[English] 日本語
Yorodumi
- EMDB-51507: Cryo-EM map of dimeric AvrSr35 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-51507
TitleCryo-EM map of dimeric AvrSr35
Map dataCryo-EM map of dimeric AvrSr35
Sample
  • Complex: Dimeric complex of wheat stem rust effector AvrSr35
    • Protein or peptide: Avirulence factor
KeywordsDimer / plant immunity / ANTIFUNGAL PROTEIN
Function / homologyAvirulence factor
Function and homology information
Biological speciesPuccinia graminis f. sp. tritici (fungus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsMacha A / Gunkel M / Lawson AW / Schulze-Lefert P / Behrmann E
Funding support Germany, 2 items
OrganizationGrant numberCountry
German Research Foundation (DFG)INST 216/949-1 FUGG Germany
German Research Foundation (DFG)INST 216/512/1 FUGG Germany
CitationJournal: To Be Published
Title: A versatile protocol for purifying recombinant proteins from Nicotiana benthamiana
Authors: Lawson AW / Macha A / Neumann U / Gunkel M / Chai JJ / Behrmann E / Schulze-Lefert P
History
DepositionSep 9, 2024-
Header (metadata) releaseSep 24, 2025-
Map releaseSep 24, 2025-
UpdateSep 24, 2025-
Current statusSep 24, 2025Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_51507.png

Downloads & links

-
Map

FileDownload / File: emd_51507.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM map of dimeric AvrSr35
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 320 pix.
= 275.84 Å		0.86 Å/pix.
x 320 pix.
= 275.84 Å		0.86 Å/pix.
x 320 pix.
= 275.84 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.862 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.35
Minimum - Maximum-6.433984 - 9.234494
Average (Standard dev.)-0.00012976183 (±0.14955808)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 275.84 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: DeepEMhancer-sharpened cryo-EM map of dimeric AvrSr35

Fileemd_51507_additional_1.map
AnnotationDeepEMhancer-sharpened cryo-EM map of dimeric AvrSr35
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Cryo-EM map of dimeric AvrSr35 - odd half-map

Fileemd_51507_half_map_1.map
AnnotationCryo-EM map of dimeric AvrSr35 - odd half-map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Cryo-EM map of dimeric AvrSr35 - even half-map

Fileemd_51507_half_map_2.map
AnnotationCryo-EM map of dimeric AvrSr35 - even half-map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Dimeric complex of wheat stem rust effector AvrSr35

EntireName: Dimeric complex of wheat stem rust effector AvrSr35
Components
  • Complex: Dimeric complex of wheat stem rust effector AvrSr35
    • Protein or peptide: Avirulence factor

-
Supramolecule #1: Dimeric complex of wheat stem rust effector AvrSr35

SupramoleculeName: Dimeric complex of wheat stem rust effector AvrSr35 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Puccinia graminis f. sp. tritici (fungus)
Molecular weightTheoretical: 120 KDa

-
Macromolecule #1: Avirulence factor

MacromoleculeName: Avirulence factor / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Puccinia graminis f. sp. tritici (fungus)
Molecular weightTheoretical: 71.213438 KDa
Recombinant expressionOrganism: Nicotiana benthamiana (plant)
SequenceString: MAMRNFAADR VHGVESVISG SKSSSNPMAL SKSMDKPDTS DLVDSNVQAK NDGSRYEEDF TAKYSEQVDH VSKILKEIEE QEPGTIIID HKAFPIQDKS PKQVVNFPFP KKMITESNSK DIREYLASTF PFEQQSTILD SVKSIAKVQI DDRKAFDLQL K FRQENLAE ...String:
MAMRNFAADR VHGVESVISG SKSSSNPMAL SKSMDKPDTS DLVDSNVQAK NDGSRYEEDF TAKYSEQVDH VSKILKEIEE QEPGTIIID HKAFPIQDKS PKQVVNFPFP KKMITESNSK DIREYLASTF PFEQQSTILD SVKSIAKVQI DDRKAFDLQL K FRQENLAE LKDQIILSLG ANNGNQNWQK LLDYTNKLDE LSNTKISPEE FIEEIQKVLY KVKLESTSTS KLYSQFNLSI QD FALQIIH SKYKSNQISQ NDLLKLITED EMLKILAKTK VLTYKMKYFD SASKMGINKY ISTEMMDLDW QFSHYKTFND ALK KNKASD SSYLGWLTHG YSIKYGLSPN NERSMFFQDG RKYAELYAFS KSPHRKIIPG EHLKDLLAKI NKSKGIFLDQ NALL DKRIY AFHELNTLET HFPGITSSFT DDLKSNYRKK MESVSLTCQV LQEIGNIHRF IESKVPYHSS TEYGLFSIPK IFSIP IDYK HGEKENLVSY VDFLYSTAHE RILQDNSINQ LCLDPLQESL NRIKSNIPVF FNLASHSSPI KPSNVHEGKL NPAFLY KVV DIKAADITSL YKKVGWSHPQ FEKGGGSGGG SGGGSWSHPQ FEKGTELGST MASYPYDVPD YA

UniProtKB: Avirulence factor

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
GridModel: C-flat-1.2/1.3 / Material: COPPER / Mesh: 400 / Support film - Material: GRAPHENE OXIDE / Support film - topology: CONTINUOUS
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV
Detailsmonodisperse sample

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 4004 / Average exposure time: 43.0 sec. / Average electron dose: 42.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 96000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 4190952
CTF correctionSoftware - Name: cryoSPARC (ver. 4.4) / Software - details: patchCTF / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4) / Software - details: non-uniform refinement / Number images used: 250926
Initial angle assignmentType: OTHER / Software - Name: cryoSPARC (ver. 4.4) / Software - details: ab initio
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.4) / Software - details: non-uniform refinement
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelPDB ID:

7xds


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-9gqn:
Cryo-EM map of dimeric AvrSr35

+
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