[English] 日本語
Yorodumi
- EMDB-42392: Cryo-EM Structure of the Helicobacter pylori cagYdAP PR -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-42392
TitleCryo-EM Structure of the Helicobacter pylori cagYdAP PR
Map data
Sample
  • Complex: Helicobacter pylori CagYdAP PR
    • Protein or peptide: Cag pathogenicity island protein (Cag8)
    • Protein or peptide: Cag pathogenicity island protein (Cag7)
KeywordsT4SS / protein translocation / MEMBRANE PROTEIN
Biological speciesHelicobacter pylori 26695 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.6 Å
AuthorsRoberts JR
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI118932 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI039657 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)CA116087 United States
CitationJournal: Life Science Alliance / Year: 2024
Title: Subdomains of the H. pylori Cag T4SS outer membrane core complex exhibit structural independence
Authors: Roberts JR / Tran SC / Frick-Cheng AF / Bryant KN / Okoye CD / Cover TL / Ohi MD
History
DepositionOct 18, 2023-
Header (metadata) releaseApr 17, 2024-
Map releaseApr 17, 2024-
UpdateApr 17, 2024-
Current statusApr 17, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_42392.png

Downloads & links

-
Map

FileDownload / File: emd_42392.map.gz / Format: CCP4 / Size: 1 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.08 Å
Density
Contour LevelBy AUTHOR: 0.075
Minimum - Maximum-0.6425841 - 1.0777255
Average (Standard dev.)0.0012483073 (±0.012570803)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions648648648
Spacing648648648
CellA=B=C: 699.84 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_42392_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_42392_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Helicobacter pylori CagYdAP PR

EntireName: Helicobacter pylori CagYdAP PR
Components
  • Complex: Helicobacter pylori CagYdAP PR
    • Protein or peptide: Cag pathogenicity island protein (Cag8)
    • Protein or peptide: Cag pathogenicity island protein (Cag7)

-
Supramolecule #1: Helicobacter pylori CagYdAP PR

SupramoleculeName: Helicobacter pylori CagYdAP PR / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Helicobacter pylori 26695 (bacteria) / Strain: 26695 / Location in cell: membrane

-
Macromolecule #1: Cag pathogenicity island protein (Cag8)

MacromoleculeName: Cag pathogenicity island protein (Cag8) / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Helicobacter pylori 26695 (bacteria)
SequenceString: MGQAFFKKIV GCFCLGYLF L SSAIEAAA LD IKNFNRG RVK VVNKKI AYLG DEKPI TIWTS LDNV TVIQLE KDE TISYITT GF NKGWSIVP N SNHIFIQPK SVKSNLMFEK EAVNFALMT R DYQEFLKT KK LIVDAPD PKE LEEQKK ALEK EKEAK ...String:
MGQAFFKKIV GCFCLGYLF L SSAIEAAA LD IKNFNRG RVK VVNKKI AYLG DEKPI TIWTS LDNV TVIQLE KDE TISYITT GF NKGWSIVP N SNHIFIQPK SVKSNLMFEK EAVNFALMT R DYQEFLKT KK LIVDAPD PKE LEEQKK ALEK EKEAK EQAQK AQKD KREKRK EER AKNRANL EN LTNAMSNP Q NLSNNKNLS EFIKQQRENE LDQMERLED M QEQAQANA LK QIEELNK KQA EETIKQ RAKD KINIK TDKPQ KSPE DNSIEL SPS DSAWRTN LV VRTNKALY Q FILRIAQKD NFASAYLTVK LEYPQRHEV S SVIEELKK RE EAKRQKE LIK QENLNT TAYI NRVMM ASNEQ IINK EKIREE KQK IILDQAK AL ETQYVHNA L KRNPVPRNY NYYQAPEKRS KHIMPSEIF D DGTFTYFG FK NITLQPA IFV VQPDGK LSMT DAAID PNMTN SGLR WYRVNE IAE KFKLIKD KA LVTVINKG Y GKNPLTKNY NIKNYGELER VIKKLPEVR D K

-
Macromolecule #2: Cag pathogenicity island protein (Cag7)

MacromoleculeName: Cag pathogenicity island protein (Cag7) / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Helicobacter pylori 26695 (bacteria)
SequenceString: MNEENDKLET SKKAQQDSPQ DLSNEEATEA NHFENLLKES KESSDHHLDN PTETQTHFDG DKSEETQTQM DSEGNETSES SNGSLADKLF KKARKLVDNK KPFTQQKNLD EETQELNEED DQENNEYQEE TQTDLIDDET SKKTQQHSPQ DLSNEEATEA NHFENLLKES ...String:
MNEENDKLET SKKAQQDSPQ DLSNEEATEA NHFENLLKES KESSDHHLDN PTETQTHFDG DKSEETQTQM DSEGNETSES SNGSLADKLF KKARKLVDNK KPFTQQKNLD EETQELNEED DQENNEYQEE TQTDLIDDET SKKTQQHSPQ DLSNEEATEA NHFENLLKES KESSDHHLDN PTETQTNFDG DKSEETQTQM DSEGNETSES SNGSLADKLF KKARKLVDNK KPFTQQKNLD EETQELNEED DQENNEYQEE TQTDLIDDET SKKTQQHSPQ DLSNEEATEA NHFENLLKES KESSDHHLDN PTETQTNFDG DKSEEITDDS NDQEIIKGSK KKYIIGGIVV AVLIVIILFS RSIFHYFMPL EDKSSRFSKD RNLYVNDEIQ IRQEYNRLLK ERNEKGNMID KNLFFNDDPN RTLYNYLNIA EIEDKNPLRA FYECISNGGN YEECLKLIKD KKLQDQMKKT LEAYNDCIKN AKTEEERIKC LDLIKDENLK KSLLNQQKVQ VALDCLKNAK TDEERNECLK LINDPEIREK FRKELELQKE LQEYKDCIKN AKTEAEKNKC LKGLSKEAIE RLKQQALDCL KNAKTDEERN ECLKNIPQDL QKELLADMSV KAYKDCVSKA RNEKEKQECE KLLTPEARKK LEQQVLDCLK NAKTDEERKK CLKDLPKDLQ SDILAKESLK AYKDCVSQAK TEAEKKECEK LLTPEAKKLL EEEAKESVKA YLDCVSQAKT EAEKKECEKL LTPEAKKKLE EAKKSVKAYL DCVSRARNEK EKKECEKLLT PEAKKLLEQQ ALDCLKNAKT DKERKKCLKD LPKDLQKKVL AKESVKAYLD CVSQAKTEAE KKECEKLLTP EARKLLEEAK KSVKAYLDCV SQAKTEAEKK ECEKLLTPEA RKLLEEXAKE SVKAYLDCVS QAKNEAEKKE CEKLLTLESK KKLEEAKKSV KAYLDCVSQA KTEAEKKECE KLLTPEAKKL LEQQALDCLK NAKTEADKKR CVKDLPKDLQ KKVLAKESLK AYKDCVSKAR NEKEKKECEK LLTPEAKKLL EEAKKSVKAY LDCVSQAKTE AEKKECEKLL TPEARKLLEE AKESVKAYKD CVSKARNEKE KKECEKLLTP EAKKLLEQQV LDCLKNAKTE ADKKRCVKDL PKDLQKKVLA KESVKAYLDC VSRARNEKEK KECEKLLTPE AKKLLEEAKE SLKAYKDCLS QARNEEERRA CEKLLTPEAR KLLEQEVKKS IKAYLDCVSR ARNEKEKKEC EKLLTPEARK FLAKQVLNCL EKAGNEEERK ACLKNLPKDL QENILAKESL KAYKDCLSQA RNEEERRACE KLLTPEARKL LEQEVKKSVK AYLDCVSRAR NEKEKKECEK LLTPEARKFL AKELQQKDKA IKDCLKNADP NDRAAIMKCL DGLSDEEKLK YLQEAREKAV ADCLAMAKTD EEKRKCQNLY SDLIQEIQNK RTQNKQNQLS KTERLHQASE CLDNLDDPTD QEAIEQCLEG LSDSERALIL GIKRQADEVD LIYSDLRNRK TFDNMAAKGY PLLPMDFKNG GDIATINATN VDADKIASDN PIYASIEPDI AKQYETEKTI KDKNLEAKLA KALGGNKKDD DKEKSKKSTA EAKAENNKID KDVAETAKNI SEIALKNKKE KSGEFVDENG NPIDDKKKAE KQDETSPVKQ AFIGKSDPTF VLAQYTPIEI TLTSKVDATL TGIVSGVVAK DVWNMNGTMI LLDKGTKVYG NYQSVKGGTP IMTRLMIVFT KAITPDGVII PLANAQAAGM LGEAGVDGYV NNMNIPPSFY KNEGDSIKIL TMDDIDFSGV YDVKITNKSV VDEIIKQSTK TLSREHEEIT TSPKGGN

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.4 mg/mL
BufferpH: 7
VitrificationCryogen name: NITROGEN

-
Electron microscopy

MicroscopeTFS KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: NONE
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.2.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.2.1)
Final reconstructionApplied symmetry - Point group: C17 (17 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 6.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.2.1) / Number images used: 22642
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