[English] 日本語
Yorodumi
- EMDB-65858: Closed state of A8 gpJ 713 central tail fiber -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-65858
TitleClosed state of A8 gpJ 713 central tail fiber
Map data
Sample
  • Complex: Closed state of central tail fiber of bacteriophage lambda A8
    • Protein or peptide: A8 gpJ 713
    • Protein or peptide: Peptidyl-prolyl cis-trans isomerase A
KeywordsPhage Tail / VIRAL PROTEIN
Function / homology
Function and homology information


peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / protein folding / periplasmic space
Similarity search - Function
Cyclophilin-type peptidyl-prolyl cis-trans isomerase, E. coli cyclophilin A-like / Cyclophilin-type peptidyl-prolyl cis-trans isomerase, conserved site / Cyclophilin-type peptidyl-prolyl cis-trans isomerase signature. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain profile. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain / Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD / Cyclophilin-like domain superfamily
Similarity search - Domain/homology
Peptidyl-prolyl cis-trans isomerase A
Similarity search - Component
Biological speciesLambdavirus / Escherichia phage Lambda (virus) / Escherichia coli O157:H7 str. EDL933 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.49 Å
AuthorsDeng TY / Ge XF / Wang JW
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32371254, 32171190 China
CitationJournal: To Be Published
Title: Closed state of A8 gpJ 713 central tail fiber
Authors: Deng TY / Ge XF / Wang JW
History
DepositionAug 16, 2025-
Header (metadata) releaseJan 28, 2026-
Map releaseJan 28, 2026-
UpdateJan 28, 2026-
Current statusJan 28, 2026Processing site: PDBc / Status: Released

-
Structure visualization

Supplemental images

emd_65858.png

Downloads & links

-
Map

FileDownload / File: emd_65858.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 384 pix.
= 412.493 Å		1.07 Å/pix.
x 384 pix.
= 412.493 Å		1.07 Å/pix.
x 384 pix.
= 412.493 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0742 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.567
Minimum - Maximum-2.144893 - 3.55533
Average (Standard dev.)-0.00020004931 (±0.044058986)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 412.4928 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #1

Fileemd_65858_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_65858_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Closed state of central tail fiber of bacteriophage lambda A8

EntireName: Closed state of central tail fiber of bacteriophage lambda A8
Components
  • Complex: Closed state of central tail fiber of bacteriophage lambda A8
    • Protein or peptide: A8 gpJ 713
    • Protein or peptide: Peptidyl-prolyl cis-trans isomerase A

-
Supramolecule #1: Closed state of central tail fiber of bacteriophage lambda A8

SupramoleculeName: Closed state of central tail fiber of bacteriophage lambda A8
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Lambdavirus

-
Macromolecule #1: A8 gpJ 713

MacromoleculeName: A8 gpJ 713 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage Lambda (virus)
Molecular weightTheoretical: 47.315691 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: HHHHHHHHAP AAPSRIELTP GYFQITATPH LAVYDPTVQF EFWFSEKQIA DIRQVETSTR YLGTALYWIA ASINIKPGHD YYFYIRSVN TVGKSAFVEA VGRASDDAEG YLDFFKGKIT ESHLGKELLE KVELTEDNAS RLEEFSKEWK DASDKWNAMW A VKIEQTKD ...String:
HHHHHHHHAP AAPSRIELTP GYFQITATPH LAVYDPTVQF EFWFSEKQIA DIRQVETSTR YLGTALYWIA ASINIKPGHD YYFYIRSVN TVGKSAFVEA VGRASDDAEG YLDFFKGKIT ESHLGKELLE KVELTEDNAS RLEEFSKEWK DASDKWNAMW A VKIEQTKD GKHYVAGIGL SMEDTEEGKL SQFLVAANRI AFIDPANGNE TPMFVAQGNQ IFMNDVFLKR LTAPTITSGG NP PAFSLTP DGKLTAKNAD ISGSVNANSG TLNNVTINEN CQIKGKLSAN QIEGDIVKTV SKSFPRTNSY ASGTITVRIS DDQ KFDRQV MIPPVLFRGG KHENFNSNNQ QSYWYSTCRL RVTRNGQEIF NQSTTDAQGV FSSVIDMPAG QGTLTLTFTV SSSG ANNWT PTTSISDLLV VVMKKSTAGI SIS

-
Macromolecule #2: Peptidyl-prolyl cis-trans isomerase A

MacromoleculeName: Peptidyl-prolyl cis-trans isomerase A / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO / EC number: peptidylprolyl isomerase
Source (natural)Organism: Escherichia coli O157:H7 str. EDL933 (bacteria)
Molecular weightTheoretical: 20.453277 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MFKSTLAAMA AVFALSALSP AAMAAKGDPH VLLTTSAGNI ELELDKQKAP VSVQNFVDYV NSGFYNNTTF HRVIPGFMIQ GGGFTEQMQ QKKPNPPIKN EADNGLRNTR GTIAMARTAD KDSATSQFFI NVADNAFLDH GQRDFGYAVF GKVVKGMDVA D KISQVPTH DVGPYQNVPS KPVVILSAKV LP

UniProtKB: Peptidyl-prolyl cis-trans isomerase A

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI POLARA 300
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

+
Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.49 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 861098
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
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://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