[English] 日本語
Yorodumi
- EMDB-38151: Cryo-EM structure of a bacteriophage tail- spike protein against ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-38151
TitleCryo-EM structure of a bacteriophage tail- spike protein against Klebsiella pneumoniae K64,ORF41(K64-ORF41) in 5 mM EDTA
Map dataCryo-EM structure of a bacteriophage tail- spike protein against Klebsiella pneumoniae K64,ORF41(K64-ORF41) in 5mM EDTA
Sample
  • Complex: K64-ORF41 in 5 mM EDTA
    • Protein or peptide: Probable tail spike protein
KeywordsK64-ORF41 / depolymerase / cryo-EM / Klebsiella pneumoniae K64 / capsule polysaccharide / EDTA / LYASE
Function / homology
Function and homology information


symbiont entry into host cell via disruption of host cell glycocalyx / symbiont entry into host cell via disruption of host cell envelope / virus tail / outer membrane / adhesion receptor-mediated virion attachment to host cell
Similarity search - Function
Tail spike TSP1/Gp66, N-terminal domain / Tail spike TSP1/Gp66 receptor binding N-terminal domain / Bacteriophage T7 tail fibre protein / Phage T7 tail fibre protein, N-terminal domain / Trimeric autotransporter adhesin YadA-like, stalk domain / Coiled stalk of trimeric autotransporter adhesin / Serralysin-like metalloprotease, C-terminal
Similarity search - Domain/homology
Probable tail spike protein
Similarity search - Component
Biological speciesKlebsiella phage SH-Kp 152410 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.5 Å
AuthorsXie Y / Huang T / Zhang Z / Tao X
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32200803 China
CitationJournal: Int J Biol Macromol / Year: 2024
Title: Structural and functional basis of bacteriophage K64-ORF41 depolymerase for capsular polysaccharide degradation of Klebsiella pneumoniae K64.
Authors: Tianyun Huang / Zhuoyuan Zhang / Xin Tao / Xinyu Shi / Peng Lin / Dan Liao / Chenyu Ma / Xinle Cai / Wei Lin / Xiaofan Jiang / Peng Luo / Shan Wu / Yuan Xie /
Abstract: Capsule polysaccharide is an important virulence factor of Klebsiella pneumoniae (K. pneumoniae), which protects bacteria against the host immune response. A promising therapeutic approach is using ...Capsule polysaccharide is an important virulence factor of Klebsiella pneumoniae (K. pneumoniae), which protects bacteria against the host immune response. A promising therapeutic approach is using phage-derived depolymerases to degrade the capsular polysaccharide and expose and sensitize the bacteria to the host immune system. Here we determined the cryo-electron microscopy (cryo-EM) structures of a bacteriophage tail-spike protein against K. pneumoniae K64, ORF41 (K64-ORF41) and ORF41 in EDTA condition (K64-ORF41), at 2.37 Å and 2.50 Å resolution, respectively, for the first time. K64-ORF41 exists as a trimer and each protomer contains a β-helix domain including a right-handed parallel β-sheet helix fold capped at both ends, an insertion domain, and one β-sheet jellyroll domain. Moreover, our structural comparison with other depolymerases of K. pneumoniae suggests that the catalytic residues (Tyr528, His574 and Arg628) are highly conserved although the substrate of capsule polysaccharide is variable. Besides that, we figured out the important residues involved in the substrate binding pocket including Arg405, Tyr526, Trp550 and Phe669. This study establishes the structural and functional basis for the promising phage-derived broad-spectrum activity depolymerase therapeutics and effective CPS-degrading agents for the treatment of carbapenem-resistant K. pneumoniae K64 infections.
History
DepositionNov 27, 2023-
Header (metadata) releaseSep 4, 2024-
Map releaseSep 4, 2024-
UpdateJun 25, 2025-
Current statusJun 25, 2025Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_38151.png

Downloads & links

-
Map

FileDownload / File: emd_38151.map.gz / Format: CCP4 / Size: 75.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of a bacteriophage tail- spike protein against Klebsiella pneumoniae K64,ORF41(K64-ORF41) in 5mM EDTA
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 270 pix.
= 229.77 Å		0.85 Å/pix.
x 270 pix.
= 229.77 Å		0.85 Å/pix.
x 270 pix.
= 229.77 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.851 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0113
Minimum - Maximum-0.035592977 - 0.07809266
Average (Standard dev.)0.00004244704 (±0.0034356304)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions270270270
Spacing270270270
CellA=B=C: 229.77 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: half1 map of ORF41(K64-ORF41) in 5mM EDTA

Fileemd_38151_half_map_1.map
Annotationhalf1 map of ORF41(K64-ORF41) in 5mM EDTA
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half2 map of ORF41(K64-ORF41) in 5mM EDTA

Fileemd_38151_half_map_2.map
Annotationhalf2 map of ORF41(K64-ORF41) in 5mM EDTA
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : K64-ORF41 in 5 mM EDTA

EntireName: K64-ORF41 in 5 mM EDTA
Components
  • Complex: K64-ORF41 in 5 mM EDTA
    • Protein or peptide: Probable tail spike protein

-
Supramolecule #1: K64-ORF41 in 5 mM EDTA

SupramoleculeName: K64-ORF41 in 5 mM EDTA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Klebsiella phage SH-Kp 152410 (virus)

-
Macromolecule #1: Probable tail spike protein

MacromoleculeName: Probable tail spike protein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Klebsiella phage SH-Kp 152410 (virus)
Molecular weightTheoretical: 112.2515 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGSSHHHHHH SSGLVPRGSH MDQDTKTIIQ YPTSGDEYDI PFDYLSRKFV RVSLVSNTQR VLLDNITDYR YVSRTRVKLL VSTDGYSRV EIRRFTSASE MVVDFSDGSV LRATDLNVSA LQSAHIAEEA RDLFSTSLSI GQLSYFDAKG LQIKNVAAGV D NTDAVTVQ ...String:
MGSSHHHHHH SSGLVPRGSH MDQDTKTIIQ YPTSGDEYDI PFDYLSRKFV RVSLVSNTQR VLLDNITDYR YVSRTRVKLL VSTDGYSRV EIRRFTSASE MVVDFSDGSV LRATDLNVSA LQSAHIAEEA RDLFSTSLSI GQLSYFDAKG LQIKNVAAGV D NTDAVTVQ QLNKIIADVV TTIPDSVADN IRGLWARVLG DIGITLVDGS FETGATITTR TQALWSISGR KCYTWAGALP KV VPENSTP ESTGGISETA WVDSSSKALG VLLAGPSGAE RVGLKQGGTV QDAINWLTFD SFDIVKDGSK DVTADIMAAC VVA NDLGLD IKQNDGTYLV SGNPVWPVYN SLDLNGVTLK LAAGFTGYFA LTQKDSTTVY GPTSPIVQAI NAAGGRTAGS GVLE GLVNS TELNGKFLFM EGADVLYYSR GTAKYWWTNT YLSNRGKLSD NLKYGVSAIT KITAVTPRTK IVYYRLPNLD FGNGP ANNG VIRVLNNTRF IMQGGSISNR PLKDVSKSPV IISLNYCAAF KAYDFFDPYP AFAVDSNNSL VYSYTLNFND IADAVF ENF NSQGYGWGVV GGQRSTNITY RDCNLNRVDM HNPYMGYLKV LDTRLGTWGI NASGMGDMYL ERVTVDLDDS AHGGHRE HE GIINARGDFG GFHDGGLYIK DLTIVGEASA FEATSGHPVA LVSAYSFNAS LAYIPESSPV TPWGFKEVIV EGLHCPFK R TGRRFNSIIS APSIQFTVYH PMRVKLEDCN FNSTAFEKFD LRGWRVTPYN PSKVGIANTL AFRPTNFVDV KDCSMVGLE FTRPTSAYDY SNFDVNLVNV KNVEEHSLSP FTLYTNQCGR YNLVGCGLQQ IVDKSMTSGE RANRRSTFSV TGGTWNSLSG NPTDITYGN GYDIPVVATG VMFVGPYSQT EVTGANLNVA EFVQASGCKF LSSGPTYIQP LLWSGAGGPT GASANFNVAR G NTLGLNIS AVNGETSQVI AATLVIPQGF STGPAAGTTY GFAVEKNINY QLGLNARSLK ANVGLVRCSD TITGVYLNA

UniProtKB: Probable tail spike protein

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 54.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 1.1 µm

+
Image processing

CTF correctionType: NONE
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 371259
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

+
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://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