[English] 日本語
Yorodumi
- EMDB-12521: MycP5-free ESX-5 inner membrane complex, state I -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-12521
TitleMycP5-free ESX-5 inner membrane complex, state I
Map data-50 Bfactor sharpening of 3D refinement map.
Sample
  • Complex: MycP5-free ESX-5 inner membrane complex, state I
    • Protein or peptide: ESX-5 secretion system ATPase EccB5
    • Protein or peptide: ESX-5 secretion system protein EccC5
    • Protein or peptide: ESX-5 secretion system protein EccD5
KeywordsT7SS / mycobacteria / protein transport / secretion / type VII secretion system / membrane / MEMBRANE PROTEIN
Function / homology
Function and homology information


Hydrolases; Acting on acid anhydrides / peptidoglycan-based cell wall / hydrolase activity / ATP hydrolysis activity / DNA binding / ATP binding / plasma membrane
Similarity search - Function
EccD-like transmembrane domain / EccD-like transmembrane domain / Type VII secretion system membrane protein EccD / YukD-like / WXG100 protein secretion system (Wss), protein YukD / EccCa-like, Actinobacteria / EccCb-like, Actinobacteria / Type VII secretion system EccB / Type VII secretion system EccB, repeat 3 domain / Type VII secretion system EccB, repeat 1 domain ...EccD-like transmembrane domain / EccD-like transmembrane domain / Type VII secretion system membrane protein EccD / YukD-like / WXG100 protein secretion system (Wss), protein YukD / EccCa-like, Actinobacteria / EccCb-like, Actinobacteria / Type VII secretion system EccB / Type VII secretion system EccB, repeat 3 domain / Type VII secretion system EccB, repeat 1 domain / Type VII secretion system ESX-1, transport TM domain B / : / FtsK domain / FtsK/SpoIIIE family / FtsK domain profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ESX-5 secretion system protein EccC5 / ESX-5 secretion system protein EccD5 / ESX-5 secretion system ATPase EccB5
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria) / Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.48 Å
AuthorsBunduc CM / Fahrenkamp D / Wald J / Ummels R / Bitter W / Houben ENG / Marlovits TC
Funding support Germany, Netherlands, European Union, 4 items
OrganizationGrant numberCountry
German Research Foundation (DFG)INST 152/774-1 FUGG Germany
Netherlands Organisation for Scientific Research (NWO)864.12.006 Netherlands
H2020 Marie Curie Actions of the European Commission101030373European Union
German Research Foundation (DFG)FA1518/2-1 Germany
CitationJournal: Nature / Year: 2021
Title: Structure and dynamics of a mycobacterial type VII secretion system.
Authors: Catalin M Bunduc / Dirk Fahrenkamp / Jiri Wald / Roy Ummels / Wilbert Bitter / Edith N G Houben / Thomas C Marlovits /
Abstract: Mycobacterium tuberculosis is the cause of one of the most important infectious diseases in humans, which leads to 1.4 million deaths every year. Specialized protein transport systems-known as ...Mycobacterium tuberculosis is the cause of one of the most important infectious diseases in humans, which leads to 1.4 million deaths every year. Specialized protein transport systems-known as type VII secretion systems (T7SSs)-are central to the virulence of this pathogen, and are also crucial for nutrient and metabolite transport across the mycobacterial cell envelope. Here we present the structure of an intact T7SS inner-membrane complex of M. tuberculosis. We show how the 2.32-MDa ESX-5 assembly, which contains 165 transmembrane helices, is restructured and stabilized as a trimer of dimers by the MycP protease. A trimer of MycP caps a central periplasmic dome-like chamber that is formed by three EccB dimers, with the proteolytic sites of MycP facing towards the cavity. This chamber suggests a central secretion and processing conduit. Complexes without MycP show disruption of the EccB periplasmic assembly and increased flexibility, which highlights the importance of MycP for complex integrity. Beneath the EccB-MycP chamber, dimers of the EccC ATPase assemble into three bundles of four transmembrane helices each, which together seal the potential central secretion channel. Individual cytoplasmic EccC domains adopt two distinctive conformations that probably reflect different secretion states. Our work suggests a previously undescribed mechanism of protein transport and provides a structural scaffold to aid in the development of drugs against this major human pathogen.
History
DepositionFeb 28, 2021-
Header (metadata) releaseJun 2, 2021-
Map releaseJun 2, 2021-
UpdateJul 10, 2024-
Current statusJul 10, 2024Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.01
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.01
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7npu
  • Surface level: 0.01
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7npu
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_12521.png

Downloads & links

-
Map

FileDownload / File: emd_12521.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation-50 Bfactor sharpening of 3D refinement map.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 400 pix.
= 440. Å		1.1 Å/pix.
x 400 pix.
= 440. Å		1.1 Å/pix.
x 400 pix.
= 440. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.01 / Movie #1: 0.01
Minimum - Maximum-0.012265803 - 0.03214824
Average (Standard dev.)0.00027374862 (±0.0014535845)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 440.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.11.11.1
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z440.000440.000440.000
α/β/γ90.00090.00090.000
start NX/NY/NZ7297100
NX/NY/NZ181127145
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-0.0120.0320.000

-
Supplemental data

-
Mask #1

Fileemd_12521_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: 3D refinement map.

Fileemd_12521_additional_1.map
Annotation3D refinement map.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: #1

Fileemd_12521_additional_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half2 of 3D refinement map.

Fileemd_12521_half_map_1.map
AnnotationHalf2 of 3D refinement map.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half1 of 3D refinement map.

Fileemd_12521_half_map_2.map
AnnotationHalf1 of 3D refinement map.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : MycP5-free ESX-5 inner membrane complex, state I

EntireName: MycP5-free ESX-5 inner membrane complex, state I
Components
  • Complex: MycP5-free ESX-5 inner membrane complex, state I
    • Protein or peptide: ESX-5 secretion system ATPase EccB5
    • Protein or peptide: ESX-5 secretion system protein EccC5
    • Protein or peptide: ESX-5 secretion system protein EccD5

-
Supramolecule #1: MycP5-free ESX-5 inner membrane complex, state I

SupramoleculeName: MycP5-free ESX-5 inner membrane complex, state I / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Mycobacterium tuberculosis H37Rv (bacteria)

-
Macromolecule #1: ESX-5 secretion system ATPase EccB5

MacromoleculeName: ESX-5 secretion system ATPase EccB5 / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO / EC number: Hydrolases; Acting on acid anhydrides
Source (natural)Organism: Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv
Molecular weightTheoretical: 53.769988 KDa
Recombinant expressionOrganism: Mycolicibacterium smegmatis MC2 155 (bacteria)
SequenceString: MAEESRGQRG SGYGLGLSTR TQVTGYQFLA RRTAMALTRW RVRMEIEPGR RQTLAVVASV SAALVICLGA LLWSFISPSG QLNESPIIA DRDSGALYVR VGDRLYPALN LASARLITGR PDNPHLVRSS QIATMPRGPL VGIPGAPSSF SPKSPPASSW L VCDTVATS ...String:
MAEESRGQRG SGYGLGLSTR TQVTGYQFLA RRTAMALTRW RVRMEIEPGR RQTLAVVASV SAALVICLGA LLWSFISPSG QLNESPIIA DRDSGALYVR VGDRLYPALN LASARLITGR PDNPHLVRSS QIATMPRGPL VGIPGAPSSF SPKSPPASSW L VCDTVATS SSIGSLQGVT VTVIDGTPDL TGHRQILSGS DAVVLRYGGD AWVIREGRRS RIEPTNRAVL LPLGLTPEQV SQ ARPMSRA LFDALPVGPE LLVPEVPNAG GPATFPGAPG PIGTVIVTPQ ISGPQQYSLV LGDGVQTLPP LVAQILQNAG SAG NTKPLT VEPSTLAKMP VVNRLDLSAY PDNPLEVVDI REHPSTCWWW ERTAGENRAR VRVVSGPTIP VAATEMNKVV SLVK ADTSG RQADQVYFGP DHANFVAVTG NNPGAQTSES LWWVTDAGAR FGVEDSKEAR DALGLTLTPS LAPWVALRLL PQGPT LSRA DALVEHDTLP MDMTPAELVV PK

UniProtKB: ESX-5 secretion system ATPase EccB5

-
Macromolecule #2: ESX-5 secretion system protein EccC5

MacromoleculeName: ESX-5 secretion system protein EccC5 / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv
Molecular weightTheoretical: 152.90075 KDa
Recombinant expressionOrganism: Mycolicibacterium smegmatis MC2 155 (bacteria)
SequenceString: MKRGFARPTP EKPPVIKPEN IVLSTPLSIP PPEGKPWWLI VVGVVVVGLL GGMVAMVFAS GSHVFGGIGS IFPLFMMVGI MMMMFRGMG GGQQQMSRPK LDAMRAQFML MLDMLRETAQ ESADSMDANY RWFHPAPNTL AAAVGSPRMW ERKPDGKDLN F GVVRVGVG ...String:
MKRGFARPTP EKPPVIKPEN IVLSTPLSIP PPEGKPWWLI VVGVVVVGLL GGMVAMVFAS GSHVFGGIGS IFPLFMMVGI MMMMFRGMG GGQQQMSRPK LDAMRAQFML MLDMLRETAQ ESADSMDANY RWFHPAPNTL AAAVGSPRMW ERKPDGKDLN F GVVRVGVG MTRPEVTWGE PQNMPTDIEL EPVTGKALQE FGRYQSVVYN LPKMVSLLVE PWYALVGERE QVLGLMRAII CQ LAFSHGP DHVQMIVVSS DLDQWDWVKW LPHFGDSRRH DAAGNARMVY TSVREFAAEQ AELFAGRGSF TPRHASSSAQ TPT PHTVII ADVDDPQWEY VISAEGVDGV TFFDLTGSSM WTDIPERKLQ FDKTGVIEAL PRDRDTWMVI DDKAWFFALT DQVS IAEAE EFAQKLAQWR LAEAYEEIGQ RVAHIGARDI LSYYGIDDPG NIDFDSLWAS RTDTMGRSRL RAPFGNRSDN GELLF LDMK SLDEGGDGPH GVMSGTTGSG KSTLVRTVIE SLMLSHPPEE LQFVLADLKG GSAVKPFAGV PHVSRIITDL EEDQAL MER FLDALWGEIA RRKAICDSAG VDDAKEYNSV RARMRARGQD MAPLPMLVVV IDEFYEWFRI MPTAVDVLDS IGRQGRA YW IHLMMASQTI ESRAEKLMEN MGYRLVLKAR TAGAAQAAGV PNAVNLPAQA GLGYFRKSLE DIIRFQAEFL WRDYFQPG V SIDGEEAPAL VHSIDYIRPQ LFTNSFTPLE VSVGGPDIEP VVAQPNGEVL ESDDIEGGED EDEEGVRTPK VGTVIIDQL RKIKFEPYRL WQPPLTQPVA IDDLVNRFLG RPWHKEYGSA CNLVFPIGII DRPYKHDQPP WTVDTSGPGA NVLILGAGGS GKTTALQTL ICSAALTHTP QQVQFYCLAY SSTALTTVSR IPHVGEVAGP TDPYGVRRTV AELLALVRER KRSFLECGIA S MEMFRRRK FGGEAGPVPD DGFGDVYLVI DNYRALAEEN EVLIEQVNVI INQGPSFGVH VVVTADRESE LRPPVRSGFG SR IELRLAA VEDAKLVRSR FAKDVPVKPG RGMVAVNYVR LDSDPQAGLH TLVARPALGS TPDNVFECDS VVAAVSRLTS AQA PPVRRL PARFGVEQVR ELASRDTRQG VGAGGIAWAI SELDLAPVYL NFAENSHLMV TGRRECGRTT TLATIMSEIG RLYA PGASS APPPAPGRPS AQVWLVDPRR QLLTALGSDY VERFAYNLDG VVAMMGELAA ALAGREPPPG LSAEELLSRS WWSGP EIFL IVDDIQQLPP GFDSPLHKAV PFVNRAADVG LHVIVTRTFG GWSSAGSDPM LRALHQANAP LLVMDADPDE GFIRGK MKG GPLPRGRGLL MAEDTGVFVQ VAATEVRR

UniProtKB: ESX-5 secretion system protein EccC5

-
Macromolecule #3: ESX-5 secretion system protein EccD5

MacromoleculeName: ESX-5 secretion system protein EccD5 / type: protein_or_peptide / ID: 3 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv
Molecular weightTheoretical: 53.480906 KDa
Recombinant expressionOrganism: Mycolicibacterium smegmatis MC2 155 (bacteria)
SequenceString: MTAVADAPQA DIEGVASPQA VVVGVMAGEG VQIGVLLDAN APVSVMTDPL LKVVNSRLRE LGEAPLEATG RGRWALCLVD GAPLRATQS LTEQDVYDGD RLWIRFIADT ERRSQVIEHI STAVASDLSK RFARIDPIVA VQVGASMVAT GVVLATGVLG W WRWHHNTW ...String:
MTAVADAPQA DIEGVASPQA VVVGVMAGEG VQIGVLLDAN APVSVMTDPL LKVVNSRLRE LGEAPLEATG RGRWALCLVD GAPLRATQS LTEQDVYDGD RLWIRFIADT ERRSQVIEHI STAVASDLSK RFARIDPIVA VQVGASMVAT GVVLATGVLG W WRWHHNTW LTTIYTAVIG VLVLAVAMLL LMRAKTDADR RVADIMLMSA IMPVTVAAAA APPGPVGSPQ AVLGFGVLTV AA ALALRFT GRRLGIYTTI VIIGALTMLA ALARMVAATS AVTLLSSLLL ICVVAYHAAP ALSRRLAGIR LPVFPSATSR WVF EARPDL PTTVVVSGGS APVLEGPSSV RDVLLQAERA RSFLSGLLTG LGVMVVVCMT SLCDPHTGQR WLPLILAGFT SGFL LLRGR SYVDRWQSIT LAGTAVIIAA AVCVRYALEL SSPLAVSIVA AILVLLPAAG MAAAAHVPHT IYSPLFRKFV EWIEY LCLM PIFPLALWLM NVYAAIRYR

UniProtKB: ESX-5 secretion system protein EccD5

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE-PROPANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 59.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.48 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 226793
Initial angle assignmentType: OTHER / Details: Rotationally averaged 3D structure.
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