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- EMDB-62294: Cryo-EM structure of Mycobacterium tuberculosis transcription act... -

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Basic information

Entry
Database: EMDB / ID: EMD-62294
TitleCryo-EM structure of Mycobacterium tuberculosis transcription activation complex with four PhoP molecules (composite map)
Map data
Sample
  • Complex: Mycobacterium tuberculosis transcription activation complex with four PhoP molecules (composite map)
    • Protein or peptide: DNA-directed RNA polymerase subunit alpha
    • Protein or peptide: DNA-directed RNA polymerase subunit beta
    • Protein or peptide: DNA-directed RNA polymerase subunit beta'
    • Protein or peptide: DNA-directed RNA polymerase subunit omega
    • DNA: Non-template strand DNA of the promoter
    • DNA: Template strand DNA of the promoter
    • Protein or peptide: RNA polymerase sigma factor SigA
    • Protein or peptide: Possible two component system response transcriptional positive regulator PhoP
  • Ligand: ZINC ION
  • Ligand: MAGNESIUM ION
Keywordsbacterial RNA polymerase / GENE REGULATION-DNA COMPLEX
Function / homology
Function and homology information


protein secretion by the type VII secretion system / glycolipid biosynthetic process / response to water / Antimicrobial action and antimicrobial resistance in Mtb / phosphorelay response regulator activity / sigma factor activity / bacterial-type RNA polymerase core enzyme binding / cytosolic DNA-directed RNA polymerase complex / positive regulation of lipid biosynthetic process / DNA-directed RNA polymerase complex ...protein secretion by the type VII secretion system / glycolipid biosynthetic process / response to water / Antimicrobial action and antimicrobial resistance in Mtb / phosphorelay response regulator activity / sigma factor activity / bacterial-type RNA polymerase core enzyme binding / cytosolic DNA-directed RNA polymerase complex / positive regulation of lipid biosynthetic process / DNA-directed RNA polymerase complex / peptidoglycan-based cell wall / DNA-templated transcription initiation / protein-DNA complex / ribonucleoside binding / : / : / : / : / : / : / DNA-directed RNA polymerase / response to oxidative stress / transcription cis-regulatory region binding / protein dimerization activity / response to antibiotic / negative regulation of DNA-templated transcription / positive regulation of gene expression / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / magnesium ion binding / DNA binding / zinc ion binding / metal ion binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
OmpR/PhoB-type DNA-binding domain / Transcriptional regulatory protein, C terminal / OmpR/PhoB-type DNA-binding domain profile. / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein WalR-like / Signal transduction response regulator, C-terminal effector / Sigma-70 factors family signature 1. / RNA polymerase sigma factor RpoD, C-terminal / RNA polymerase sigma factor RpoD / : ...OmpR/PhoB-type DNA-binding domain / Transcriptional regulatory protein, C terminal / OmpR/PhoB-type DNA-binding domain profile. / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein WalR-like / Signal transduction response regulator, C-terminal effector / 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 / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / 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 / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb6 / RNA polymerase, subunit omega/Rpo6/RPB6 / RNA polymerase Rpb6 / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase Rpb1, domain 3 superfamily / RPB6/omega subunit-like superfamily / 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 / RNA polymerase Rpb1, clamp domain superfamily / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 1 / RNA polymerase, beta subunit, protrusion / RNA polymerase beta subunit / RNA polymerase, alpha subunit / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb1, domain 2 / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / DNA-directed RNA polymerase, insert domain superfamily / RNA polymerase, N-terminal / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase I subunit A N-terminus / RNA polymerase Rpb2, domain 2 / RNA polymerase Rpb2, domain 2 / RNA polymerase, RBP11-like subunit / 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
Possible two component system response transcriptional positive regulator PhoP / RNA polymerase sigma factor SigA / DNA-directed RNA polymerase subunit omega / DNA-directed RNA polymerase subunit beta' / DNA-directed RNA polymerase subunit beta / DNA-directed RNA polymerase subunit alpha
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria) / Mycobacterium tuberculosis H37Rv (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsLin W / Feng Y
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nat Commun / Year: 2025
Title: Structural insights into transcription regulation of the global OmpR/PhoB family regulator PhoP from Mycobacterium tuberculosis.
Authors: Jing Shi / Zhenzhen Feng / Qian Song / Aijia Wen / Tianyu Liu / Liqiao Xu / Zonghang Ye / Simin Xu / Fei Gao / Liuxiang Xiao / Jiapeng Zhu / Kalyan Das / Guoping Zhao / Jie Li / Yu Feng / Wei Lin /
Abstract: As a global transcription activator or repressor, the representative OmpR/PhoB family response regulator PhoP plays a crucial role in regulating bacterial pathogenicity and stress adaptation. ...As a global transcription activator or repressor, the representative OmpR/PhoB family response regulator PhoP plays a crucial role in regulating bacterial pathogenicity and stress adaptation. However, the molecular mechanisms underlying the transcriptional regulation that define its differential functions remain largely unclear. In the present study, we determine three cryo-EM structures of Mycobacterium tuberculosis (Mtb) PhoP-dependent transcription activation complexes (PhoP-TACs) and build one preliminary cryo-EM structure model of Mtb PhoP-dependent transcription repression complex (PhoP-TRC). In PhoP-TACs, tandem PhoP dimers cooperatively recognize various types of promoters through conserved PhoP-PHO box interactions, which displace the canonical interactions between the -35 element and σR4 of RNA polymerase (RNAP), unraveling complex transcription activation mechanisms of PhoP. In PhoP-TRC, one PhoP dimer binds and significantly distorts the upstream PHO box of the promoter cross-talked with the global nitrogen regulator GlnR through the PhoP-PHO box, PhoP-GlnR and αCTD-DNA interactions. This unique binding of PhoP creates steric hindrances that prevent additional GlnR binding, positioning PhoP within a unique 'competitive occluding model', as supported by prior biochemical observations. Collectively, these findings reveal the dual molecular mechanisms of PhoP-dependent transcription regulation, and offer valuable insights for further exploration of the enormous PhoP-like OmpR/PhoB family response regulators.
History
DepositionNov 5, 2024-
Header (metadata) releaseMar 5, 2025-
Map releaseMar 5, 2025-
UpdateMar 12, 2025-
Current statusMar 12, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_62294.png

Downloads & links

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Map

FileDownload / File: emd_62294.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.2 Å/pix.
x 256 pix.
= 307.2 Å		1.2 Å/pix.
x 256 pix.
= 307.2 Å		1.2 Å/pix.
x 256 pix.
= 307.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.2 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04
Minimum - Maximum-0.19266506 - 0.39808488
Average (Standard dev.)-0.0012295464 (±0.01890109)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 307.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Mycobacterium tuberculosis transcription activation complex with ...

EntireName: Mycobacterium tuberculosis transcription activation complex with four PhoP molecules (composite map)
Components
  • Complex: Mycobacterium tuberculosis transcription activation complex with four PhoP molecules (composite map)
    • Protein or peptide: DNA-directed RNA polymerase subunit alpha
    • Protein or peptide: DNA-directed RNA polymerase subunit beta
    • Protein or peptide: DNA-directed RNA polymerase subunit beta'
    • Protein or peptide: DNA-directed RNA polymerase subunit omega
    • DNA: Non-template strand DNA of the promoter
    • DNA: Template strand DNA of the promoter
    • Protein or peptide: RNA polymerase sigma factor SigA
    • Protein or peptide: Possible two component system response transcriptional positive regulator PhoP
  • Ligand: ZINC ION
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Mycobacterium tuberculosis transcription activation complex with ...

SupramoleculeName: Mycobacterium tuberculosis transcription activation complex with four PhoP molecules (composite map)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#8
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)

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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 H37Rv (bacteria)
Molecular weightTheoretical: 37.745328 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
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

UniProtKB: DNA-directed RNA polymerase subunit alpha

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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 H37Rv (bacteria)
Molecular weightTheoretical: 130.018828 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MLEGCILADS RQSKTAASPS PSRPQSSSNN SVPGAPNRVS FAKLREPLEV PGLLDVQTDS FEWLIGSPRW RESAAERGDV NPVGGLEEV LYELSPIEDF SGSMSLSFSD PRFDDVKAPV DECKDKDMTY AAPLFVTAEF INNNTGEIKS QTVFMGDFPM M TEKGTFII ...String:
MLEGCILADS RQSKTAASPS PSRPQSSSNN SVPGAPNRVS FAKLREPLEV PGLLDVQTDS FEWLIGSPRW RESAAERGDV NPVGGLEEV LYELSPIEDF SGSMSLSFSD PRFDDVKAPV DECKDKDMTY AAPLFVTAEF INNNTGEIKS QTVFMGDFPM M TEKGTFII NGTERVVVSQ LVRSPGVYFD ETIDKSTDKT LHSVKVIPSR GAWLEFDVDK RDTVGVRIDR KRRQPVTVLL KA LGWTSEQ IVERFGFSEI MRSTLEKDNT VGTDEALLDI YRKLRPGEPP TKESAQTLLE NLFFKEKRYD LARVGRYKVN KKL GLHVGE PITSSTLTEE DVVATIEYLV RLHEGQTTMT VPGGVEVPVE TDDIDHFGNR RLRTVGELIQ NQIRVGMSRM ERVV RERMT TQDVEAITPQ TLINIRPVVA AIKEFFGTSQ LSQFMDQNNP LSGLTHKRRL SALGPGGLSR ERAGLEVRDV HPSHY GRMC PIETPEGPNI GLIGSLSVYA RVNPFGFIET PYRKVVDGVV SDEIVYLTAD EEDRHVVAQA NSPIDADGRF VEPRVL VRR KAGEVEYVPS SEVDYMDVSP RQMVSVATAM IPFLEHDDAN RALMGANMQR QAVPLVRSEA PLVGTGMELR AAIDAGD VV VAEESGVIEE VSADYITVMH DNGTRRTYRM RKFARSNHGT CANQCPIVDA GDRVEAGQVI ADGPCTDDGE MALGKNLL V AIMPWEGHNY EDAIILSNRL VEEDVLTSIH IEEHEIDARD TKLGAEEITR DIPNISDEVL ADLDERGIVR IGAEVRDGD ILVGKVTPKG ETELTPEERL LRAIFGEKAR EVRDTSLKVP HGESGKVIGI RVFSREDEDE LPAGVNELVR VYVAQKRKIS DGDKLAGRH GNKGVIGKIL PVEDMPFLAD GTPVDIILNT HGVPRRMNIG QILETHLGWC AHSGWKVDAA KGVPDWAARL P DELLEAQP NAIVSTPVFD GAQEAELQGL LSCTLPNRDG DVLVDADGKA MLFDGRSGEP FPYPVTVGYM YIMKLHHLVD DK IHARSTG PYSMITQQPL GGKAQFGGQR FGEMECWAMQ AYGAAYTLQE LLTIKSDDTV GRVKVYEAIV KGENIPEPGI PES FKVLLK ELQSLCLNVE VLSSDGAAIE LREGEDEDLE RAAANLGINL SRNESASVED LA

UniProtKB: DNA-directed RNA polymerase subunit beta

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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 H37Rv (bacteria)
Molecular weightTheoretical: 146.968969 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MLDVNFFDEL RIGLATAEDI RQWSYGEVKK PETINYRTLK PEKDGLFCEK IFGPTRDWEC YCGKYKRVRF KGIICERCGV EVTRAKVRR ERMGHIELAA PVTHIWYFKG VPSRLGYLLD LAPKDLEKII YFAAYVITSV DEEMRHNELS TLEAEMAVER K AVEDQRDG ...String:
MLDVNFFDEL RIGLATAEDI RQWSYGEVKK PETINYRTLK PEKDGLFCEK IFGPTRDWEC YCGKYKRVRF KGIICERCGV EVTRAKVRR ERMGHIELAA PVTHIWYFKG VPSRLGYLLD LAPKDLEKII YFAAYVITSV DEEMRHNELS TLEAEMAVER K AVEDQRDG ELEARAQKLE ADLAELEAEG AKADARRKVR DGGEREMRQI RDRAQRELDR LEDIWSTFTK LAPKQLIVDE NL YRELVDR YGEYFTGAMG AESIQKLIEN FDIDAEAESL RDVIRNGKGQ KKLRALKRLK VVAAFQQSGN SPMGMVLDAV PVI PPELRP MVQLDGGRFA TSDLNDLYRR VINRNNRLKR LIDLGAPEII VNNEKRMLQE SVDALFDNGR RGRPVTGPGN RPLK SLSDL LKGKQGRFRQ NLLGKRVDYS GRSVIVVGPQ LKLHQCGLPK LMALELFKPF VMKRLVDLNH AQNIKSAKRM VERQR PQVW DVLEEVIAEH PVLLNRAPTL HRLGIQAFEP MLVEGKAIQL HPLVCEAFNA DFDGDQMAVH LPLSAEAQAE ARILML SSN NILSPASGRP LAMPRLDMVT GLYYLTTEVP GDTGEYQPAS GDHPETGVYS SPAEAIMAAD RGVLSVRAKI KVRLTQL RP PVEIEAELFG HSGWQPGDAW MAETTLGRVM FNELLPLGYP FVNKQMHKKV QAAIINDLAE RYPMIVVAQT VDKLKDAG F YWATRSGVTV SMADVLVPPR KKEILDHYEE RADKVEKQFQ RGALNHDERN EALVEIWKEA TDEVGQALRE HYPDDNPII TIVDSGATGN FTQTRTLAGM KGLVTNPKGE FIPRPVKSSF REGLTVLEYF INTHGARKGL ADTALRTADS GYLTRRLVDV SQDVIVREH DCQTERGIVV ELAERAPDGT LIRDPYIETS AYARTLGTDA VDEAGNVIVE RGQDLGDPEI DALLAAGITQ V KVRSVLTC ATSTGVCATC YGRSMATGKL VDIGEAVGIV AAQSIGEPGT QLTMRTFHQG GVGEDITGGL PRVQELFEAR VP RGKAPIA DVTGRVRLED GERFYKITIV PDDGGEEVVY DKISKRQRLR VFKHEDGSER VLSDGDHVEV GQQLMEGSAD PHE VLRVQG PREVQIHLVR EVQEVYRAQG VSIHDKHIEV IVRQMLRRVT IIDSGSTEFL PGSLIDRAEF EAENRRVVAE GGEP AAGRP VLMGITKASL ATDSWLSAAS FQETTRVLTD AAINCRSDKL NGLKENVIIG KLIPAGTGIN RYRNIAVQPT EEARA AAYT IPSYEDQYYS PDFGAATGAA VPLDDYGYSD YR

UniProtKB: DNA-directed RNA polymerase subunit beta'

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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 H37Rv (bacteria)
Molecular weightTheoretical: 11.85114 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MSISQSDASL AAVPAVDQFD PSSGASGGYD TPLGITNPPI DELLDRVSSK YALVIYAAKR ARQINDYYNQ LGEGILEYVG PLVEPGLQE KPLSIALREI HADLLEHTEG E

UniProtKB: DNA-directed RNA polymerase subunit omega

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Macromolecule #7: RNA polymerase sigma factor SigA

MacromoleculeName: RNA polymerase sigma factor SigA / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis H37Rv (bacteria)
Molecular weightTheoretical: 57.87716 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MAATKASTAT DEPVKRTATK SPAASASGAK TGAKRTAAKS ASGSPPAKRA TKPAARSVKP ASAPQDTTTS TIPKRKTRAA AKSAAAKAP SARGHATKPR APKDAQHEAA TDPEDALDSV EELDAEPDLD VEPGEDLDLD AADLNLDDLE DDVAPDADDD L DSGDDEDH ...String:
MAATKASTAT 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

UniProtKB: RNA polymerase sigma factor SigA

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Macromolecule #8: Possible two component system response transcriptional positive r...

MacromoleculeName: Possible two component system response transcriptional positive regulator PhoP
type: protein_or_peptide / ID: 8 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis H37Rv (bacteria)
Molecular weightTheoretical: 27.550488 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MRKGVDLVTA GTPGENTTPE ARVLVVDDEA NIVELLSVSL KFQGFEVYTA TNGAQALDRA RETRPDAVIL DVMMPGMDGF GVLRRLRAD GIDAPALFLT ARDSLQDKIA GLTLGGDDYV TKPFSLEEVV ARLRVILRRA GKGNKEPRNV RLTFADIELD E ETHEVWKA ...String:
MRKGVDLVTA GTPGENTTPE ARVLVVDDEA NIVELLSVSL KFQGFEVYTA TNGAQALDRA RETRPDAVIL DVMMPGMDGF GVLRRLRAD GIDAPALFLT ARDSLQDKIA GLTLGGDDYV TKPFSLEEVV ARLRVILRRA GKGNKEPRNV RLTFADIELD E ETHEVWKA GQPVSLSPTE FTLLRYFVIN AGTVLSKPKI LDHVWRYDFG GDVNVVESYV SYLRRKIDTG EKRLLHTLRG VG YVLREPR

UniProtKB: Possible two component system response transcriptional positive regulator PhoP

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Macromolecule #5: Non-template strand DNA of the promoter

MacromoleculeName: Non-template strand DNA of the promoter / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Mycobacterium tuberculosis H37Rv (bacteria)
Molecular weightTheoretical: 30.421381 KDa
SequenceString: (DC)(DT)(DC)(DG)(DT)(DC)(DG)(DC)(DC)(DC) (DA)(DG)(DA)(DG)(DT)(DT)(DC)(DA)(DC)(DC) (DT)(DT)(DG)(DG)(DA)(DG)(DC)(DC)(DA) (DG)(DG)(DG)(DA)(DC)(DG)(DG)(DT)(DT)(DC) (DA) (DT)(DT)(DT)(DG)(DG)(DG) ...String:
(DC)(DT)(DC)(DG)(DT)(DC)(DG)(DC)(DC)(DC) (DA)(DG)(DA)(DG)(DT)(DT)(DC)(DA)(DC)(DC) (DT)(DT)(DG)(DG)(DA)(DG)(DC)(DC)(DA) (DG)(DG)(DG)(DA)(DC)(DG)(DG)(DT)(DT)(DC) (DA) (DT)(DT)(DT)(DG)(DG)(DG)(DG)(DT) (DG)(DC)(DC)(DG)(DG)(DA)(DA)(DA)(DC)(DG) (DG)(DA) (DC)(DG)(DC)(DG)(DT)(DA)(DC) (DA)(DG)(DG)(DC)(DC)(DG)(DT)(DA)(DT)(DA) (DA)(DT)(DG) (DG)(DG)(DA)(DG)(DC)(DT) (DG)(DT)(DC)(DA)(DC)(DG)(DG)(DA)(DT)(DG) (DC)(DA)

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Macromolecule #6: Template strand DNA of the promoter

MacromoleculeName: Template strand DNA of the promoter / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Mycobacterium tuberculosis H37Rv (bacteria)
Molecular weightTheoretical: 30.854664 KDa
SequenceString: (DT)(DG)(DC)(DA)(DT)(DC)(DC)(DG)(DT)(DG) (DA)(DG)(DT)(DC)(DG)(DA)(DG)(DG)(DG)(DT) (DA)(DA)(DT)(DA)(DA)(DC)(DG)(DG)(DC) (DC)(DT)(DG)(DT)(DA)(DC)(DG)(DC)(DG)(DT) (DC) (DC)(DG)(DT)(DT)(DT)(DC) ...String:
(DT)(DG)(DC)(DA)(DT)(DC)(DC)(DG)(DT)(DG) (DA)(DG)(DT)(DC)(DG)(DA)(DG)(DG)(DG)(DT) (DA)(DA)(DT)(DA)(DA)(DC)(DG)(DG)(DC) (DC)(DT)(DG)(DT)(DA)(DC)(DG)(DC)(DG)(DT) (DC) (DC)(DG)(DT)(DT)(DT)(DC)(DC)(DG) (DG)(DC)(DA)(DC)(DC)(DC)(DC)(DA)(DA)(DA) (DT)(DG) (DA)(DA)(DC)(DC)(DG)(DT)(DC) (DC)(DC)(DT)(DG)(DG)(DC)(DT)(DC)(DC)(DA) (DA)(DG)(DG) (DT)(DG)(DA)(DA)(DC)(DT) (DC)(DT)(DG)(DG)(DG)(DC)(DG)(DA)(DC)(DG) (DA)(DG)(DT)(DG)

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Macromolecule #9: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 9 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #10: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 10 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.9
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 52.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6vvy

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 46239
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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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

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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

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