[English] 日本語
Yorodumi
- EMDB-43404: Cryo-EM structure of the cysteine-free ABC transporter PCAT1 boun... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-43404
TitleCryo-EM structure of the cysteine-free ABC transporter PCAT1 bound with ADP and Substrate
Map data
Sample
  • Complex: PCAT1
    • Protein or peptide: ABC-type bacteriocin transporter
    • Protein or peptide: Bacteriocin-type signal sequence-containing protein
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: 3-[oxidanyl-[2-(trimethyl-$l^{4}-azanyl)ethoxy]phosphoryl]oxypropyl hexadecanoate
KeywordsABC transporter / Nucleotide / Membrane Protein / TRANSPORT PROTEIN
Function / homology
Function and homology information


ABC-type bacteriocin transporter activity / ABC-type oligopeptide transporter activity / cysteine-type peptidase activity / ATP hydrolysis activity / proteolysis / ATP binding / plasma membrane
Similarity search - Function
Peptidase C39, ABC-type bacteriocin transporter / Peptidase family C39 domain profile. / Peptidase C39 family / Peptidase C39, bacteriocin processing / Type 1 protein exporter / ABC transporter transmembrane region / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily / ABC transporter ...Peptidase C39, ABC-type bacteriocin transporter / Peptidase family C39 domain profile. / Peptidase C39 family / Peptidase C39, bacteriocin processing / Type 1 protein exporter / ABC transporter transmembrane region / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ABC-type bacteriocin transporter / Bacteriocin-type signal sequence-containing protein
Similarity search - Component
Biological speciesAcetivibrio thermocellus ATCC 27405 (bacteria)
Methodsingle particle reconstruction / Resolution: 3.18 Å
AuthorsZhang R / Jagessar KL / Polasa A / Brownd M / Stein R / Moradi M / Karakas E / Mchaourab HS
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 128087 United States
CitationJournal: J Gen Virol / Year: 1984
Title: Investigation of varicella-zoster virus-infected cell proteins that elicit antibody production during primary varicella using the immune transfer method.
Abstract: The varicella-zoster virus-infected cell proteins (VZV-ICPs) against which IgG, IgM and IgA antibodies were made in the course of primary varicella-zoster virus (VZV) infection were analysed by the ...The varicella-zoster virus-infected cell proteins (VZV-ICPs) against which IgG, IgM and IgA antibodies were made in the course of primary varicella-zoster virus (VZV) infection were analysed by the immune transfer method. IgG antibodies were made against one or more of 18 VZV-ICPs by patients with varicella. IgM antibodies were produced which reacted with 21 VZV-ICPs. The spectrum of IgG antibody production during the first week after the onset of infection was limited to an average of three VZV-ICPs while IgM antibodies which reacted with an average of seven VZV-ICPs were detectable in the acute phase of varicella. Equivalent VZV IgG or IgM antibody titres by radioimmunoassay did not correlate with a similar pattern of antibody specificity for VZV-ICPs by immune transfer. A detectable immune response to all VZV-ICPs was not required for the recovery of individual patients from primary VZV infection.
History
DepositionJan 16, 2024-
Header (metadata) releaseOct 30, 2024-
Map releaseOct 30, 2024-
UpdateOct 30, 2024-
Current statusOct 30, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_43404.png

Downloads & links

-
Map

FileDownload / File: emd_43404.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.)
0.65 Å/pix.
x 360 pix.
= 232.92 Å		0.65 Å/pix.
x 360 pix.
= 232.92 Å		0.65 Å/pix.
x 360 pix.
= 232.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.647 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.07
Minimum - Maximum-1.3299949 - 2.2521493
Average (Standard dev.)0.0054170215 (±0.05613908)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 232.92 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_43404_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_43404_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : PCAT1

EntireName: PCAT1
Components
  • Complex: PCAT1
    • Protein or peptide: ABC-type bacteriocin transporter
    • Protein or peptide: Bacteriocin-type signal sequence-containing protein
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: 3-[oxidanyl-[2-(trimethyl-$l^{4}-azanyl)ethoxy]phosphoryl]oxypropyl hexadecanoate

-
Supramolecule #1: PCAT1

SupramoleculeName: PCAT1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Acetivibrio thermocellus ATCC 27405 (bacteria)
Molecular weightTheoretical: 1.62 MDa

-
Macromolecule #1: ABC-type bacteriocin transporter

MacromoleculeName: ABC-type bacteriocin transporter / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Acetivibrio thermocellus ATCC 27405 (bacteria)
Molecular weightTheoretical: 83.610172 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MGHHHHHHHH HHSSGHIDDD DKHMLRRLFK KKYVSVRQYD LTDSGAAVLS SIAQYYGLKM SLAKIREMTG TDTQGTNAYG LIHAAKQLG FSAKGVKASK EDLLKDFRLP AIANVIVDNR LAHFVVIYSI KNRIITVADP GKGIVRYSMD DFFSIWTGGL V LLEPGEAF ...String:
MGHHHHHHHH HHSSGHIDDD DKHMLRRLFK KKYVSVRQYD LTDSGAAVLS SIAQYYGLKM SLAKIREMTG TDTQGTNAYG LIHAAKQLG FSAKGVKASK EDLLKDFRLP AIANVIVDNR LAHFVVIYSI KNRIITVADP GKGIVRYSMD DFFSIWTGGL V LLEPGEAF QKGDYTQNMM VKFAGFLKPL KKTVLAIFLA SLLYTALGIA GSFYIKFLFD DLIKFEKLND LHIISAGFAV IF LLQIFLN YYRSILVTKL GMSIDKSIMM EYYSHVLKLP MNFFNSRKVG EIISRFMDAS KIRQAISGAT LTIMIDTIMA VIG GILLYI QNSSLFFISF IIILLYGIIV TVFNKPIQNA NRQIMEDNAK LTSALVESVK GIETIKSFGA EEQTEKSTRD KIET VMKSS FKEGMLYINL SSLTGIVAGL GGIVILWAGA YNVIKGNMSG GQLLAFNALL AYFLTPVKNL IDLQPLIQTA VVASN RLGE ILELATEKEL REDSDDFVIS LKGDIEFRNV DFRYGLRKPV LKNINLTIPK GKTVAIVGES GSGKTTLAKL LMNFYS PEK GDILINGHSI KNISLELIRK KIAFVSQDVF IFSGTVKENL ALGNENVDMD EIIKAAKMAN AHDFIEKLPL KYDTFLN ES GANLSEGQKQ RLAIARALLK KPDILILDEA TSNLDSITEN HIKDAIYGLE DDVTVIIIAH RLSTIVNADK IYLLKDGE I VESGSHTELI ALKGLYFKMW KQTENTLAS

UniProtKB: ABC-type bacteriocin transporter

-
Macromolecule #2: Bacteriocin-type signal sequence-containing protein

MacromoleculeName: Bacteriocin-type signal sequence-containing protein / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Acetivibrio thermocellus ATCC 27405 (bacteria)
Molecular weightTheoretical: 12.725521 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MGHHHHHHHH HHSSGHIDDD DKHMSEAKKL NIGRELTDEE LMEMTGGSTF SIQCQKDYTY KPSLPVVKYG VVIDEPEVVI KYGVGPIVG IKYGVEPIGP IQPMYGIKPV ETLK

UniProtKB: Bacteriocin-type signal sequence-containing protein

-
Macromolecule #3: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 2 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

-
Macromolecule #4: 3-[oxidanyl-[2-(trimethyl-$l^{4}-azanyl)ethoxy]phosphoryl]oxyprop...

MacromoleculeName: 3-[oxidanyl-[2-(trimethyl-$l^{4}-azanyl)ethoxy]phosphoryl]oxypropyl hexadecanoate
type: ligand / ID: 4 / Number of copies: 3 / Formula: A1ACX
Molecular weightTheoretical: 480.639 Da

-
Experimental details

-
Structure determination

Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.5 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
50.0 mMMOPS3-(N-morpholino)propanesulfonic acid
50.0 mMNaClSodium chloride

Details: 50mM MOPS, 50mM NaCl, PH 7.4
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec.

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 15861 / Average electron dose: 1.06312 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 4616621
Startup modelType of model: OTHER / Details: Model Angelo
Final reconstructionNumber classes used: 1 / Resolution.type: BY AUTHOR / Resolution: 3.18 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.2.1) / Number images used: 311347
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
Final 3D classificationNumber classes: 4 / Software - Name: cryoSPARC (ver. 4.2.1)

+
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