[English] 日本語
Yorodumi
- EMDB-22886: Mycobacterium tuberculosis WT RNAP transcription open promoter co... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-22886
TitleMycobacterium tuberculosis WT RNAP transcription open promoter complex with WhiB7 transcription factor
Map data
Sample
  • Complex: Mycobacterium tuberculosis WT RNAP transcription open promoter complex with WhiB7 transcription factor
    • Protein or peptide: x 8 types
    • DNA: x 2 types
  • Ligand: x 3 types
Function / homology
Function and homology information


dinitrosyl-iron complex binding / protein-disulfide reductase (NAD(P)H) activity / bacterial-type RNA polymerase core enzyme binding / response to fatty acid / sigma factor activity / cell redox homeostasis / DNA-directed RNA polymerase complex / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity ...dinitrosyl-iron complex binding / protein-disulfide reductase (NAD(P)H) activity / bacterial-type RNA polymerase core enzyme binding / response to fatty acid / sigma factor activity / cell redox homeostasis / DNA-directed RNA polymerase complex / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / 4 iron, 4 sulfur cluster binding / protein dimerization activity / response to antibiotic / negative regulation of DNA-templated transcription / DNA-templated transcription / positive regulation of DNA-templated transcription / magnesium ion binding / DNA binding / zinc ion binding / metal ion binding / cytoplasm
Similarity search - Function
AT hook motif / Transcription factor WhiB / WhiB-like iron-sulfur binding domain / Transcription factor WhiB / 4Fe-4S WhiB-like (Wbl)-type iron-sulfur binding domain profile. / : / CarD, C-terminal / CarD-like, C-terminal domain / RNA polymerase-binding protein RbpA / RbpA superfamily ...AT hook motif / Transcription factor WhiB / WhiB-like iron-sulfur binding domain / Transcription factor WhiB / 4Fe-4S WhiB-like (Wbl)-type iron-sulfur binding domain profile. / : / CarD, C-terminal / CarD-like, C-terminal domain / RNA polymerase-binding protein RbpA / RbpA superfamily / RNA polymerase-binding protein / CarD-like/TRCF, RNAP-interacting domain / CarD-like/TRCF, RNAP-interacting domain superfamily / CarD-like/TRCF RID domain / CarD-like/TRCF domain / AT hook, DNA-binding motif / Sigma-70 factors family signature 1. / RNA polymerase sigma factor RpoD, C-terminal / RNA polymerase sigma factor RpoD / RNA polymerase sigma-70 region 1.2 / Sigma-70 factor, region 1.2 / RNA polymerase sigma-70 region 3 / Sigma-70 region 3 / Sigma-70 factors family signature 2. / RNA polymerase sigma-70 / RNA polymerase sigma-70 region 4 / Sigma-70, region 4 / RNA polymerase sigma-70 region 2 / RNA polymerase sigma-70 like domain / Sigma-70 region 2 / RNA polymerase sigma factor, region 2 / RNA polymerase sigma factor, region 3/4-like / DNA-directed RNA polymerase, omega subunit / DNA-directed RNA polymerase, subunit beta-prime, bacterial type / DNA-directed RNA polymerase, beta subunit, external 1 domain superfamily / DNA-directed RNA polymerase, beta subunit, external 1 domain / RNA polymerase beta subunit external 1 domain / RNA polymerase, alpha subunit, C-terminal / Bacterial RNA polymerase, alpha chain C terminal domain / DNA-directed RNA polymerase, alpha subunit / DNA-directed RNA polymerase beta subunit, bacterial-type / RNA polymerase Rpb6 / RNA polymerase, subunit omega/Rpo6/RPB6 / RNA polymerase Rpb6 / RNA polymerase Rpb1, domain 3 superfamily / RNA polymerase Rpb1, clamp domain superfamily / RPB6/omega subunit-like superfamily / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 1 / RNA polymerase, alpha subunit / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb1, domain 2 / RNA polymerase Rpb1, domain 4 / RNA polymerase, N-terminal / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase I subunit A N-terminus / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 5 / RNA polymerase, beta subunit, protrusion / RNA polymerase beta subunit / DNA-directed RNA polymerase, insert domain / DNA-directed RNA polymerase, RpoA/D/Rpb3-type / RNA polymerase Rpb3/RpoA insert domain / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerases D / DNA-directed RNA polymerase, insert domain superfamily / RNA polymerase, RBP11-like subunit / RNA polymerase Rpb2, domain 2 / RNA polymerase Rpb2, domain 2 / RNA polymerase, beta subunit, conserved site / RNA polymerase Rpb2, domain 7 / RNA polymerase Rpb2, domain 3 / RNA polymerase Rpb2, OB-fold / RNA polymerase Rpb2, domain 7 / RNA polymerase Rpb2, domain 3 / RNA polymerases beta chain signature. / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain / DNA-directed RNA polymerase, subunit 2 / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain superfamily / RNA polymerase Rpb2, domain 6 / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
DNA-directed RNA polymerase subunit beta' / RNA polymerase sigma factor SigA / DNA-directed RNA polymerase subunit omega / DNA-directed RNA polymerase subunit beta / DNA-directed RNA polymerase subunit alpha / RNA polymerase-binding protein RbpA / RNA polymerase-binding transcription factor CarD / Probable transcriptional regulator WhiB7
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.94 Å
AuthorsLilic M / Darst SA / Campbell EA
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Mol Cell / Year: 2021
Title: Structural basis of transcriptional activation by the Mycobacterium tuberculosis intrinsic antibiotic-resistance transcription factor WhiB7.
Authors: Mirjana Lilic / Seth A Darst / Elizabeth A Campbell /
Abstract: In pathogenic mycobacteria, transcriptional responses to antibiotics result in induced antibiotic resistance. WhiB7 belongs to the Actinobacteria-specific family of Fe-S-containing transcription ...In pathogenic mycobacteria, transcriptional responses to antibiotics result in induced antibiotic resistance. WhiB7 belongs to the Actinobacteria-specific family of Fe-S-containing transcription factors and plays a crucial role in inducible antibiotic resistance in mycobacteria. Here, we present cryoelectron microscopy structures of Mycobacterium tuberculosis transcriptional regulatory complexes comprising RNA polymerase σ-holoenzyme, global regulators CarD and RbpA, and WhiB7, bound to a WhiB7-regulated promoter. The structures reveal how WhiB7 interacts with σ-holoenzyme while simultaneously interacting with an AT-rich sequence element via its AT-hook. Evidently, AT-hooks, rare elements in bacteria yet prevalent in eukaryotes, bind to target AT-rich DNA sequences similarly to the nuclear chromosome binding proteins. Unexpectedly, a subset of particles contained a WhiB7-stabilized closed promoter complex, revealing this intermediate's structure, and we apply kinetic modeling and biochemical assays to rationalize how WhiB7 activates transcription. Altogether, our work presents a comprehensive view of how WhiB7 serves to activate gene expression leading to antibiotic resistance.
History
DepositionOct 23, 2020-
Header (metadata) releaseApr 21, 2021-
Map releaseApr 21, 2021-
UpdateNov 3, 2021-
Current statusNov 3, 2021Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 4
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 4
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7kif
  • Surface level: 4
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22886.png

Downloads & links

-
Map

FileDownload / File: emd_22886.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.1 Å
Density
Contour LevelBy AUTHOR: 3.6 / Movie #1: 4
Minimum - Maximum-19.15075 - 44.35031
Average (Standard dev.)0.0012538907 (±1.0080861)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 330.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.11.11.1
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z330.000330.000330.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-19.15144.3500.001

-
Supplemental data

-
Sample components

+
Entire : Mycobacterium tuberculosis WT RNAP transcription open promoter co...

EntireName: Mycobacterium tuberculosis WT RNAP transcription open promoter complex with WhiB7 transcription factor
Components
  • Complex: Mycobacterium tuberculosis WT RNAP transcription open promoter complex with WhiB7 transcription factor
    • Protein or peptide: DNA-directed RNA polymerase subunit alphaPolymerase
    • Protein or peptide: DNA-directed RNA polymerase subunit betaPolymerase
    • Protein or peptide: DNA-directed RNA polymerase subunit beta'Polymerase
    • Protein or peptide: DNA-directed RNA polymerase subunit omegaPolymerase
    • Protein or peptide: RNA polymerase sigma factor SigA
    • Protein or peptide: RNA polymerase-binding protein RbpA
    • Protein or peptide: RNA polymerase-binding transcription factor CarD
    • DNA: DNA (63-MER)
    • DNA: DNA (55-MER)
    • Protein or peptide: Probable transcriptional regulator WhiB7
  • Ligand: ZINC ION
  • Ligand: MAGNESIUM ION
  • Ligand: IRON/SULFUR CLUSTERIron–sulfur cluster

+
Supramolecule #1: Mycobacterium tuberculosis WT RNAP transcription open promoter co...

SupramoleculeName: Mycobacterium tuberculosis WT RNAP transcription open promoter complex with WhiB7 transcription factor
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#10
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)

+
Macromolecule #1: DNA-directed RNA polymerase subunit alpha

MacromoleculeName: DNA-directed RNA polymerase subunit alpha / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Molecular weightTheoretical: 37.745328 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MLISQRPTLS EDVLTDNRSQ FVIEPLEPGF GYTLGNSLRR TLLSSIPGAA VTSIRIDGVL HEFTTVPGVK EDVTEIILNL KSLVVSSEE DEPVTMYLRK QGPGEVTAGD IVPPAGVTVH NPGMHIATLN DKGKLEVELV VERGRGYVPA VQNRASGAEI G RIPVDSIY ...String:
MLISQRPTLS EDVLTDNRSQ FVIEPLEPGF GYTLGNSLRR TLLSSIPGAA VTSIRIDGVL HEFTTVPGVK EDVTEIILNL KSLVVSSEE DEPVTMYLRK QGPGEVTAGD IVPPAGVTVH NPGMHIATLN DKGKLEVELV VERGRGYVPA VQNRASGAEI G RIPVDSIY SPVLKVTYKV DATRVEQRTD FDKLILDVET KNSISPRDAL ASAGKTLVEL FGLARELNVE AEGIEIGPSP AE ADHIASF ALPIDDLDLT VRSYNCLKRE GVHTVGELVA RTESDLLDIR NFGQKSIDEV KIKLHQLGLS LKDSPPSFDP SEV AGYDVA TGTWSTEGAY DEQDYAETEQ L

+
Macromolecule #2: DNA-directed RNA polymerase subunit beta

MacromoleculeName: DNA-directed RNA polymerase subunit beta / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Molecular weightTheoretical: 129.372031 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: LADSRQSKTA ASPSPSRPQS SSNNSVPGAP NRVSFAKLRE PLEVPGLLDV QTDSFEWLIG SPRWRESAAE RGDVNPVGGL EEVLYELSP IEDFSGSMSL SFSDPRFDDV KAPVDECKDK DMTYAAPLFV TAEFINNNTG EIKSQTVFMG DFPMMTEKGT F IINGTERV ...String:
LADSRQSKTA ASPSPSRPQS SSNNSVPGAP NRVSFAKLRE PLEVPGLLDV QTDSFEWLIG SPRWRESAAE RGDVNPVGGL EEVLYELSP IEDFSGSMSL SFSDPRFDDV KAPVDECKDK DMTYAAPLFV TAEFINNNTG EIKSQTVFMG DFPMMTEKGT F IINGTERV VVSQLVRSPG VYFDETIDKS TDKTLHSVKV IPSRGAWLEF DVDKRDTVGV RIDRKRRQPV TVLLKALGWT SE QIVERFG FSEIMRSTLE KDNTVGTDEA LLDIYRKLRP GEPPTKESAQ TLLENLFFKE KRYDLARVGR YKVNKKLGLH VGE PITSST LTEEDVVATI EYLVRLHEGQ TTMTVPGGVE VPVETDDIDH FGNRRLRTVG ELIQNQIRVG MSRMERVVRE RMTT QDVEA ITPQTLINIR PVVAAIKEFF GTSQLSQFMD QNNPLSGLTH KRRLSALGPG GLSRERAGLE VRDVHPSHYG RMCPI ETPE GPNIGLIGSL SVYARVNPFG FIETPYRKVV DGVVSDEIVY LTADEEDRHV VAQANSPIDA DGRFVEPRVL VRRKAG EVE YVPSSEVDYM DVSPRQMVSV ATAMIPFLEH DDANRALMGA NMQRQAVPLV RSEAPLVGTG MELRAAIDAG DVVVAEE SG VIEEVSADYI TVMHDNGTRR TYRMRKFARS NHGTCANQCP IVDAGDRVEA GQVIADGPCT DDGEMALGKN LLVAIMPW E GHNYEDAIIL SNRLVEEDVL TSIHIEEHEI DARDTKLGAE EITRDIPNIS DEVLADLDER GIVRIGAEVR DGDILVGKV TPKGETELTP EERLLRAIFG EKAREVRDTS LKVPHGESGK VIGIRVFSRE DEDELPAGVN ELVRVYVAQK RKISDGDKLA GRHGNKGVI GKILPVEDMP FLADGTPVDI ILNTHGVPRR MNIGQILETH LGWCAHSGWK VDAAKGVPDW AARLPDELLE A QPNAIVST PVFDGAQEAE LQGLLSCTLP NRDGDVLVDA DGKAMLFDGR SGEPFPYPVT VGYMYIMKLH HLVDDKIHAR ST GPYSMIT QQPLGGKAQF GGQRFGEMEC WAMQAYGAAY TLQELLTIKS DDTVGRVKVY EAIVKGENIP EPGIPESFKV LLK ELQSLC LNVEVLSSDG AAIELREGED EDLERAAANL GINLSRNESA SVEDLA

+
Macromolecule #3: DNA-directed RNA polymerase subunit beta'

MacromoleculeName: DNA-directed RNA polymerase subunit beta' / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Molecular weightTheoretical: 147.097094 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GAMLDVNFFD ELRIGLATAE DIRQWSYGEV KKPETINYRT LKPEKDGLFC EKIFGPTRDW ECYCGKYKRV RFKGIICERC GVEVTRAKV RRERMGHIEL AAPVTHIWYF KGVPSRLGYL LDLAPKDLEK IIYFAAYVIT SVDEEMRHNE LSTLEAEMAV E RKAVEDQR ...String:
GAMLDVNFFD ELRIGLATAE DIRQWSYGEV KKPETINYRT LKPEKDGLFC EKIFGPTRDW ECYCGKYKRV RFKGIICERC GVEVTRAKV RRERMGHIEL AAPVTHIWYF KGVPSRLGYL LDLAPKDLEK IIYFAAYVIT SVDEEMRHNE LSTLEAEMAV E RKAVEDQR DGELEARAQK LEADLAELEA EGAKADARRK VRDGGEREMR QIRDRAQREL DRLEDIWSTF TKLAPKQLIV DE NLYRELV DRYGEYFTGA MGAESIQKLI ENFDIDAEAE SLRDVIRNGK GQKKLRALKR LKVVAAFQQS GNSPMGMVLD AVP VIPPEL RPMVQLDGGR FATSDLNDLY RRVINRNNRL KRLIDLGAPE IIVNNEKRML QESVDALFDN GRRGRPVTGP GNRP LKSLS DLLKGKQGRF RQNLLGKRVD YSGRSVIVVG PQLKLHQCGL PKLMALELFK PFVMKRLVDL NHAQNIKSAK RMVER QRPQ VWDVLEEVIA EHPVLLNRAP TLHRLGIQAF EPMLVEGKAI QLHPLVCEAF NADFDGDQMA VHLPLSAEAQ AEARIL MLS SNNILSPASG RPLAMPRLDM VTGLYYLTTE VPGDTGEYQP ASGDHPETGV YSSPAEAIMA ADRGVLSVRA KIKVRLT QL RPPVEIEAEL FGHSGWQPGD AWMAETTLGR VMFNELLPLG YPFVNKQMHK KVQAAIINDL AERYPMIVVA QTVDKLKD A GFYWATRSGV TVSMADVLVP PRKKEILDHY EERADKVEKQ FQRGALNHDE RNEALVEIWK EATDEVGQAL REHYPDDNP IITIVDSGAT GNFTQTRTLA GMKGLVTNPK GEFIPRPVKS SFREGLTVLE YFINTHGARK GLADTALRTA DSGYLTRRLV DVSQDVIVR EHDCQTERGI VVELAERAPD GTLIRDPYIE TSAYARTLGT DAVDEAGNVI VERGQDLGDP EIDALLAAGI T QVKVRSVL TCATSTGVCA TCYGRSMATG KLVDIGEAVG IVAAQSIGEP GTQLTMRTFH QGGVGEDITG GLPRVQELFE AR VPRGKAP IADVTGRVRL EDGERFYKIT IVPDDGGEEV VYDKISKRQR LRVFKHEDGS ERVLSDGDHV EVGQQLMEGS ADP HEVLRV QGPREVQIHL VREVQEVYRA QGVSIHDKHI EVIVRQMLRR VTIIDSGSTE FLPGSLIDRA EFEAENRRVV AEGG EPAAG RPVLMGITKA SLATDSWLSA ASFQETTRVL TDAAINCRSD KLNGLKENVI IGKLIPAGTG INRYRNIAVQ PTEEA RAAA YTIPSYEDQY YSPDFGAATG AAVPLDDYGY SDYR

+
Macromolecule #4: DNA-directed RNA polymerase subunit omega

MacromoleculeName: DNA-directed RNA polymerase subunit omega / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Molecular weightTheoretical: 11.819075 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
VSISQSDASL AAVPAVDQFD PSSGASGGYD TPLGITNPPI DELLDRVSSK YALVIYAAKR ARQINDYYNQ LGEGILEYVG PLVEPGLQE KPLSIALREI HADLLEHTEG E

+
Macromolecule #5: RNA polymerase sigma factor SigA

MacromoleculeName: RNA polymerase sigma factor SigA / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Molecular weightTheoretical: 57.845098 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: VAATKASTAT DEPVKRTATK SPAASASGAK TGAKRTAAKS ASGSPPAKRA TKPAARSVKP ASAPQDTTTS TIPKRKTRAA AKSAAAKAP SARGHATKPR APKDAQHEAA TDPEDALDSV EELDAEPDLD VEPGEDLDLD AADLNLDDLE DDVAPDADDD L DSGDDEDH ...String:
VAATKASTAT DEPVKRTATK SPAASASGAK TGAKRTAAKS ASGSPPAKRA TKPAARSVKP ASAPQDTTTS TIPKRKTRAA AKSAAAKAP SARGHATKPR APKDAQHEAA TDPEDALDSV EELDAEPDLD VEPGEDLDLD AADLNLDDLE DDVAPDADDD L DSGDDEDH EDLEAEAAVA PGQTADDDEE IAEPTEKDKA SGDFVWDEDE SEALRQARKD AELTASADSV RAYLKQIGKV AL LNAEEEV ELAKRIEAGL YATQLMTELS ERGEKLPAAQ RRDMMWICRD GDRAKNHLLE ANLRLVVSLA KRYTGRGMAF LDL IQEGNL GLIRAVEKFD YTKGYKFSTY ATWWIRQAIT RAMADQARTI RIPVHMVEVI NKLGRIQREL LQDLGREPTP EELA KEMDI TPEKVLEIQQ YAREPISLDQ TIGDEGDSQL GDFIEDSEAV VAVDAVSFTL LQDQLQSVLD TLSEREAGVV RLRFG LTDG QPRTLDEIGQ VYGVTRERIR QIESKTMSKL RHPSRSQVLR DYLD

+
Macromolecule #6: RNA polymerase-binding protein RbpA

MacromoleculeName: RNA polymerase-binding protein RbpA / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Molecular weightTheoretical: 12.993695 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MADRVLRGSR LGAVSYETDR NHDLAPRQIA RYRTDNGEEF EVPFADDAEI PGTWLCRNGM EGTLIEGDLP EPKKVKPPRT HWDMLLERR SIEELEELLK ERLELIRSRR RG

+
Macromolecule #7: RNA polymerase-binding transcription factor CarD

MacromoleculeName: RNA polymerase-binding transcription factor CarD / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Molecular weightTheoretical: 17.933361 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MIFKVGDTVV YPHHGAALVE AIETRTIKGE QKEYLVLKVA QGDLTVRVPA ENAEYVGVRD VVGQEGLDKV FQVLRAPHTE EPTNWSRRY KANLEKLASG DVNKVAEVVR DLWRRDQERG LSAGEKRMLA KARQILVGEL ALAESTDDAK AETILDEVLA A AS

+
Macromolecule #10: Probable transcriptional regulator WhiB7

MacromoleculeName: Probable transcriptional regulator WhiB7 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Molecular weightTheoretical: 10.153804 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSVLTVPRQT PRQRLPVLPC HVGDPDLWFA DTPAGLEVAK TLCVSCPIRR QCLAAALQRA EPWGVWGGEI FDQGSIVSHK RPRGRPRKD AVA

+
Macromolecule #8: DNA (63-MER)

MacromoleculeName: DNA (63-MER) / type: dna / ID: 8 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Molecular weightTheoretical: 30.844654 KDa
SequenceString: (DC)(DT)(DG)(DT)(DA)(DC)(DC)(DG)(DG)(DC) (DA)(DA)(DA)(DC)(DG)(DC)(DG)(DC)(DA)(DG) (DG)(DT)(DC)(DA)(DG)(DA)(DA)(DA)(DA) (DT)(DC)(DG)(DG)(DT)(DT)(DG)(DT)(DG)(DG) (DT) (DC)(DA)(DG)(DC)(DT)(DG) ...String:
(DC)(DT)(DG)(DT)(DA)(DC)(DC)(DG)(DG)(DC) (DA)(DA)(DA)(DC)(DG)(DC)(DG)(DC)(DA)(DG) (DG)(DT)(DC)(DA)(DG)(DA)(DA)(DA)(DA) (DT)(DC)(DG)(DG)(DT)(DT)(DG)(DT)(DG)(DG) (DT) (DC)(DA)(DG)(DC)(DT)(DG)(DC)(DT) (DG)(DC)(DC)(DA)(DC)(DC)(DG)(DG)(DT)(DT) (DA)(DA) (DC)(DC)(DT)(DC)(DC)(DA)(DG) (DG)(DT)(DC)(DG)(DC)(DA)(DT)(DT)(DC)(DT) (DG)(DC)(DT) (DG)(DC)(DC)(DA)(DG)(DC) (DC)(DT)(DG)(DG)(DA)(DG)(DA)(DT)(DG)(DG) (DC)(DA)(DT)(DT)

+
Macromolecule #9: DNA (55-MER)

MacromoleculeName: DNA (55-MER) / type: dna / ID: 9 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Molecular weightTheoretical: 30.862684 KDa
SequenceString: (DA)(DA)(DT)(DG)(DC)(DC)(DA)(DT)(DC)(DT) (DC)(DC)(DA)(DG)(DG)(DC)(DT)(DG)(DG)(DC) (DA)(DG)(DC)(DA)(DG)(DA)(DA)(DT)(DG) (DC)(DG)(DA)(DC)(DC)(DT)(DG)(DG)(DA)(DG) (DG) (DT)(DT)(DA)(DA)(DC)(DC) ...String:
(DA)(DA)(DT)(DG)(DC)(DC)(DA)(DT)(DC)(DT) (DC)(DC)(DA)(DG)(DG)(DC)(DT)(DG)(DG)(DC) (DA)(DG)(DC)(DA)(DG)(DA)(DA)(DT)(DG) (DC)(DG)(DA)(DC)(DC)(DT)(DG)(DG)(DA)(DG) (DG) (DT)(DT)(DA)(DA)(DC)(DC)(DG)(DG) (DT)(DG)(DG)(DC)(DA)(DG)(DC)(DA)(DG)(DC) (DT)(DG) (DA)(DC)(DC)(DA)(DC)(DA)(DA) (DC)(DC)(DG)(DA)(DT)(DT)(DT)(DT)(DC)(DT) (DG)(DA)(DC) (DC)(DT)(DG)(DC)(DG)(DC) (DG)(DT)(DT)(DT)(DG)(DC)(DC)(DG)(DG)(DT) (DA)(DC)(DA)(DG)

+
Macromolecule #11: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 11 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

+
Macromolecule #12: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 12 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

+
Macromolecule #13: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 13 / Number of copies: 1 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER / Iron–sulfur cluster

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 66.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.94 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 87743

+
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