLG ALPVTLDLTN LQAKVAGVIS DVIGVEPVIN LGSMPLMSDV TPQQHEAAEN A REAKIKDR ETDYARIVKL EADNTSLSQR LAIAENLLIE NGIIS

UniProtKB: PHIKZ161

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Macromolecule #4: PHIKZ088

MacromoleculeName: PHIKZ088 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas phage phiKZ (virus)
Molecular weightTheoretical: 40.503461 KDa
SequenceString: MAASEFLDQI IQNIGQSPRD KAISDSIRGL NIIGRNSTIA PNTENHGFTF FTRPILNLSY DNCKIDRKLT MLLNDNPYSL SRSIRAILD PWSNRDGMNA VDVDPLNPFI PLLSNNLVSL TGWEDFQLNL ATTNPGIYRD AMSYVDDVPY QFNTFDLQAS F RNMEGDPI ...String:
MAASEFLDQI IQNIGQSPRD KAISDSIRGL NIIGRNSTIA PNTENHGFTF FTRPILNLSY DNCKIDRKLT MLLNDNPYSL SRSIRAILD PWSNRDGMNA VDVDPLNPFI PLLSNNLVSL TGWEDFQLNL ATTNPGIYRD AMSYVDDVPY QFNTFDLQAS F RNMEGDPI TNLLYMWERY SALVKEGRLW PYPEMILLKE VDYNTRVWRI VTDVTRTYIT RIFCSGASIF MNANTGRTGD FI GDGSETP FQNANDLLSV SIRCMGMDVY DYILFYEFND LVEDFNPNMS DERRYTQMQK IKIYEREYFS RSKVYPYINT DNS ELEWWI SKEDYNAMLP GLLRNPPPPQ KEG

UniProtKB: PHIKZ088

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Macromolecule #5: PHIKZ182

MacromoleculeName: PHIKZ182 / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas phage phiKZ (virus)
Molecular weightTheoretical: 73.539461 KDa
SequenceString: MATDSKPIWL RQAFLLPTPD ERQVGFGSRS KRRNAASAAF KFTNTSPGGN WAINPLPQYT RYADIRLPGI GRTYDERHLG MGRYYSEAH DDTAQLIHMS FGVPRFSSWA SFFTNFYDRS AAQFANSGTT SRAWYELGNA AGYLVSLPLQ PFIIGVTAAN R VINFLAKT ...String:
MATDSKPIWL RQAFLLPTPD ERQVGFGSRS KRRNAASAAF KFTNTSPGGN WAINPLPQYT RYADIRLPGI GRTYDERHLG MGRYYSEAH DDTAQLIHMS FGVPRFSSWA SFFTNFYDRS AAQFANSGTT SRAWYELGNA AGYLVSLPLQ PFIIGVTAAN R VINFLAKT QPSKWYYFKP TMHAYWSAVN TLANEFAINL GIRPRVFDGI QKDLEIPGQT VTPADLANFH RMFPGLIRED GS FDIMSLS GRTQRKSDEA KKIWDTLVEK ARNQDDLHNV VDNYLRSSFK DNGDSKVSAR DYLLSYIEVD RKPGAGVIDS ENF SSWSKL KNVYDFVVGA QRDGSQFVTF RVEHNGEVSE SFTNTTTDIG VAQTLNSKVQ EGRAAQFNFM QGNVTEMMGN VTRG VMDFI GGALDSVNMA GLATLAGSAF VDVPEHWENS VASLPTASYT IPLVCPYGNV MSRFLDIFIP LAMILPMGLP RSAGR SAYT SPFICQIFHQ GRVQRQLGIV DSITIRRGTG NIGWNAENHM LNCEVQINVK DLSKIMHIPL KAGFADGSII DTAFKA AGA TIGEAVAEGI GADGDRGIGV GLALTDGSVW DEQSLFQDYT ATLTSQSWSD FYYVGKRMNL NITRATQSFK NWRSPSN FL SWVLDGEPAR ALSAFANTTG RF

UniProtKB: PHIKZ182

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Macromolecule #6: PHIKZ049

MacromoleculeName: PHIKZ049 / type: protein_or_peptide / ID: 6 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas phage phiKZ (virus)
Molecular weightTheoretical: 15.212229 KDa
SequenceString:
MAVNIRDIQA GDRISFEVYP YAILGTNFKN VTVEGIVTAS VASAMGFDVA AAGQQVYPSL PAGSAPVDPT QYNYIRVRMA NNESVMFIG IPWIVANTLE RVDGKRLTLV WDDVDNKMYD RILLAVRQNN APPTSVTYE

UniProtKB: PHIKZ049

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Macromolecule #7: PHIKZ029

MacromoleculeName: PHIKZ029 / type: protein_or_peptide / ID: 7 / Number of copies: 4 / 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 #8: PHIKZ062

MacromoleculeName: PHIKZ062 / type: protein_or_peptide / ID: 8 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas phage phiKZ (virus)
Molecular weightTheoretical: 15.352444 KDa
SequenceString:
MPKTIPTVSV SGWIDTPEQV ADKTISYFIL SNPSQDIINR ERSTSLPYLL KVYANDYPQL EIELRRILSD KFNIVFGNEL IDSNVIVKD ESNTGDGKMS ITFTATILVQ GKPVQIGKLV RYQYSNILEI ARLNNGE

UniProtKB: PHIKZ062

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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: 3.65 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 22539
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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