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- EMDB-36914: Cryo-EM structure of Streptomyces coelicolor transcription initia... -

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Basic information

Entry
Database: EMDB / ID: EMD-36914
TitleCryo-EM structure of Streptomyces coelicolor transcription initiation complex with the global transcription factor AfsR
Map data
Sample
  • Complex: Streptomyces coelicolor transcription initiation complex with the global transcription factor AfsR
    • 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 principal sigma factor HrdB
    • DNA: Non-template strand DNA for AfsS promoter
    • DNA: Template strand DNA for AfsS promoter
    • Protein or peptide: Regulatory protein AfsR
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION
Keywordstranscription factor / TRANSCRIPTION-DNA complex / GENE REGULATION
Function / homology
Function and homology information


pigment binding / bacterial-type RNA polymerase holo enzyme binding / nucleoid / phosphorelay signal transduction system / sigma factor activity / antibiotic biosynthetic process / DNA-directed RNA polymerase complex / DNA-templated transcription initiation / ribonucleoside binding / ADP binding ...pigment binding / bacterial-type RNA polymerase holo enzyme binding / nucleoid / phosphorelay signal transduction system / sigma factor activity / antibiotic biosynthetic process / DNA-directed RNA polymerase complex / DNA-templated transcription initiation / ribonucleoside binding / ADP binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / protein dimerization activity / DNA-templated transcription / regulation of DNA-templated transcription / magnesium ion binding / DNA binding / zinc ion binding / ATP binding / cytoplasm
Similarity search - Function
Bacterial transcriptional activator domain / Bacterial transcriptional activator domain / Bacterial transcriptional activator domain / Tetratricopeptide repeat / NB-ARC / NB-ARC domain / OmpR/PhoB-type DNA-binding domain profile. / OmpR/PhoB-type DNA-binding domain / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein, C terminal ...Bacterial transcriptional activator domain / Bacterial transcriptional activator domain / Bacterial transcriptional activator domain / Tetratricopeptide repeat / NB-ARC / NB-ARC domain / OmpR/PhoB-type DNA-binding domain profile. / OmpR/PhoB-type DNA-binding domain / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein, C terminal / Tetratricopeptide repeat / 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 / 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 / TPR repeat region circular profile. / DNA-directed RNA polymerase, alpha subunit / DNA-directed RNA polymerase beta subunit, bacterial-type / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / RNA polymerase Rpb6 / RNA polymerase, subunit omega/Rpo6/RPB6 / RNA polymerase Rpb6 / RNA polymerase Rpb1, domain 3 superfamily / RPB6/omega subunit-like superfamily / RNA polymerase Rpb1, clamp domain 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 5 / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb1, domain 2 / RNA polymerase Rpb1, domain 5 / 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 / 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 / Tetratricopeptide-like helical domain superfamily / Winged helix-like DNA-binding domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
RNA polymerase principal sigma factor HrdB / Regulatory protein AfsR / DNA-directed RNA polymerase subunit alpha / DNA-directed RNA polymerase subunit beta' / DNA-directed RNA polymerase subunit omega / DNA-directed RNA polymerase subunit beta
Similarity search - Component
Biological speciesStreptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsLin W / Shi J / Xu JC
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81903526 China
CitationJournal: Iscience / Year: 2024
Title: Structural insights into transcription activation of the Streptomyces antibiotic regulatory protein, AfsR
Authors: Shi J / Ye Z / Feng Z / Wen A / Wang L / Zhang Z / Xu L / Song Q / Wang F / Liu T / Wang S / Feng Y / Lin W
History
DepositionJul 24, 2023-
Header (metadata) releaseJul 31, 2024-
Map releaseJul 31, 2024-
UpdateJul 31, 2024-
Current statusJul 31, 2024Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_36914.png

Downloads & links

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Map

FileDownload / File: emd_36914.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 280 pix.
= 308. Å		1.1 Å/pix.
x 280 pix.
= 308. Å		1.1 Å/pix.
x 280 pix.
= 308. Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.007
Minimum - Maximum-0.029425224 - 0.057714265
Average (Standard dev.)0.000018430344 (±0.002237157)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 308.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_36914_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_36914_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : Streptomyces coelicolor transcription initiation complex with the...

EntireName: Streptomyces coelicolor transcription initiation complex with the global transcription factor AfsR
Components
  • Complex: Streptomyces coelicolor transcription initiation complex with the global transcription factor AfsR
    • 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 principal sigma factor HrdB
    • DNA: Non-template strand DNA for AfsS promoter
    • DNA: Template strand DNA for AfsS promoter
    • Protein or peptide: Regulatory protein AfsR
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION

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Supramolecule #1: Streptomyces coelicolor transcription initiation complex with the...

SupramoleculeName: Streptomyces coelicolor transcription initiation complex with the global transcription factor AfsR
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#8
Source (natural)Organism: Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145) (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: Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145) (bacteria)
Molecular weightTheoretical: 36.734641 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MLIAQRPSLT EEVVDEFRSR FVIEPLEPGF GYTLGNSLRR TLLSSIPGAA VTSIRIDGVL HEFTTVPGVK EDVTDLILNI KQLVVSSEH DEPVVMYLRK QGPGLVTAAD IAPPAGVEVH NPDLVLATLN GKGKLEMELT VERGRGYVSA VQNKQVGQEI G RIPVDSIY ...String:
MLIAQRPSLT EEVVDEFRSR FVIEPLEPGF GYTLGNSLRR TLLSSIPGAA VTSIRIDGVL HEFTTVPGVK EDVTDLILNI KQLVVSSEH DEPVVMYLRK QGPGLVTAAD IAPPAGVEVH NPDLVLATLN GKGKLEMELT VERGRGYVSA VQNKQVGQEI G RIPVDSIY SPVLKVTYKV EATRVEQRTD FDKLIVDVET KQAMRPRDAM ASAGKTLVEL FGLARELNID AEGIDMGPSP TD AALAADL ALPIEELELT VRSYNCLKRE GIHSVGELVA RSEADLLDIR NFGAKSIDEV KAKLAGMGLA LKDSPPGFDP TAA ADAFGA DDDADAGFVE TEQY

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: Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145) (bacteria)
Molecular weightTheoretical: 128.644945 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MAASRNASTA NTNNAASTAP LRISFAKIKE PLEVPNLLAL QTESFDWLLG NDAWKARVES ALESGQDVPT KSGLEEIFEE ISPIEDFSG SMSLTFRDHR FEPPKNSIDE CKDRDFTYAA PLFVTAEFTN NETGEIKSQT VFMGDFPLMT NKGTFVINGT E RVVVSQLV ...String:
MAASRNASTA NTNNAASTAP LRISFAKIKE PLEVPNLLAL QTESFDWLLG NDAWKARVES ALESGQDVPT KSGLEEIFEE ISPIEDFSG SMSLTFRDHR FEPPKNSIDE CKDRDFTYAA PLFVTAEFTN NETGEIKSQT VFMGDFPLMT NKGTFVINGT E RVVVSQLV RSPGVYFDSS IDKTSDKDIF SAKIIPSRGA WLEMEIDKRD MVGVRIDRKR KQSVTVLLKA LGWTTEQILE EF GEYESMR ATLEKDHTQG QDDALLDIYR KLRPGEPPTR EAAQTLLENL YFNPKRYDLA KVGRYKVNKK LGADEPLDAG VLT TDDVIA TIKYLVKLHA GETETVGESG REIVVETDDI DHFGNRRIRN VGELIQNQVR TGLARMERVV RERMTTQDVE AITP QTLIN IRPVVASIKE FFGTSQLSQF MDQNNPLSGL THKRRLNALG PGGLSRERAG FEVRDVHPSH YGRMCPIETP EGPNI GLIG SLASYGRINP FGFIETPYRK VVEGQVTDDV DYLTADEEDR FVIAQANAAL GDDMRFAEAR VLVRRRGGEV DYVPGD DVD YMDVSPRQMV SVATAMIPFL EHDDANRALM GANMMRQAVP LIKSESPLVG TGMEYRSAAD AGDVVKAEKA GVVQEVS AD YITTTNDDGT YITYRLAKFS RSNQGTSVNQ KVIVAEGDRI IEGQVLADGP ATENGEMALG KNLLVAFMPW EGHNYEDA I ILSQRLVQDD VLSSIHIEEH EVDARDTKLG PEEITRDIPN VSEEVLADLD ERGIIRIGAE VVAGDILVGK VTPKGETEL TPEERLLRAI FGEKAREVRD TSLKVPHGEI GKVIGVRVFD REEGDELPPG VNQLVRVYVA QKRKITDGDK LAGRHGNKGV ISKINPIED MPFLEDGTPV DIILNPLAVP SRMNPGQVLE IHLGWLASRG WDVSGLAEEW AQRLQVIGAD KVEPGTNVAT P VFDGARED ELAGLLQHTI PNRDGERMVL PSGKARLFDG RSGEPFPEPI SVGYMYILKL HHLVDDKLHA RSTGPYSMIT QQ PLGGKAQ FGGQRFGEME VWALEAYGAA YALQELLTIK SDDVTGRVKV YEAIVKGENI PEPGIPESFK VLIKEMQSLC LNV EVLSSD GMSIEMRDTD EDVFRAAEEL GIDLSRREPS SVEEV

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: Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145) (bacteria)
Molecular weightTheoretical: 144.807078 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MLDVNFFDEL RIGLATADDI RQWSHGEVKK PETINYRTLK PEKDGLFCEK IFGPTRDWEC YCGKYKRVRF KGIICERCGV EVTRAKVRR ERMGHIELAA PVTHIWYFKG VPSRLGYLLD LAPKDLEKVI YFAAYMITFV DEERRTRDLP SLEAHVSVER Q QIEQRRDS ...String:
MLDVNFFDEL RIGLATADDI RQWSHGEVKK PETINYRTLK PEKDGLFCEK IFGPTRDWEC YCGKYKRVRF KGIICERCGV EVTRAKVRR ERMGHIELAA PVTHIWYFKG VPSRLGYLLD LAPKDLEKVI YFAAYMITFV DEERRTRDLP SLEAHVSVER Q QIEQRRDS DLEARAKKLE TDLAELEAEG AKADVRRKVR EGAEREMKQL RDRAQREIDR LDEVWNRFKN LKVQDLEGDE LL YRELRDR FGTYFDGSMG AAALQKRLES FDLDEEAERL REIIRTGKGQ KKTRALKRLK VVSAFLQTSN SPKGMVLDCV PVI PPDLRP MVQLDGGRFA TSDLNDLYRR VINRNNRLKR LLDLGAPEII VNNEKRMLQE AVDALFDNGR RGRPVTGPGN RPLK SLSDM LKGKQGRFRQ NLLGKRVDYS ARSVIVVGPQ LKLHQCGLPK AMALELFKPF VMKRLVDLNH AQNIKSAKRM VERGR TVVY DVLEEVIAEH PVLLNRAPTL HRLGIQAFEP QLVEGKAIQI HPLVCTAFNA DFDGDQMAVH LPLSAEAQAE ARILML SSN NILKPADGRP VTMPTQDMVL GLFFLTTDSE GRSPKGEGRA FGSSAEAIMA FDAGDLTLQA KIDIRFPVGT IPPRGFE PP AREEGEPEWQ QGDTFTLKTT LGRALFNELL PEDYPFVDYE VGKKQLSEIV NDLAERYPKV IVAATLDNLK AAGFFWAT R SGVTVAISDI VVPDAKKEIV KGYEGQDEKV QKQYERGLIT KEERTQELIA IWTKATNEVA EAMNDNFPKT NPVSMMVNS GARGNMMQMR QIAGMRGLVS NAKNETIPRP IKASFREGLS VLEYFISTHG ARKGLADTAL RTADSGYLTR RLVDVSQDVI IREEDCGTE RGLKLPIATR DADGTLRKAE DVETSVYARM LAEDVVIDGK VIAPANVDLG DVLIDALVAH GVEEVKTRSI L TCESQVGT CAMCYGRSLA TGKLVDIGEA VGIIAAQSIG EPGTQLTMRT FHTGGVAGDD ITQGLPRVVE LFEARTPKGV AP ISEASGR VRIEETEKTK KIVVTPDDGS DETAFPISKR ARLLVGEGDH VEVGQKLTVG ATNPHDVLRI LGQRAVQVHL VGE VQKVYN SQGVSIHDKH IEIIIRQMLR RVTIIESGDA ELLPGELVER TKFETENRRV VQEGGHPASG RPQLMGITKA SLAT ESWLS AASFQETTRV LTDAAINAKS DSLIGLKENV IIGKLIPAGT GLSRYRNIRV EPTEEAKAAM YSAVGYDDID YSPFG TGSG QAVPLEDYDY GPYNQ

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: Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145) (bacteria)
Molecular weightTheoretical: 9.716941 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MSSSISAPEG IINPPIDELL EATDSKYSLV IYAAKRARQI NAYYSQLGEG LLEYVGPLVD THVHEKPLSI ALREINAGLL TSEAIEGPA Q

UniProtKB: DNA-directed RNA polymerase subunit omega

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Macromolecule #5: RNA polymerase principal sigma factor HrdB

MacromoleculeName: RNA polymerase principal sigma factor HrdB / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145) (bacteria)
Molecular weightTheoretical: 56.017578 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MSASTSRTLP PEIAESVSVM ALIERGKAEG QIAGDDVRRA FEADQIPATQ WKNVLRSLNQ ILEEEGVTLM VSAAEPKRTR KSVAAKSPA KRTATKAVAA KPVTSRKATA PAAPAAPATE PAAVEEEAPA KKAAAKKTTA KKATAKKTTA KKAAAKKTTA K KEDGELLE ...String:
MSASTSRTLP PEIAESVSVM ALIERGKAEG QIAGDDVRRA FEADQIPATQ WKNVLRSLNQ ILEEEGVTLM VSAAEPKRTR KSVAAKSPA KRTATKAVAA KPVTSRKATA PAAPAAPATE PAAVEEEAPA KKAAAKKTTA KKATAKKTTA KKAAAKKTTA K KEDGELLE DEATEEPKAA TEEPEGTENA GFVLSDEDED DAPAQQVAAA GATADPVKDY LKQIGKVPLL NAEQEVELAK RI EAGLFAE DKLANSDKLA PKLKRELEII AEDGRRAKNH LLEANLRLVV SLAKRYTGRG MLFLDLIQEG NLGLIRAVEK FDY TKGYKF STYATWWIRQ AITRAMADQA RTIRIPVHMV EVINKLARVQ RQMLQDLGRE PTPEELAKEL DMTPEKVIEV QKYG REPIS LHTPLGEDGD SEFGDLIEDS EAVVPADAVS FTLLQEQLHS VLDTLSEREA GVVSMRFGLT DGQPKTLDEI GKVYG VTRE RIRQIESKTM SKLRHPSRSQ VLRDYLD

UniProtKB: RNA polymerase principal sigma factor HrdB

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Macromolecule #8: Regulatory protein AfsR

MacromoleculeName: Regulatory protein AfsR / type: protein_or_peptide / ID: 8 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145) (bacteria)
Molecular weightTheoretical: 105.842578 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MDGGPRVPEQ RRPGFPAEEE ESGALRFGVL GPVRAWRDGE TLATGSPQQR ALLAALLLRE GRTATAGELI DALWGEEPPS QALAAVRTY ASRLRKVLDP GVLVSESGGY AVRGLAEGAL DLARAQDLAS AAEKARSAGD LCHARDLLRR ALDLWDGEVL A GVPGPYAQ ...String:
MDGGPRVPEQ RRPGFPAEEE ESGALRFGVL GPVRAWRDGE TLATGSPQQR ALLAALLLRE GRTATAGELI DALWGEEPPS QALAAVRTY ASRLRKVLDP GVLVSESGGY AVRGLAEGAL DLARAQDLAS AAEKARSAGD LCHARDLLRR ALDLWDGEVL A GVPGPYAQ TQRVRLGEWR LQLLETRLDM DLDQGCHAEA VSELTALTAA HPLRERLREL LMLALYRSGR QAEALAVYAD TR RLLADEL GVDPRPGLQE LQQRILQADP ALAELSAATA ETATATLRPA QLPATVSDFT GRAAFVRELS DVLSAASGES ASG RVMAVS ALAGIGGVGK TTLAVHVAHR ARAAFPDGQL YVDLQGAGAR PAEPETVLGS FLRALGTADS AIPDSLEERA ALYR SVLDG RRVLVLLDNA RDAAQVRPLL PGTDGCAALV TARVRMVDLA GAHLVDLDVM APEEALALFT KIVGEERVAS ERQAA LDVV GACGFLPLAI RIAASRLAAR RTWTVSVLAA KLADERRRLD ELQAGDQAVE ATFELGYGQL EPAQARAFRL LGLADG PDI SLAAAAAVLD LPAQDTEDLL ESLVDTSLLE SAAPGRYRFH DLVRLYARAC AERTERDGNA PSERGAALSR LLDFYLA TA AGVYAIERPG DRLVDGLEPT EYPGLTFTEG SAALDWLYTE AAPLLACVRQ SAGTARLRRA VDLLWAAKDL TESGANSH Q YEATARAMCD ATGSAADTRA EGRARTVLSD VLLVSGRIEH AEEEARLAMR LAGSAEDSAA VSWVANNRGL VCLHQRRYA EGKGLFHQAI AGFRATDNRA GEASALSNLS RAQLGMGNVA EAVDIARQGL AVYAELGRTM RLANGHFALG VALTRAGRHE EALGEFAEA LDLFGDHRQR LWEGATNFRL AEVHLAAGRP SSAAQHAEQA LALGCIGGDR MRGNVLALLG RALSALGQAD R ARACWREA LSLYEQHDAQ EVGEVRALLA RSVAR

UniProtKB: Regulatory protein AfsR

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Macromolecule #6: Non-template strand DNA for AfsS promoter

MacromoleculeName: Non-template strand DNA for AfsS promoter / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145) (bacteria)
Molecular weightTheoretical: 18.177602 KDa
SequenceString: (DC)(DC)(DG)(DG)(DA)(DG)(DC)(DG)(DT)(DT) (DC)(DA)(DG)(DC)(DG)(DT)(DT)(DC)(DG)(DT) (DT)(DT)(DA)(DT)(DC)(DT)(DC)(DC)(DC) (DC)(DC)(DT)(DG)(DG)(DT)(DA)(DT)(DA)(DA) (DT) (DG)(DG)(DG)(DA)(DG)(DC) ...String:
(DC)(DC)(DG)(DG)(DA)(DG)(DC)(DG)(DT)(DT) (DC)(DA)(DG)(DC)(DG)(DT)(DT)(DC)(DG)(DT) (DT)(DT)(DA)(DT)(DC)(DT)(DC)(DC)(DC) (DC)(DC)(DT)(DG)(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 #7: Template strand DNA for AfsS promoter

MacromoleculeName: Template strand DNA for AfsS promoter / type: dna / ID: 7 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145) (bacteria)
Molecular weightTheoretical: 18.36077 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)(DC)(DA)(DG) (DG)(DG)(DG)(DG)(DA)(DG)(DA)(DT)(DA)(DA) (DA) (DC)(DG)(DA)(DA)(DC)(DG) ...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)(DC)(DA)(DG) (DG)(DG)(DG)(DG)(DA)(DG)(DA)(DT)(DA)(DA) (DA) (DC)(DG)(DA)(DA)(DC)(DG)(DC)(DT) (DG)(DA)(DA)(DC)(DG)(DC)(DT)(DC)(DC)(DG) (DG)

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Macromolecule #9: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 9 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #10: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 10 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 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 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:

7vpd

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 231221
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

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External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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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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