[English] 日本語
Yorodumi
- EMDB-38301: Cryo-EM structure of the ATP-bound Mtb DppABCD with the D445A mut... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-38301
TitleCryo-EM structure of the ATP-bound Mtb DppABCD with the D445A mutation of DppA
Map data
Sample
  • Complex: DppABCD
    • Protein or peptide: Probable dipeptide-transport integral membrane protein ABC transporter DppB
    • Protein or peptide: Probable dipeptide-transport integral membrane protein ABC transporter DppC
    • Protein or peptide: Probable dipeptide-transport ATP-binding protein ABC transporter DppD
    • Protein or peptide: Probable periplasmic dipeptide-binding lipoprotein DppA
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
KeywordsDppABCD / ABC importer / Mycobacterium tuberculosis / MEMBRANE PROTEIN
Function / homology
Function and homology information


peptide transmembrane transporter activity / peptide transport / ATP-binding cassette (ABC) transporter complex / transmembrane transport / periplasmic space / ATP hydrolysis activity / ATP binding / plasma membrane
Similarity search - Function
ABC transporter type 1, GsiC-like, N-terminal domain / : / : / Binding-prot-dependent transport system membrane comp, N-term / Oligopeptide/dipeptide ABC transporter, C-terminal / Oligopeptide/dipeptide transporter, C-terminal region / ABC transporter type 1, transmembrane domain MetI-like / MetI-like superfamily / Binding-protein-dependent transport system inner membrane component / ABC transporter integral membrane type-1 domain profile. ...ABC transporter type 1, GsiC-like, N-terminal domain / : / : / Binding-prot-dependent transport system membrane comp, N-term / Oligopeptide/dipeptide ABC transporter, C-terminal / Oligopeptide/dipeptide transporter, C-terminal region / ABC transporter type 1, transmembrane domain MetI-like / MetI-like superfamily / Binding-protein-dependent transport system inner membrane component / ABC transporter integral membrane type-1 domain profile. / Peptide/nickel binding protein, MppA-type / Solute-binding protein family 5 domain / Solute-binding protein family 5 / Bacterial extracellular solute-binding proteins, family 5 Middle / ABC transporter-like, conserved site / ABC transporters family signature. / 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
Probable periplasmic dipeptide-binding lipoprotein DppA / Probable dipeptide-transport ATP-binding protein ABC transporter DppD / Probable dipeptide-transport integral membrane protein ABC transporter DppB / Probable dipeptide-transport integral membrane protein ABC transporter DppC
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria) / Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.89 Å
AuthorsHu T / Zhang B / Rao Z
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32171217 China
CitationJournal: To Be Published
Title: Cryo-EM structure of the ATP-bound Mtb DppABCD with the D445A mutation of DppA
Authors: Hu T / Zhang B / Rao Z
History
DepositionDec 13, 2023-
Header (metadata) releaseSep 18, 2024-
Map releaseSep 18, 2024-
UpdateSep 18, 2024-
Current statusSep 18, 2024Processing site: PDBc / Status: Released

-
Structure visualization

Supplemental images

emd_38301.png

Downloads & links

-
Map

FileDownload / File: emd_38301.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.)
0.82 Å/pix.
x 384 pix.
= 314.88 Å		0.82 Å/pix.
x 384 pix.
= 314.88 Å		0.82 Å/pix.
x 384 pix.
= 314.88 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.82 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.129
Minimum - Maximum-0.41512728 - 1.1814481
Average (Standard dev.)-0.0013144836 (±0.035004485)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 314.88 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_38301_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_38301_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : DppABCD

EntireName: DppABCD
Components
  • Complex: DppABCD
    • Protein or peptide: Probable dipeptide-transport integral membrane protein ABC transporter DppB
    • Protein or peptide: Probable dipeptide-transport integral membrane protein ABC transporter DppC
    • Protein or peptide: Probable dipeptide-transport ATP-binding protein ABC transporter DppD
    • Protein or peptide: Probable periplasmic dipeptide-binding lipoprotein DppA
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE

-
Supramolecule #1: DppABCD

SupramoleculeName: DppABCD / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Mycobacterium tuberculosis H37Rv (bacteria)

-
Macromolecule #1: Probable dipeptide-transport integral membrane protein ABC transp...

MacromoleculeName: Probable dipeptide-transport integral membrane protein ABC transporter DppB
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Molecular weightTheoretical: 32.563557 KDa
Recombinant expressionOrganism: Mycolicibacterium smegmatis MC2 155 (bacteria)
SequenceString: MGWYVARRVA VMVPVFLGAT LLIYGMVFLL PGDPVAALAG DRPLTPAVAA QLRSHYHLDD PFLVQYLRYL GGILHGDLGR AYSGLPVSA VLAHAFPVTI RLALIALAVE AVLGIGFGVI AGLRQGGIFD SAVLVTGLVI IAIPIFVLGF LAQFLFGVQL E IAPVTVGE ...String:
MGWYVARRVA VMVPVFLGAT LLIYGMVFLL PGDPVAALAG DRPLTPAVAA QLRSHYHLDD PFLVQYLRYL GGILHGDLGR AYSGLPVSA VLAHAFPVTI RLALIALAVE AVLGIGFGVI AGLRQGGIFD SAVLVTGLVI IAIPIFVLGF LAQFLFGVQL E IAPVTVGE RASVGRLLLP GIVLGAMSFA YVVRLTRSAV AANAHADYVR TATAKGLSRP RVVTVHILRN SLIPVVTFLG AD LGALMGG AIVTEGIFNI HGVGGVLYQA VTRQETPTVV SIVTVLVLIY LITNLLVDLL YAALDPRIRY G

UniProtKB: Probable dipeptide-transport integral membrane protein ABC transporter DppB

-
Macromolecule #2: Probable dipeptide-transport integral membrane protein ABC transp...

MacromoleculeName: Probable dipeptide-transport integral membrane protein ABC transporter DppC
type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Molecular weightTheoretical: 30.48573 KDa
Recombinant expressionOrganism: Mycolicibacterium smegmatis MC2 155 (bacteria)
SequenceString: MAEHTGFWLD AWRGLRRRPK FVIAAALILL ILVVAAFPSL FTAADPTYAD PSQSMLAPSA AHWFGTDLQG HDIYSRTVYG ARASVTVGL GATLAVFVVG GALGALAGFY GSWIDAVVSR VTDVFLGLPL LLAAIVLMQV MHHRTVWTVI AILALFGWPQ V ARIARGAV ...String:
MAEHTGFWLD AWRGLRRRPK FVIAAALILL ILVVAAFPSL FTAADPTYAD PSQSMLAPSA AHWFGTDLQG HDIYSRTVYG ARASVTVGL GATLAVFVVG GALGALAGFY GSWIDAVVSR VTDVFLGLPL LLAAIVLMQV MHHRTVWTVI AILALFGWPQ V ARIARGAV LEVRASDYVL AAKALGLNRF QILLRHALPN AVGPVIAVAT VALGIFIVTE ATLSYLGVGL PTSVVSWGGD IN VAQTRLR SGSPILFYPA GALAITVLAF MMMGDALRDA LDPASRAWRA

UniProtKB: Probable dipeptide-transport integral membrane protein ABC transporter DppC

-
Macromolecule #3: Probable dipeptide-transport ATP-binding protein ABC transporter DppD

MacromoleculeName: Probable dipeptide-transport ATP-binding protein ABC transporter DppD
type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Molecular weightTheoretical: 59.018547 KDa
Recombinant expressionOrganism: Mycolicibacterium smegmatis MC2 155 (bacteria)
SequenceString: MSVPAAPLLS VEGLEVTFGT DAPAVCGVDL AVRSGQTVAV VGESGSGKST TAAAILGLLP AGGRITAGRV VFDGRDITGA DAKRLRSIR GREIGYVPQD PMTNLNPVWK VGFQVTEALR ANTDGRAARR RAVELLAEAG LPDPAKQAGR YPHQLSGGMC Q RALIAIGL ...String:
MSVPAAPLLS VEGLEVTFGT DAPAVCGVDL AVRSGQTVAV VGESGSGKST TAAAILGLLP AGGRITAGRV VFDGRDITGA DAKRLRSIR GREIGYVPQD PMTNLNPVWK VGFQVTEALR ANTDGRAARR RAVELLAEAG LPDPAKQAGR YPHQLSGGMC Q RALIAIGL AGRPRLLIAD QPTSALDVTV QRQVLDHLQG LTDELGTALL LITHDLALAA QRAEAVVVVR RGVVVESGAA QS ILQSPQH EYTRRLVAAA PSLTARSRRP PESRSRATTQ AGDILVVSEL TKIYRESRGA PWRRVESRAV DGVSFRLPRA STL AIVGES GSGKSTLARM VLGLLQPTSG TVVFDGTYDV GALARDQVLA FRRRVQPVFQ NPYSSLDPMY SVFRAIEEPL RVHH VGDRR QRQRAVRELV DQVALPSSIL GRRPRELSGG QRQRVAIARA LALRPEVLVC DQAVSALDVL VQAQILDLLA DLQAD LGLT YLFISHDLAV IRQIADDVLV MRAGRVVEHA STEEVFSRPR HEYTRQLLQA IPGAPSAPRK VGNL

UniProtKB: Probable dipeptide-transport ATP-binding protein ABC transporter DppD

-
Macromolecule #4: Probable periplasmic dipeptide-binding lipoprotein DppA

MacromoleculeName: Probable periplasmic dipeptide-binding lipoprotein DppA
type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Molecular weightTheoretical: 56.013234 KDa
Recombinant expressionOrganism: Mycolicibacterium smegmatis MC2 155 (bacteria)
SequenceString: CGGGVLSPDV VLVNGGEPPN PLIPTGTNDS NGGRIIDRLF AGLMSYDAVG KPSLEVAQSI ESADNVNYRI TVKPGWKFTD GSPVTAHSF VDAWNYGALS TNAQLQQHFF SPIEGFDDVA GAPGDKSRTT MSGLRVVNDL EFTVRLKAPT IDFTLRLGHS S FYPLPDSA ...String:
CGGGVLSPDV VLVNGGEPPN PLIPTGTNDS NGGRIIDRLF AGLMSYDAVG KPSLEVAQSI ESADNVNYRI TVKPGWKFTD GSPVTAHSF VDAWNYGALS TNAQLQQHFF SPIEGFDDVA GAPGDKSRTT MSGLRVVNDL EFTVRLKAPT IDFTLRLGHS S FYPLPDSA FRDMAAFGRN PIGNGPYKLA DGPAGPAWEH NVRIDLVPNP DYHGNRKPRN KGLRFEFYAN LDTAYADLLS GN LDVLDTI PPSALTVYQR DLGDHATSGP AAINQTLDTP LRLPHFGGEE GRLRRLALSA AINRPQICQQ IFAGTRSPAR DFT ARSLPG FDPNLPGNEV LDYDPQRARR LWAQADAISP WSGRYAIAYN ADAGHRDWVD AVANSIKNVL GIDAVAAPQP TFAG FRTQI TNRAIDSAFR AGWRGAYPSM IEFLAPLFTA GAGSNDVGYI NPEFDAALAA AEAAPTLTES HELVNDAQRI LFHDM PVVP LWDYISVVGW SSQVSNVTVT WNGLPDYENI VKA

UniProtKB: Probable periplasmic dipeptide-binding lipoprotein DppA

-
Macromolecule #5: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 5 / Number of copies: 2 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.4000000000000001 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.89 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 71498
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

+
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