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Entry
Database: EMDB / ID: EMD-34816
TitleCryo-EM structure of Mycobacterium tuberculosis transcription initiation complex with transcription factor GlnR
Map data
Sample
  • Complex: Mycobacterium tuberculosis transcription initiation complex with transcription factor GlnR
    • 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
    • Protein or peptide: RNA polymerase sigma factor SigA
    • DNA: Non-template strand DNA of amtB promoter
    • DNA: Template strand DNA of amtB promoter
    • Protein or peptide: Transcriptional regulatory protein
  • Ligand: ZINC ION
  • Ligand: MAGNESIUM ION
Keywordstranscription factor / TRANSCRIPTION-DNA complex
Function / homology
Function and homology information


response to water / Antimicrobial action and antimicrobial resistance in Mtb / phosphorelay response regulator activity / sigma factor activity / nitrate assimilation / DNA-directed RNA polymerase complex / peptidoglycan-based cell wall / DNA-templated transcription initiation / protein-DNA complex / ribonucleoside binding ...response to water / Antimicrobial action and antimicrobial resistance in Mtb / phosphorelay response regulator activity / sigma factor activity / nitrate assimilation / DNA-directed RNA polymerase complex / peptidoglycan-based cell wall / DNA-templated transcription initiation / protein-DNA complex / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / protein dimerization activity / transcription cis-regulatory region binding / response to antibiotic / DNA-templated transcription / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / magnesium ion binding / DNA binding / zinc ion binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
: / Transcription regulator GlnR, N-terminal domain / OmpR/PhoB-type DNA-binding domain profile. / OmpR/PhoB-type DNA-binding domain / Transcriptional regulatory protein, C terminal / 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 ...: / Transcription regulator GlnR, N-terminal domain / OmpR/PhoB-type DNA-binding domain profile. / OmpR/PhoB-type DNA-binding domain / Transcriptional regulatory protein, C terminal / 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 / 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 / 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 Rpb2, domain 2 superfamily / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 3 / 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, beta subunit, protrusion / RNA polymerase beta subunit / 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 / 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
Transcriptional regulatory protein / 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: 3.66 Å
AuthorsLin W / Shi J / Xu JC
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81903526 China
CitationJournal: Proc Natl Acad Sci U S A / Year: 2023
Title: Structural insights into the transcription activation mechanism of the global regulator GlnR from actinobacteria.
Authors: Jing Shi / Zhenzhen Feng / Juncao Xu / Fangfang Li / Yuqiong Zhang / Aijia Wen / Fulin Wang / Qian Song / Lu Wang / Hong Cui / Shujuan Tong / Peiying Chen / Yejin Zhu / Guoping Zhao / Shuang ...Authors: Jing Shi / Zhenzhen Feng / Juncao Xu / Fangfang Li / Yuqiong Zhang / Aijia Wen / Fulin Wang / Qian Song / Lu Wang / Hong Cui / Shujuan Tong / Peiying Chen / Yejin Zhu / Guoping Zhao / Shuang Wang / Yu Feng / Wei Lin /
Abstract: In actinobacteria, an OmpR/PhoB subfamily protein called GlnR acts as an orphan response regulator and globally coordinates the expression of genes responsible for nitrogen, carbon, and phosphate ...In actinobacteria, an OmpR/PhoB subfamily protein called GlnR acts as an orphan response regulator and globally coordinates the expression of genes responsible for nitrogen, carbon, and phosphate metabolism in actinobacteria. Although many researchers have attempted to elucidate the mechanisms of GlnR-dependent transcription activation, progress is impeded by lacking of an overall structure of GlnR-dependent transcription activation complex (GlnR-TAC). Here, we report a co-crystal structure of the C-terminal DNA-binding domain of GlnR (GlnR_DBD) in complex with its regulatory -element DNA and a cryo-EM structure of GlnR-TAC which comprises RNA polymerase, GlnR, and a promoter containing four well-characterized conserved GlnR binding sites. These structures illustrate how four GlnR protomers coordinate to engage promoter DNA in a head-to-tail manner, with four N-terminal receiver domains of GlnR (GlnR-RECs) bridging GlnR_DBDs and the RNAP core enzyme. Structural analysis also unravels that GlnR-TAC is stabilized by complex protein-protein interactions between GlnR and the conserved β flap, σR4, αCTD, and αNTD domains of RNAP, which are further confirmed by our biochemical assays. Taken together, these results reveal a global transcription activation mechanism for the master regulator GlnR and other OmpR/PhoB subfamily proteins and present a unique mode of bacterial transcription regulation.
History
DepositionNov 20, 2022-
Header (metadata) releaseJun 7, 2023-
Map releaseJun 7, 2023-
UpdateJul 3, 2024-
Current statusJul 3, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_34816.png

Downloads & links

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Map

FileDownload / File: emd_34816.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.19 Å
Density
Contour LevelBy AUTHOR: 0.011
Minimum - Maximum-0.04860257 - 0.090691775
Average (Standard dev.)0.00031850976 (±0.0070348834)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 238.00002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_34816_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_34816_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : Mycobacterium tuberculosis transcription initiation complex with ...

EntireName: Mycobacterium tuberculosis transcription initiation complex with transcription factor GlnR
Components
  • Complex: Mycobacterium tuberculosis transcription initiation complex with transcription factor GlnR
    • 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
    • Protein or peptide: RNA polymerase sigma factor SigA
    • DNA: Non-template strand DNA of amtB promoter
    • DNA: Template strand DNA of amtB promoter
    • Protein or peptide: Transcriptional regulatory protein
  • Ligand: ZINC ION
  • Ligand: MAGNESIUM ION

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

SupramoleculeName: Mycobacterium tuberculosis transcription initiation complex with transcription factor GlnR
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: 3 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Mycobacterium tuberculosis (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 (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 (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) / Strain: H37Rv
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 #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 H37Rv (bacteria) / Strain: H37Rv
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: Transcriptional regulatory protein

MacromoleculeName: Transcriptional regulatory protein / type: protein_or_peptide / ID: 8 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis H37Rv (bacteria) / Strain: H37Rv
Molecular weightTheoretical: 27.631398 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MLELLLLTSE LYPDPVLPAL SLLPHTVRTA PAEASSLLEA GNADAVLVDA RNDLSSGRGL CRLLSSTGRS IPVLAVVSEG GLVAVSADW GLDEILLLST GPAEIDARLR LVVGRRGDLA DQESLGKVSL GELVIDEGTY TARLRGRPLD LTYKEFELLK Y LAQHAGRV ...String:
MLELLLLTSE LYPDPVLPAL SLLPHTVRTA PAEASSLLEA GNADAVLVDA RNDLSSGRGL CRLLSSTGRS IPVLAVVSEG GLVAVSADW GLDEILLLST GPAEIDARLR LVVGRRGDLA DQESLGKVSL GELVIDEGTY TARLRGRPLD LTYKEFELLK Y LAQHAGRV FTRAQLLHEV WGYDFFGGTR TVDVHVRRLR AKLGPEHEAL IGTVRNVGYK AVRPARGRPP AADPDDEDAD PG RDGMQEP LVDPLRSQ

UniProtKB: Transcriptional regulatory protein

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Macromolecule #6: Non-template strand DNA of amtB promoter

MacromoleculeName: Non-template strand DNA of amtB promoter / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Molecular weightTheoretical: 33.588414 KDa
SequenceString: (DG)(DG)(DC)(DC)(DG)(DT)(DT)(DC)(DA)(DC) (DC)(DC)(DA)(DC)(DG)(DC)(DG)(DT)(DA)(DA) (DC)(DA)(DC)(DG)(DC)(DA)(DC)(DC)(DG) (DT)(DG)(DC)(DC)(DT)(DT)(DC)(DG)(DT)(DC) (DA) (DC)(DG)(DG)(DC)(DG)(DG) ...String:
(DG)(DG)(DC)(DC)(DG)(DT)(DT)(DC)(DA)(DC) (DC)(DC)(DA)(DC)(DG)(DC)(DG)(DT)(DA)(DA) (DC)(DA)(DC)(DG)(DC)(DA)(DC)(DC)(DG) (DT)(DG)(DC)(DC)(DT)(DT)(DC)(DG)(DT)(DC) (DA) (DC)(DG)(DG)(DC)(DG)(DG)(DC)(DG) (DA)(DA)(DA)(DC)(DA)(DA)(DC)(DG)(DA)(DG) (DG)(DG) (DG)(DC)(DT)(DT)(DC)(DC)(DA) (DC)(DC)(DG)(DA)(DA)(DA)(DC)(DC)(DG)(DC) (DG)(DC)(DT) (DG)(DC)(DG)(DT)(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 #7: Template strand DNA of amtB promoter

MacromoleculeName: Template strand DNA of amtB promoter / type: dna / ID: 7 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Molecular weightTheoretical: 33.854512 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)(DA)(DC)(DG)(DC) (DA)(DG)(DC)(DG)(DC)(DG)(DG)(DT)(DT)(DT) (DC) (DG)(DG)(DT)(DG)(DG)(DA) ...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)(DA)(DC)(DG)(DC) (DA)(DG)(DC)(DG)(DC)(DG)(DG)(DT)(DT)(DT) (DC) (DG)(DG)(DT)(DG)(DG)(DA)(DA)(DG) (DC)(DC)(DC)(DC)(DT)(DC)(DG)(DT)(DT)(DG) (DT)(DT) (DT)(DC)(DG)(DC)(DC)(DG)(DC) (DC)(DG)(DT)(DG)(DA)(DC)(DG)(DA)(DA)(DG) (DG)(DC)(DA) (DC)(DG)(DG)(DT)(DG)(DC) (DG)(DT)(DG)(DT)(DT)(DA)(DC)(DG)(DC)(DG) (DT)(DG)(DG)(DG) (DT)(DG)(DA)(DA)(DC) (DG)(DG)(DC)(DC)

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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

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 57.0 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: 3.66 Å / Resolution method: FSC 0.143 CUT-OFF
Details: The higher resolution region than depositor's reported resolution of the data is reflected by CTF correction or temperature factor correction.
Number images used: 202298
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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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

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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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