[English] 日本語
Yorodumi
- EMDB-33032: Cryo-EM structure of Streptomyces coelicolor RNAP-promoter open c... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-33032
TitleCryo-EM structure of Streptomyces coelicolor RNAP-promoter open complex with three Zur dimers
Map data
Sample
  • Complex: Cryo-EM structure of Streptomyces coelicolor RNAP-promoter open complex with three Zur dimers
    • 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
    • Protein or peptide: Putative metal uptake regulation protein
    • DNA: DNA (84-MER)
    • DNA: DNA (84-MER)
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION
Keywordsrna polymerase / zinc uptake regulator / GENE REGULATION
Function / homology
Function and homology information


regulation of secondary metabolite biosynthetic process / bacterial-type RNA polymerase holo enzyme binding / DNA-binding transcription repressor activity / sigma factor activity / DNA-directed RNA polymerase complex / protein-DNA complex / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase ...regulation of secondary metabolite biosynthetic process / bacterial-type RNA polymerase holo enzyme binding / DNA-binding transcription repressor activity / sigma factor activity / DNA-directed RNA polymerase complex / protein-DNA complex / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / protein dimerization activity / transcription cis-regulatory region binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / DNA-templated transcription / magnesium ion binding / DNA binding / zinc ion binding / cytosol / cytoplasm
Similarity search - Function
Ferric-uptake regulator, C-terminal domain / Ferric-uptake regulator / Ferric uptake regulator family / 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 ...Ferric-uptake regulator, C-terminal domain / Ferric-uptake regulator / Ferric uptake regulator family / 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 / RPB6/omega subunit-like superfamily / RNA polymerase Rpb1, clamp domain superfamily / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 3 / DNA-directed RNA polymerase, subunit beta-prime / 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 / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
DNA-directed RNA polymerase subunit alpha / RNA polymerase principal sigma factor HrdB / DNA-directed RNA polymerase subunit beta' / DNA-directed RNA polymerase subunit omega / DNA-directed RNA polymerase subunit beta / Metal uptake regulation protein
Similarity search - Component
Biological speciesStreptomyces coelicolor A3(2) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.45 Å
AuthorsYang X / Zheng J
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31770068, 32070040 China
CitationJournal: Nucleic Acids Res / Year: 2022
Title: Structural basis of Streptomyces transcription activation by zinc uptake regulator.
Authors: Xu Yang / Yiqun Wang / Guiyang Liu / Zixin Deng / Shuangjun Lin / Jianting Zheng /
Abstract: Streptomyces coelicolor (Sc) is a model organism of actinobacteria to study morphological differentiation and production of bioactive metabolites. Sc zinc uptake regulator (Zur) affects both ...Streptomyces coelicolor (Sc) is a model organism of actinobacteria to study morphological differentiation and production of bioactive metabolites. Sc zinc uptake regulator (Zur) affects both processes by controlling zinc homeostasis. It activates transcription by binding to palindromic Zur-box sequences upstream of -35 elements. Here we deciphered the molecular mechanism by which ScZur interacts with promoter DNA and Sc RNA polymerase (RNAP) by cryo-EM structures and biochemical assays. The ScZur-DNA structures reveal a sequential and cooperative binding of three ScZur dimers surrounding a Zur-box spaced 8 nt upstream from a -35 element. The ScRNAPσHrdB-Zur-DNA structures define protein-protein and protein-DNA interactions involved in the principal housekeeping σHrdB-dependent transcription initiation from a noncanonical promoter with a -10 element lacking the critical adenine residue at position -11 and a TTGCCC -35 element deviating from the canonical TTGACA motif. ScZur interacts with the C-terminal domain of ScRNAP α subunit (αCTD) in a complex structure trapped in an active conformation. Key ScZur-αCTD interfacial residues accounting for ScZur-dependent transcription activation were confirmed by mutational studies. Together, our structural and biochemical results provide a comprehensive model for transcription activation of Zur family regulators.
History
DepositionMar 9, 2022-
Header (metadata) releaseAug 3, 2022-
Map releaseAug 3, 2022-
UpdateJun 26, 2024-
Current statusJun 26, 2024Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_33032.png

Downloads & links

-
Map

FileDownload / File: emd_33032.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 384 pix.
= 403.2 Å		1.05 Å/pix.
x 384 pix.
= 403.2 Å		1.05 Å/pix.
x 384 pix.
= 403.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.05 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03
Minimum - Maximum-1.7577894 - 2.8994122
Average (Standard dev.)0.002692491 (±0.044910464)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 403.19998 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_33032_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_33032_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_33032_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

+
Entire : Cryo-EM structure of Streptomyces coelicolor RNAP-promoter open c...

EntireName: Cryo-EM structure of Streptomyces coelicolor RNAP-promoter open complex with three Zur dimers
Components
  • Complex: Cryo-EM structure of Streptomyces coelicolor RNAP-promoter open complex with three Zur dimers
    • 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
    • Protein or peptide: Putative metal uptake regulation protein
    • DNA: DNA (84-MER)
    • DNA: DNA (84-MER)
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION

+
Supramolecule #1: Cryo-EM structure of Streptomyces coelicolor RNAP-promoter open c...

SupramoleculeName: Cryo-EM structure of Streptomyces coelicolor RNAP-promoter open complex with three Zur dimers
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#8
Source (natural)Organism: Streptomyces coelicolor A3(2) (bacteria)
Molecular weightTheoretical: 560 KDa

+
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 A3(2) (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

+
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 A3(2) (bacteria) / Strain: ATCC BAA-471 / A3(2) / M145
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

+
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 A3(2) (bacteria) / Strain: ATCC BAA-471 / A3(2) / M145
Molecular weightTheoretical: 145.912219 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 GPYNQHHHHH HHH

UniProtKB: DNA-directed RNA polymerase subunit beta'

+
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 A3(2) (bacteria) / Strain: ATCC BAA-471 / A3(2) / M145
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

+
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 A3(2) (bacteria) / Strain: ATCC BAA-471 / A3(2) / M145
Molecular weightTheoretical: 58.188953 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MGSSHHHHHH SSGLVPRGSH MSASTSRTLP PEIAESVSVM ALIERGKAEG QIAGDDVRRA FEADQIPATQ WKNVLRSLNQ ILEEEGVTL MVSAAEPKRT RKSVAAKSPA KRTATKAVAA KPVTSRKATA PAAPAAPATE PAAVEEEAPA KKAAAKKTTA K KATAKKTT ...String:
MGSSHHHHHH SSGLVPRGSH MSASTSRTLP PEIAESVSVM ALIERGKAEG QIAGDDVRRA FEADQIPATQ WKNVLRSLNQ ILEEEGVTL MVSAAEPKRT RKSVAAKSPA KRTATKAVAA KPVTSRKATA PAAPAAPATE PAAVEEEAPA KKAAAKKTTA K KATAKKTT AKKAAAKKTT AKKEDGELLE DEATEEPKAA TEEPEGTENA GFVLSDEDED DAPAQQVAAA GATADPVKDY LK QIGKVPL LNAEQEVELA KRIEAGLFAE DKLANSDKLA PKLKRELEII AEDGRRAKNH LLEANLRLVV SLAKRYTGRG MLF LDLIQE GNLGLIRAVE KFDYTKGYKF STYATWWIRQ AITRAMADQA RTIRIPVHMV EVINKLARVQ RQMLQDLGRE PTPE ELAKE LDMTPEKVIE VQKYGREPIS LHTPLGEDGD SEFGDLIEDS EAVVPADAVS FTLLQEQLHS VLDTLSEREA GVVSM RFGL TDGQPKTLDE IGKVYGVTRE RIRQIESKTM SKLRHPSRSQ VLRDYLD

UniProtKB: RNA polymerase principal sigma factor HrdB

+
Macromolecule #6: Putative metal uptake regulation protein

MacromoleculeName: Putative metal uptake regulation protein / type: protein_or_peptide / ID: 6 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Streptomyces coelicolor A3(2) (bacteria) / Strain: ATCC BAA-471 / A3(2) / M145
Molecular weightTheoretical: 16.90484 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MGSSHHHHHH SSGLVPRGSH MTTAGPPVKG RATRQRAAVS AALQEVEEFR SAQELHDMLK HKGDAVGLTT VYRTLQSLAD AGEVDVLRT AEGESVYRRC STGDHHHHLV CRACGKAVEV EGPAVEKWAE AIAAEHGYVN VAHTVEIFGT CADCAGASGG

UniProtKB: Metal uptake regulation protein

+
Macromolecule #7: DNA (84-MER)

MacromoleculeName: DNA (84-MER) / type: dna / ID: 7 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Streptomyces coelicolor A3(2) (bacteria)
Molecular weightTheoretical: 25.808424 KDa
SequenceString: (DC)(DA)(DA)(DG)(DG)(DC)(DA)(DC)(DA)(DT) (DG)(DA)(DC)(DA)(DA)(DC)(DG)(DG)(DT)(DG) (DT)(DT)(DC)(DA)(DG)(DT)(DG)(DC)(DC) (DG)(DC)(DG)(DT)(DT)(DG)(DC)(DC)(DC)(DG) (DA) (DT)(DA)(DC)(DC)(DC)(DC) ...String:
(DC)(DA)(DA)(DG)(DG)(DC)(DA)(DC)(DA)(DT) (DG)(DA)(DC)(DA)(DA)(DC)(DG)(DG)(DT)(DG) (DT)(DT)(DC)(DA)(DG)(DT)(DG)(DC)(DC) (DG)(DC)(DG)(DT)(DT)(DG)(DC)(DC)(DC)(DG) (DA) (DT)(DA)(DC)(DC)(DC)(DC)(DC)(DT) (DA)(DC)(DC)(DC)(DG)(DT)(DA)(DG)(DT)(DT) (DG)(DA) (DC)(DT)(DG)(DG)(DC)(DA)(DT) (DC)(DC)(DG)(DG)(DG)(DC)(DG)(DC)(DC)(DG) (DG)(DG)(DT) (DC)(DG)(DC)(DC)

GENBANK: GENBANK: AL939129.1

+
Macromolecule #8: DNA (84-MER)

MacromoleculeName: DNA (84-MER) / type: dna / ID: 8 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Streptomyces coelicolor A3(2) (bacteria)
Molecular weightTheoretical: 26.017555 KDa
SequenceString: (DG)(DG)(DC)(DG)(DA)(DC)(DC)(DC)(DG)(DG) (DC)(DG)(DC)(DC)(DC)(DG)(DC)(DT)(DA)(DC) (DG)(DG)(DA)(DG)(DT)(DC)(DA)(DA)(DC) (DT)(DA)(DC)(DG)(DG)(DG)(DT)(DA)(DG)(DG) (DG) (DG)(DG)(DT)(DA)(DT)(DC) ...String:
(DG)(DG)(DC)(DG)(DA)(DC)(DC)(DC)(DG)(DG) (DC)(DG)(DC)(DC)(DC)(DG)(DC)(DT)(DA)(DC) (DG)(DG)(DA)(DG)(DT)(DC)(DA)(DA)(DC) (DT)(DA)(DC)(DG)(DG)(DG)(DT)(DA)(DG)(DG) (DG) (DG)(DG)(DT)(DA)(DT)(DC)(DG)(DG) (DG)(DC)(DA)(DA)(DC)(DG)(DC)(DG)(DG)(DC) (DA)(DC) (DT)(DG)(DA)(DA)(DC)(DA)(DC) (DC)(DG)(DT)(DT)(DG)(DT)(DC)(DA)(DT)(DG) (DT)(DG)(DC) (DC)(DT)(DT)(DG)

+
Macromolecule #9: MAGNESIUM ION

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

+
Macromolecule #10: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 10 / Number of copies: 20 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.8 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
20.0 mMHEPESHEPES
100.0 mMKClKCl
2.0 mMDTTDTT
5.0 mMMgCl2MgCl2
0.02 mMZnSO4ZnSO4
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 289 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 40.0 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

+
Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.45 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 30218
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

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

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more