[English] 日本語
Yorodumi
- EMDB-39002: Composite cryo-EM map of PhiKZ capsid after applying the "block-b... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-39002
TitleComposite cryo-EM map of PhiKZ capsid after applying the "block-based" reconstruction method
Map data
Sample
  • Virus: Phikzvirus phiKZ
    • Protein or peptide: x 11 types
KeywordsphiKZ / capsid protein / viral assembly / Pseudomonas aeruginosa / jumbo phage / VIRUS
Biological speciesPhikzvirus phiKZ
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsYang Y / Shao Q / Guo M / Han L / Zhao X / Wang A / Li X / Wang B / Pan J / Chen Z ...Yang Y / Shao Q / Guo M / Han L / Zhao X / Wang A / Li X / Wang B / Pan J / Chen Z / Fokine A / Sun L / Fang Q
Funding support China, 4 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2021YFC2302500 China
Shenzhen Medical Research FundD2301008 China
Shenzhen Science and Technology ProgramZDSYS20230626091203007 China
R&D Program of Guangzhou LaboratorySRPG22-003 China
CitationJournal: Nat Commun / Year: 2024
Title: Capsid structure of bacteriophage ΦKZ provides insights into assembly and stabilization of jumbo phages.
Authors: Yashan Yang / Qianqian Shao / Mingcheng Guo / Lin Han / Xinyue Zhao / Aohan Wang / Xiangyun Li / Bo Wang / Ji-An Pan / Zhenguo Chen / Andrei Fokine / Lei Sun / Qianglin Fang /
Abstract: Jumbo phages are a group of tailed bacteriophages with large genomes and capsids. As a prototype of jumbo phage, ΦKZ infects Pseudomonas aeruginosa, a multi-drug-resistant (MDR) opportunistic ...Jumbo phages are a group of tailed bacteriophages with large genomes and capsids. As a prototype of jumbo phage, ΦKZ infects Pseudomonas aeruginosa, a multi-drug-resistant (MDR) opportunistic pathogen leading to acute or chronic infection in immunocompromised individuals. It holds potential to be used as an antimicrobial agent and as a model for uncovering basic phage biology. Although previous low-resolution structural studies have indicated that jumbo phages may have more complicated capsid structures than smaller phages such as HK97, the detailed structures and the assembly mechanism of their capsids remain largely unknown. Here, we report a 3.5-Å-resolution cryo-EM structure of the ΦKZ capsid. The structure unveiled ten minor capsid proteins, with some decorating the outer surface of the capsid and the others forming a complex network attached to the capsid's inner surface. This network seems to play roles in driving capsid assembly and capsid stabilization. Similar mechanisms of capsid assembly and stabilization are probably employed by many other jumbo viruses.
History
DepositionFeb 3, 2024-
Header (metadata) releaseAug 14, 2024-
Map releaseAug 14, 2024-
UpdateAug 14, 2024-
Current statusAug 14, 2024Processing site: PDBc / Status: Released

-
Structure visualization

Downloads & links

-
Map

FileDownload / File: emd_39002.map.gz / Format: CCP4 / Size: 3.7 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.6 Å
Density
Contour LevelBy AUTHOR: 0.0165
Minimum - Maximum-0.08208482 - 0.12954655
Average (Standard dev.)0.0005346959 (±0.0042417184)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-500-500-500
Dimensions100010001000
Spacing100010001000
CellA=B=C: 1600.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Sample components

+
Entire : Phikzvirus phiKZ

EntireName: Phikzvirus phiKZ
Components
  • Virus: Phikzvirus phiKZ
    • Protein or peptide: gp28
    • Protein or peptide: gp35
    • Protein or peptide: gp85
    • Protein or peptide: gp86
    • Protein or peptide: gp91
    • Protein or peptide: gp93
    • Protein or peptide: gp119
    • Protein or peptide: gp120
    • Protein or peptide: gp162
    • Protein or peptide: gp184
    • Protein or peptide: gp244

+
Supramolecule #1: Phikzvirus phiKZ

SupramoleculeName: Phikzvirus phiKZ / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 169683 / Sci species name: Phikzvirus phiKZ / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Pseudomonas aeruginosa (bacteria)
Virus shellShell ID: 1 / T number (triangulation number): 27

+
Macromolecule #1: gp28

MacromoleculeName: gp28 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Phikzvirus phiKZ
Molecular weightTheoretical: 36.511871 KDa
SequenceString: MFLLPYETTV CKTLYNPTGG GKLYPKQYVD QIENAIKKAN VYLPIPPVDA RNGETLEHSG QITPVDDFED IKKFTQIVNI GDRDNPKLV VDARLYKKIE QRTGIPRIIQ QNEWQFQYIR MALNIKLLRE GPDFLHRLGD IPVKVFYNWI SGILTQKYSL P PESTQAIW ...String:
MFLLPYETTV CKTLYNPTGG GKLYPKQYVD QIENAIKKAN VYLPIPPVDA RNGETLEHSG QITPVDDFED IKKFTQIVNI GDRDNPKLV VDARLYKKIE QRTGIPRIIQ QNEWQFQYIR MALNIKLLRE GPDFLHRLGD IPVKVFYNWI SGILTQKYSL P PESTQAIW VICAVYYFAM QDDDLTEPGQ ERDRLIPIIS RLTYIPAGFI ADVIDTLGPL HNAGDLAYEI STNGRSIRMG KL KFSDLQL LVSPSWFGTA SRENVGVALE HMPTYITLIY MALADRSYRK TVLSQKVEMI SRSDDASRFI NLVNEAVSSQ FVK

+
Macromolecule #2: gp35

MacromoleculeName: gp35 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Phikzvirus phiKZ
Molecular weightTheoretical: 29.713783 KDa
SequenceString: MAKRKARAVS APVTLSEISE IPNEVTNAED SVNELETTPT EIVSTESSEN ENTTADSENT AATDSTTDEE SEDTSSTEAN GDGESEEPD LSENQEDPKE PIETPEEPVE DDDGSGDPDG GTSEEKPTEG DPEDPEEPTE PTDPEEPTDP VDPVEPPPEE P KAFQLNLA ...String:
MAKRKARAVS APVTLSEISE IPNEVTNAED SVNELETTPT EIVSTESSEN ENTTADSENT AATDSTTDEE SEDTSSTEAN GDGESEEPD LSENQEDPKE PIETPEEPVE DDDGSGDPDG GTSEEKPTEG DPEDPEEPTE PTDPEEPTDP VDPVEPPPEE P KAFQLNLA TVKSQFGDLP TYWAIELIKR YFSAPPAIYI PDVVDNPDFK IMVQQVKFFG NGLRPIYNSK NMITFTTMLE GA SEATILE DMKKQQPALL SLLPWYDPNA EIDK

+
Macromolecule #3: gp85

MacromoleculeName: gp85 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Phikzvirus phiKZ
Molecular weightTheoretical: 16.438799 KDa
SequenceString:
MQQLGFELSR ILKQLPNLGG SDRKTRAMLL ANAVALQIPF ETLLDFDEQQ DKAVAKFKKI LSKVNENIAV DTKLAVTYFN NILRIRQSL ITGITDPCLV KAVLTSDTAN DYLTVDDVNI VSAVVNGPDY NRIQADMGNA LNQLIGSIDE

+
Macromolecule #4: gp86

MacromoleculeName: gp86 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Phikzvirus phiKZ
Molecular weightTheoretical: 48.893793 KDa
SequenceString: MSEVKPMSHV KEVDVEEEKL FFDENQPEMV EGEEETVSSA SAPEVLAKMC VAVEAIHQLS DIYAITKLEG VSKPDVDGIR ALVKRMSTE GFEAPKKAVA SLEQYASMFT PTRSTLNVTI SQEAVMATII NTLKTWFEKL MELFAKLIRW ISDFKKRDVV V ATRYGKIV ...String:
MSEVKPMSHV KEVDVEEEKL FFDENQPEMV EGEEETVSSA SAPEVLAKMC VAVEAIHQLS DIYAITKLEG VSKPDVDGIR ALVKRMSTE GFEAPKKAVA SLEQYASMFT PTRSTLNVTI SQEAVMATII NTLKTWFEKL MELFAKLIRW ISDFKKRDVV V ATRYGKIV RAVDQARTLF QELLVKNRLG NRKDALLEKF DAIAQSIIDD PKILASRIYA AAFGSVYYQK EIININNEAR TE LGTMEKL VGTIIEYVNY NGDDYRALMP IANIREIGKL ATRCNELSTV YPDRSSIPDF PDKNFWKNSH LLKDRFVAPL DDL LKAYRN SSDALRKLKQ LSRNYSQETI DAIGESVQLI NTSLEGMRRI TDTMFEYSQA QYLAASCVLN YYGKCAQVVS EDYK IHGFN DAIREWQRRF DKVIDDFKRG YAM

+
Macromolecule #5: gp91

MacromoleculeName: gp91 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Phikzvirus phiKZ
Molecular weightTheoretical: 20.817568 KDa
SequenceString:
MEGIDMPATN AVRPFGRNYS GGQQQAISRF TARPGDPQVE ELYLIFTNFP AQTAYWEFHK KVLACAIRLF SGNYNWFILQ DNNSNIDSY NYQFLLDTVR YIATGHRRIS ITQWPMLLAT EPDAGAQLIE PRAEIATLFN ELKLDLDTVS MIQNWVKHKN G MNDLMYTL HLLFGSVEVI DKD

+
Macromolecule #6: gp93

MacromoleculeName: gp93 / type: protein_or_peptide / ID: 6 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Phikzvirus phiKZ
Molecular weightTheoretical: 47.656105 KDa
SequenceString: MSLLKMLDKL SLESIEDQGT TIHGDVELVV ENETSADVSS VLAEVDQIEN NPVEEVLDAD DAVQPTALDT EVTIVQAEDE LGLIEDAKE ALEKFQGLLL QAGEDGISRQ AAAFMHVGME SIDRILGIEK SGLTAALENY DASPRSAIQK AAVISLEDLK E KLKEAGKK ...String:
MSLLKMLDKL SLESIEDQGT TIHGDVELVV ENETSADVSS VLAEVDQIEN NPVEEVLDAD DAVQPTALDT EVTIVQAEDE LGLIEDAKE ALEKFQGLLL QAGEDGISRQ AAAFMHVGME SIDRILGIEK SGLTAALENY DASPRSAIQK AAVISLEDLK E KLKEAGKK ALEIIKKIVA MIKQKIKDFN PKLIALDMRI TKTIDAIKSL KAGDLKKEEI KFTPSEYMVS SSGFIANNPK TI ADFMTVF STQYVSALRK YGELGVRYLK GDKSIDIDQV TSDLQAKMAE DINKAVEKAP GNVKLEVTSS KSGVNKWEVV EGD GETDLH EVEVDVRAPS KILAHLNILK GLVIKLQDFN KIDYKIAENL EKALADWNPD EAGMSKETAR DALNIGGIDN SALV NYIAK CIAAQYTFIV KHELAAYGKE TSKAPENDEK

+
Macromolecule #7: gp119

MacromoleculeName: gp119 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Phikzvirus phiKZ
Molecular weightTheoretical: 20.25399 KDa
SequenceString:
MTQVLVMPKA VFESYKTAGV QFNKLLDTNY IVSETSVNDL AEIHQALTAF PFLLPEKLDI KLAVSPIIKV AELGEIDGPE QFKMKDLHN RLESRLATNE LRDAGNRNLV YDYYLYPVDE NLWVAVQQSA HIASSDPRRV SIQLNHTFFD SMINEMLNTR P RESVASTQ IFTYYLESC

+
Macromolecule #8: gp120

MacromoleculeName: gp120 / type: protein_or_peptide / ID: 8 / Number of copies: 27 / Enantiomer: LEVO
Source (natural)Organism: Phikzvirus phiKZ
Molecular weightTheoretical: 83.022883 KDa
SequenceString: MSVHALRELF KHKGEKNYEV FSMEDFIGRL ESEIGLNDSV VSQGRSLISS ISHENFGTVQ ATDIQDAAAI YNKMQMLVND YGFERVSSS DPQVRAREER VRENQITAAT MAAIACADET KYIRALRGIT KAKASNEDHV KVVQHQFNGP AGGIQVFENG V GLENYNEK ...String:
MSVHALRELF KHKGEKNYEV FSMEDFIGRL ESEIGLNDSV VSQGRSLISS ISHENFGTVQ ATDIQDAAAI YNKMQMLVND YGFERVSSS DPQVRAREER VRENQITAAT MAAIACADET KYIRALRGIT KAKASNEDHV KVVQHQFNGP AGGIQVFENG V GLENYNEK SQRDFRVVTI GYNLAASRQD EFAERIYPTT VINPIEGGVV QVLPYIAVMK DVYHEVSGVK MDNEEVNMVE AY RDPSILD DESIALIPAL DPAGSNADFF VDPALVPPYT IKNEQNLTIT TAPLKANVRL DLMGNSNANL LIQRGMLEVS DTI DPAGRL KNLFVLLGGK VVKFKVDRLP RAVFQPDLVG DTRNAVIRFD SDDLVVSGDT TFIDGSADGV INDLKTAKLS LRLS VGFGG TISLSKGDSK FGATDTYVDK VLNEDGQVMD NADPAVKAIL DQLTDLAVIG FELDTRFTNT NRRQRGHLLQ TRALQ FRHP IPMHAPVTLP MDTMTDEGPG EVVKALTVNT NIRNSNNAVK RMLNYLAQLR EVVHNGYNRP KFGIIEGALS AVMRPT YRY KELDLEKVID TIKSKDRWDD VCAAILNCVK AELFPAHRDS NIEAAFRVIS GNQDETPMYL FCSDKEIANY LMTKGDD RT LGAYLKYDIV STNNQLFDGK LVVIPTRAVQ QENDILSWGQ FFYVSTVIAD LPITRGGHQV TREIAAIPFN LHVNNIPF A LEFKITGFQK VMGETQFNGK LADLKP

+
Macromolecule #9: gp162

MacromoleculeName: gp162 / type: protein_or_peptide / ID: 9 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Phikzvirus phiKZ
Molecular weightTheoretical: 57.705137 KDa
SequenceString: MAKKKTVPAM DFFASLERVS DAEDKNVNLD VGKELPEQLK DDEDGKVNPC DEVTNVVTNT PIDVCKGPDV DGTADKINDK KIHVSQGLK EFQVAKGDRV ENEITETADE MITKVSDTKD LNVSTKKPHQ IADVPSNEDI SIMEANETEQ LDHGYDATAL L ETTEDIIT ...String:
MAKKKTVPAM DFFASLERVS DAEDKNVNLD VGKELPEQLK DDEDGKVNPC DEVTNVVTNT PIDVCKGPDV DGTADKINDK KIHVSQGLK EFQVAKGDRV ENEITETADE MITKVSDTKD LNVSTKKPHQ IADVPSNEDI SIMEANETEQ LDHGYDATAL L ETTEDIIT GELDDHLESL SVEMFTIVNE LTKVESVQTA LENYIGLVSN RHHRGHDVDH DLAKAISIAL ESFDYKYFNN TV PSMESFI SPLTRPKASI EVLDNLQAKA KEVSTVALDF IKKLIRIVVE TYQRIRQNVS NQIERVNKIM KRVKENELPD EVR TIAIPR DLILGDTGES WVGVDPVQGV TVIRNLFDSI EKNGLRALKA ALAGKTTDDK ALALAKGMFG TATKINANGV RYAS PVVPG NRVYTFGKDK AAVDFSILDA PGKPNYGITV ELLVDKNVVM AQLKAVHNLL NHLNNIRGIS KESTAEIIAQ MTDKE ATNV GKAYLTGTTE ASNDLFKCVM IWITVLEKLV DSEIKETE

+
Macromolecule #10: gp184

MacromoleculeName: gp184 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Phikzvirus phiKZ
Molecular weightTheoretical: 25.300836 KDa
SequenceString: MSKPNLEWLA SLESKEAKST VDSSDMDNDQ KEGSDKSQQD EATEPEKKIT ATDVQIAIEE YARIRALTTT KDLPTDPEPG DTYHVNGVD WIYQEDGGWV TMQGIYGHEH FDENGLNIEA SGIDQKSGAT KRYVVTGYNA QTNPAAMPGD NLTECVILMQ N GLVPEVGV ...String:
MSKPNLEWLA SLESKEAKST VDSSDMDNDQ KEGSDKSQQD EATEPEKKIT ATDVQIAIEE YARIRALTTT KDLPTDPEPG DTYHVNGVD WIYQEDGGWV TMQGIYGHEH FDENGLNIEA SGIDQKSGAT KRYVVTGYNA QTNPAAMPGD NLTECVILMQ N GLVPEVGV NGLTADCLLK IVKDLFEGYQ AGPFACEENQ VVINSMDRAL SAIHQRLVRR KEQGTEGTYS GN

+
Macromolecule #11: gp244

MacromoleculeName: gp244 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Phikzvirus phiKZ
Molecular weightTheoretical: 13.427183 KDa
SequenceString:
MPTYIELINI VNDDTPEDDA VISDLMSQMN DKQTVLDSCR INHKGNAYFK FHVKGSISKD KLKALNETLK DSNLVVTDAS TQRGFMPPN KFDDITYTEE SVGYRAMVWT SFTIEKLLV

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
GridModel: EMS Lacey Carbon / Material: COPPER / Support film - Material: CARBON / Support film - topology: LACEY
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (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: 2.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 64000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 903900
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlc1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more