[English] 日本語
Yorodumi
- EMDB-63716: Cryo-EM structure of bacteriophage NF5 baseplate -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-63716
TitleCryo-EM structure of bacteriophage NF5 baseplate
Map data
Sample
  • Complex: Brochothrix phage NF5
    • Protein or peptide: Gp11
    • Protein or peptide: Gp15
    • Protein or peptide: Gp14
    • Protein or peptide: Gp18
Keywordsbaseplate / phage / Viral gene product / VIRAL PROTEIN
Function / homology: / : / : / :
Function and homology information
Biological speciesBrochothrix phage NF5 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.44 Å
AuthorsPeng YN / Liu HR
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)32071209 China
CitationJournal: To Be Published
Title: structure of bacteriophage NF5
Authors: Peng YN / Liu HR
History
DepositionMar 12, 2025-
Header (metadata) releaseDec 17, 2025-
Map releaseDec 17, 2025-
UpdateDec 17, 2025-
Current statusDec 17, 2025Processing site: PDBc / Status: Released

-
Structure visualization

Supplemental images

emd_63716.png

Downloads & links

-
Map

FileDownload / File: emd_63716.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.2 Å/pix.
x 360 pix.
= 432. Å		1.2 Å/pix.
x 360 pix.
= 432. Å		1.2 Å/pix.
x 360 pix.
= 432. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.2 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.26
Minimum - Maximum-0.7965131 - 1.5610489
Average (Standard dev.)0.0023735997 (±0.065369435)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-180-180-180
Dimensions360360360
Spacing360360360
CellA=B=C: 432.00003 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_63716_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_63716_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_63716_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Brochothrix phage NF5

EntireName: Brochothrix phage NF5 (virus)
Components
  • Complex: Brochothrix phage NF5
    • Protein or peptide: Gp11
    • Protein or peptide: Gp15
    • Protein or peptide: Gp14
    • Protein or peptide: Gp18

-
Supramolecule #1: Brochothrix phage NF5

SupramoleculeName: Brochothrix phage NF5 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Brochothrix phage NF5 (virus)

-
Macromolecule #1: Gp11

MacromoleculeName: Gp11 / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Brochothrix phage NF5 (virus)
Molecular weightTheoretical: 18.744686 KDa
SequenceString:
MAEAKKGIDV ILLYRVLKNE AKEAAWKMAF QTEHSNGKSR DADSTATKDG PIQNMAAIEY DFSATSIVAV GDKHIDELDD AFDNSELVE IWEIDKAEKG TDKDVDKYKA TYFQGYVSSF SKTPNSEDAL ELEIEFAING IGQKGYATLT TDQAEVVSYV F KDTVKVEE G

UniProtKB: UNIPROTKB: D7RWD5

-
Macromolecule #2: Gp15

MacromoleculeName: Gp15 / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Brochothrix phage NF5 (virus)
Molecular weightTheoretical: 28.827814 KDa
SequenceString: MYYFKDTKKY PLETFKFIPT SAMFYDGLLL EDLIEGYTTL KVEGREMTSL TIDSTAVKVG AIVNGQKINT RSITVTYQLK NKSSQAIQD DFKKMMAHLY REEDVAIYFE DEPTTLYYGR YQSAESVDGS SNSIISSFTI FCSDPYKYGS QIVSTGVINT V LRQPVMPT ...String:
MYYFKDTKKY PLETFKFIPT SAMFYDGLLL EDLIEGYTTL KVEGREMTSL TIDSTAVKVG AIVNGQKINT RSITVTYQLK NKSSQAIQD DFKKMMAHLY REEDVAIYFE DEPTTLYYGR YQSAESVDGS SNSIISSFTI FCSDPYKYGS QIVSTGVINT V LRQPVMPT KIETTVTKSG PMKIVKGSQS ISMSRANFKS GDKVVIDFVV GKVFVNNLNR TRFLDLDSDF SNFKINSNDK VT CSSANLK IYYRSVDL

UniProtKB: UNIPROTKB: D7RWD9

-
Macromolecule #3: Gp14

MacromoleculeName: Gp14 / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Brochothrix phage NF5 (virus)
Molecular weightTheoretical: 71.315227 KDa
SequenceString: METHKIEAIL SADDRNFSSG MSRAEKAAGA VGNGADKAGK ATGKMGIGLG TMLKGAGVFA VVSAGINGVK GATSGAIDRF DTLNNSTRS FENMGFKTKE ITGTMDALKG SIQGLPTPLD GAIKNVQLLA ASTGDLGKSQ EVFAAMNNAI LGFGGTTDQV Q NTVTQLSQ ...String:
METHKIEAIL SADDRNFSSG MSRAEKAAGA VGNGADKAGK ATGKMGIGLG TMLKGAGVFA VVSAGINGVK GATSGAIDRF DTLNNSTRS FENMGFKTKE ITGTMDALKG SIQGLPTPLD GAIKNVQLLA ASTGDLGKSQ EVFAAMNNAI LGFGGTTDQV Q NTVTQLSQ ALSNGKVDAE TWNSMINGGM GPTLNALAKT FKMTTGEMKA ALSDGTISVE QFQDSLIQLN EKGGGGLKPL AK IAQDAMG GIKTGVSNAK TAVVRGLTTV ITAINDNLQK MNLGSIGEII GKIGSAAEKA LTSLATYIPV IMTAIGTFVS FFQ KHSDVL IPIITGVAAA FLALGIINTV LSIATGAVAL FGATIAFVTS PIGIVVLAIA ALVAIGMYLY RNWSSIGPLL SGIW QIFKD KTIEIFNSVI EFFKKWGPTM LIALGGPVVW IVALIVKNWE KIKAFTITIW DAIKTYYSTV WNGIKSIFTT VINFI VRFF VSQFKAAVDL MKTIWGGVSG FFKGMWDKVV SLFQGGVNNV RGWIDKLLGV FDKIKNFSLA DAGKAIIDGF VNGLKA AWE KGKKFVSGIG DWIKDHKGPI SYDKKLLIEN GQSIMFGLDK GLQGGFGDVM GNVNGMAKSI SGSFTADANQ ANRTAVT PL DLSVKIGKQD FKYFVEDISQ QMGGDAQINE QF

UniProtKB: UNIPROTKB: D7RWD8

-
Macromolecule #4: Gp18

MacromoleculeName: Gp18 / type: protein_or_peptide / ID: 4 / Number of copies: 18 / Enantiomer: LEVO
Source (natural)Organism: Brochothrix phage NF5 (virus)
Molecular weightTheoretical: 70.224508 KDa
SequenceString: MSITKISKSV MEVTADYQKL SDLNVAFYNQ DINTAILQFN VTRNDAPVPL GKSNVDGYIV LLHEDGSRIQ DNLVIEDEEH GVIQYTIPR EFLKHTGKVL GQVYIAVKGR DDTAVMRKIS FDIKQDLMTA FSAAVKLEYI KTFDDLQTKI KQRVEAIEEA I ANGEDYVA ...String:
MSITKISKSV MEVTADYQKL SDLNVAFYNQ DINTAILQFN VTRNDAPVPL GKSNVDGYIV LLHEDGSRIQ DNLVIEDEEH GVIQYTIPR EFLKHTGKVL GQVYIAVKGR DDTAVMRKIS FDIKQDLMTA FSAAVKLEYI KTFDDLQTKI KQRVEAIEEA I ANGEDYVA QMAETLNTGK KEIAATVSKA TTDVNKAATD ATKKITDTSN TAVATVNAKG DEVVKKITDA DVVQKKDALF YT DGKGFSR PVPNGITDWY QISTAGNYSI TKIEVPTNAP PVGVYFNLIV NTRTSTTRDL TAINVTTGVI YTNAMTGVDN WSG WSKVAT DKEAQMQKIT ADDGAAKVYI KATMDVYEEL LKLERGFYSI YISAGASNSP SMTVRGSVFV EAKAQWLSVQ GVGS NGKVY SIHYTGSAWI GWLIAASESI AQIPKITNDD GSSITLTNYD LLNTTDVSNF DGYVTSASNV PTTSNSGYFK RKYRS GYIE ITFAPHSQKD VFRNAYNFST KNWTGWEKIV NQSDLDKLIS DTGWITYNTV NGVLANTAFK ASGENGYNCA YRKITS NGI TRLLLRVNIS NITTASGIFA NLPNNIVVNS QTGVARTNGA NQKTVVTLRP SGDLSINIPV DFKAPDYVYQ QFEWTL

UniProtKB: UNIPROTKB: D7RWE2

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 32.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.0 µm / Nominal defocus min: 0.2 µm

+
Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.44 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 38436
Initial angle assignmentType: COMMON LINE
Final angle assignmentType: COMMON LINE
FSC plot (resolution estimation)

+
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://pdbjlvh1.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