[English] 日本語
Yorodumi
- EMDB-71615: The cryo-EM structure of C. crescentus DriD-ssDNA-RNAP-Sigma73-CC... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-71615
TitleThe cryo-EM structure of C. crescentus DriD-ssDNA-RNAP-Sigma73-CCNA_03891/CCNA_01149 promoter transcription activation complex
Map data
Sample
  • Complex: The cryo-EM structure of C. crescentus DriD-ssDNA-RNAP-Sigma73-CCNA_03891/CCNA_01149 promoter transcription activation complex
    • Protein or peptide: x 6 types
    • DNA: x 3 types
  • Ligand: x 2 types
KeywordsCCNA_03891-CCNA_01149 promoter Transcription Activation Complex / DriD / Caulobacter / TRANSCRIPTION / TRANSCRIPTION-DNA complex
Function / homology
Function and homology information


sigma factor activity / DNA-directed RNA polymerase complex / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed RNA polymerase / DNA-directed RNA polymerase activity / protein dimerization activity / DNA-templated transcription / magnesium ion binding / DNA binding ...sigma factor activity / DNA-directed RNA polymerase complex / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed RNA polymerase / DNA-directed RNA polymerase activity / protein dimerization activity / DNA-templated transcription / magnesium ion binding / DNA binding / zinc ion binding / cytoplasm
Similarity search - Function
: / WCX domain / : / WYL domain profile. / WYL domain / WYL domain / RNA polymerase sigma factor 70, non-essential domain / Sigma-70, non-essential region / RNA polymerase sigma factor 70, region 1.1 / Sigma-70 factor, region 1.1 superfamily ...: / WCX domain / : / WYL domain profile. / WYL domain / WYL domain / RNA polymerase sigma factor 70, non-essential domain / Sigma-70, non-essential region / RNA polymerase sigma factor 70, region 1.1 / Sigma-70 factor, region 1.1 superfamily / Sigma-70 factor, region 1.1 / 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 beta subunit, bacterial-type / DNA-directed RNA polymerase, alpha subunit / 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, beta subunit, protrusion / RNA polymerase beta subunit / 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 / DNA-directed RNA polymerase, insert domain superfamily / RNA polymerase Rpb2, domain 2 / RNA polymerase Rpb2, domain 2 / RNA polymerase, N-terminal / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase I subunit A N-terminus / 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
RNA polymerase sigma factor RpoD / DNA-directed RNA polymerase subunit omega / DNA-directed RNA polymerase subunit alpha / Uncharacterized protein / DNA-directed RNA polymerase subunit beta' / DNA-directed RNA polymerase subunit beta
Similarity search - Component
Biological speciesCaulobacter vibrioides NA1000 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsSingh RR / Schumacher MA
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM130290 United States
Citation
Journal: To Be Published
Title: The cryo-EM structure of C. crescentus RNAP-Sigma73-CCNA_03891/CCNA_01149 promoter complex
Authors: Singh RR / Schumacher MA
#1: Journal: To Be Published
Title: The cryo-EM structure of C. crescentus RNAP-Sigma73-CCNA_03891/CCNA_01149 promoter complex
Authors: Singh RR / Schumacher MA
#2: Journal: To Be Published
Title: The cryo-EM structure of C. crescentus DriD-ssDNA-RNAP-Sigma73-didA promoter transcription activation complex
Authors: Singh RR / Schumacher MA
#3: Journal: To Be Published
Title: The cryo-EM structure of C. crescentus DriD-ssDNA-RNAP-Sigma73-bapE promoter transcription activation complex
Authors: Singh RR / Schumacher MA
History
DepositionJul 6, 2025-
Header (metadata) releaseFeb 25, 2026-
Map releaseFeb 25, 2026-
UpdateFeb 25, 2026-
Current statusFeb 25, 2026Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_71615.png

Downloads & links

-
Map

FileDownload / File: emd_71615.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.08 Å/pix.
x 384 pix.
= 414.72 Å		1.08 Å/pix.
x 384 pix.
= 414.72 Å		1.08 Å/pix.
x 384 pix.
= 414.72 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0128
Minimum - Maximum-0.35544467 - 0.5504555
Average (Standard dev.)0.000000000000002 (±0.009786629)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 414.72003 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_71615_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_71615_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_71615_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

+
Entire : The cryo-EM structure of C. crescentus DriD-ssDNA-RNAP-Sigma73-CC...

EntireName: The cryo-EM structure of C. crescentus DriD-ssDNA-RNAP-Sigma73-CCNA_03891/CCNA_01149 promoter transcription activation complex
Components
  • Complex: The cryo-EM structure of C. crescentus DriD-ssDNA-RNAP-Sigma73-CCNA_03891/CCNA_01149 promoter transcription activation complex
    • 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 RpoD
    • DNA: DNA (66-MER)-non template
    • DNA: DNA (53-MER)-template
    • Protein or peptide: WYL domain-containing protein
    • DNA: DNA (5'-D(P*GP*TP*C)-3')
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION

+
Supramolecule #1: The cryo-EM structure of C. crescentus DriD-ssDNA-RNAP-Sigma73-CC...

SupramoleculeName: The cryo-EM structure of C. crescentus DriD-ssDNA-RNAP-Sigma73-CCNA_03891/CCNA_01149 promoter transcription activation complex
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#9
Source (natural)Organism: Caulobacter vibrioides NA1000 (bacteria) / Strain: ML2315 (BSL1)

+
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: Caulobacter vibrioides NA1000 (bacteria) / Strain: ML2315 (BSL1)
Molecular weightTheoretical: 37.315523 KDa
SequenceString: MIERNWNELI RPEKPQIETG ADATRKARIV AEPLERGFGV TLGNALRRVL LSSLQGAAVT AIQIDGVVHE FSSLEGVRED VVDIVLNIK QLAVRMHAEG PKRMTLRATG PGPVTAGQIE TPADIEILNP DHVLCTLDDG ASVRMEFTVN NGKGYVPADR N RPEDAPIG ...String:
MIERNWNELI RPEKPQIETG ADATRKARIV AEPLERGFGV TLGNALRRVL LSSLQGAAVT AIQIDGVVHE FSSLEGVRED VVDIVLNIK QLAVRMHAEG PKRMTLRATG PGPVTAGQIE TPADIEILNP DHVLCTLDDG ASVRMEFTVN NGKGYVPADR N RPEDAPIG LIAVDALYSP VKRVAYRVEP TRQGQSLDYD KLILEVETNG AVTPVDAVAY AARILQDQLQ IFITFEEPKA KS ADESKPE LPFNPALLKK VDELELSVRS ANCLKNDNIV YIGDLIQKTE AEMLRTPNFG RKSLNEIKEV LAGMGLHLGM DVP NWPPEN IEDLAKKFED QI

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: Caulobacter vibrioides NA1000 (bacteria) / Strain: ML2315 (BSL1)
Molecular weightTheoretical: 151.085609 KDa
SequenceString: MAQSFTGKKR IRKSFGRIPE AVQMPNLIEV QRSSYEQFLQ RETRPGLRRD EGVEAVFKSV FPIKDFNERA VLEYVSYEFE EPKYDVEEC IQRDMTFAAP LKVKLRLIVF ETEEETGARS VKDIKEQDVY MGDIPLMTDK GTFIVNGTER VIVSQMHRSP G VFFDHDKG ...String:
MAQSFTGKKR IRKSFGRIPE AVQMPNLIEV QRSSYEQFLQ RETRPGLRRD EGVEAVFKSV FPIKDFNERA VLEYVSYEFE EPKYDVEEC IQRDMTFAAP LKVKLRLIVF ETEEETGARS VKDIKEQDVY MGDIPLMTDK GTFIVNGTER VIVSQMHRSP G VFFDHDKG KTHASGKLLF AARVIPYRGS WLDFEFDAKD IVYVRIDRRR KLPATTFLYA LGMDGEEILT TFYDVVPFEK RS GGWATPY KPERWRGVKP EFPLVDADTG EEVAPAGTKI TARQAKKFAD GGLKTLLLAP EALTGRYLAR DAVNMATGEI YAE AGDELD VTSIQALADQ GFSTIDVLDI DHVTVGAYMR NTLRVDKNAI REDALFDIYR VMRPGEPPTV EAAEAMFKSL FFDA ERYDL SSVGRVKMNM RLEQDVSDEV RILRKEDVLA VLKVLVGLRD GRGEIDDIDN LGNRRVRSVG ELLENQYRVG LLRME RAIK ERMSSVDIDT VMPHDLINAK PAAAAVREFF GSSQLSQFMD QTNPLSEITH KRRLSALGPG GLTRERAGFE VRDVHP THY GRICPIETPE GPNIGLINSL ATHARVNKYG FIESPYRRVK DGKPQDEVVY MSAMEESKHV IAQSNIKVAE GEIVEDL VP GRINGEPTLL QKETVDLMDV SPRQVVSVAA ALIPFLENDD ANRALMGSNM QRQAVPLVQS DAPLVGTGME AVVARDSG A VVIAKRTGVV EQIDGTRIVI RATEETDPAR SGVDIYRMSK FQRSNQSTCI NQRPLVKVGD RIVAGDIIAD GPSTELGEL ALGRNALVAF MPWNGYNFED SILISERIVR DDVFTSIHIE EFEVMARDTK LGPEEITRDI PNVGEEALRN LDEAGIVAIG AEVQPGDIL VGKVTPKGES PMTPEEKLLR AIFGEKASDV RDTSLRLPPG VAGTIVDVRV FNRHGVDKDE RALAIERAEI D RLGKDRDD EFAILNRNIS GRLKELLIGK VALSGPKGLS RGEITAEGLA QVASGLWWQI ALEDEKAMGE LESLRRLFDE NR KRLDRRF EDKVDKLQRG DELPPGVMKM VKVFVAVKRK LQPGDKMAGR HGNKGVISRI LPIEDMPFLA DGTHVDVVLN PLG VPSRMN VGQIFETHLG WACANLGKQI TNLLEDWQQG GQKQALVERL TEIYGPDEEL PDTEEGLVEL ARNLGKGVPI ATPV FDGAR MDDIEGHLEM AGVNKSGQSI LFDGLTGEQF KRPVTVGYIY MLKLHHLVDD KIHARSIGPY SLVTQQPLGG KAQFG GQRF GEMEVWALEA YGAAYTLQEM LTVKSDDVAG RTKVYESIVR GDDTFEAGIP ESFNVLVKEM RSLGLNVELE NS

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: Caulobacter vibrioides NA1000 (bacteria) / Strain: ML2315 (BSL1)
Molecular weightTheoretical: 154.467 KDa
SequenceString: MNQEVLNIFN PVQAAPTFDQ IRISLASPEK IRSWSFGEIK KPETINYRTF KPERDGLFCA RIFGPTKDYE CLCGKYKRMK YKGIICEKC GVEVTLARVR RERMGHIELA SPVAHIWFLK SLPSRIAMML DMPLKDIERV LYFEYYIVTE PGLTPLKQHQ L LSEDDYMR ...String:
MNQEVLNIFN PVQAAPTFDQ IRISLASPEK IRSWSFGEIK KPETINYRTF KPERDGLFCA RIFGPTKDYE CLCGKYKRMK YKGIICEKC GVEVTLARVR RERMGHIELA SPVAHIWFLK SLPSRIAMML DMPLKDIERV LYFEYYIVTE PGLTPLKQHQ L LSEDDYMR AQEEYGDDSF TAEIGAEAIQ NLLKAIDLEK EAERLREELS GTVSDMKQKK FSKRLKILEA FQESGNRPEW MV LTVVPVI PPELRPLVPL DGGRFATSDL NDLYRRVINR NNRLKRLIEL RAPDIIIRNE KRMLQESVDA LFDNGRRGRV ITG ANKRPL KSLADMLKGK QGRFRQNLLG KRVDYSGRSV IVVGPELKLH ECGLPKKMAL ELFKPFIYAR LDAKGLSGTV KQSK RMVER EQPQVWDILE EVIREHPVLL NRAPTLHRLG IQAFEPKLIE GKAIQLHPLV CAAFNADFDG DQMAVHVPLS LEAQL EARV LMMSTNNILS PANGRPIIVP SQDIVLGLYY LSVARDGEPG EGKIFADLGE IEAAMDAGVV SLHAKIKARH TEMTPE GVL LRKVIDTTPG RMKIAALLPH HPQIGHRLIE KALTKKEIGN LIDIVYRHCG QKATVIFADK VMGLGFKEAA KAGISFG KD DIIIPVRKTA IVEETRKLAE EYEQQYADGL ITKGEKYNKV VDAWAKATDR VADEMMAELQ MKHKDENGRE KEINAIYM M AHSGARGSQA QMKQLGGMRG LMAKPSGEII ETPIVSNFKE GLTVQEYFNS THGARKGLAD TALKTANSGY LTRRLVDVA QDCIIVEEDC GTTKGITLRA VVEGGDVLVS LGSRVLGRFT AEDVKDPGTG ELVVPADTYI DENIADAIEA AVVQSVKVRS VLTCEAKIG VCGACYGRDL ARGTPVNIGE AVGVIAAQSI GEPGTQLTMR TFHIGGTAQV AEQSFFEASN EGTVRVIGPT V VGSDGALV IMSRNTSVSV LVDGKERETY KPPYGARLRV KDGDLVKRGQ RLGDWDPYTT PIITEVAGKI RAEDLVDGLS IR EEVDEAT GIAQRVVADW RTSARGSDLR PAMGVLSEDG SYKRLSNGGE ARYLLSAGAI LSVADGDEVK PGEVIARIPT EGA KTRDIT GGLPRVAELF EARRPKDCAV IAEMDGRVEF GKDYKNKRRI KITPDVDADG NQPEAVEFLI PKGKHIAVHD GDYI TKGEY IIDGNPDPHD ILRILGVEAL ANFLVDEIQE VYRLQGVPIN DKHIETIVRQ MLQKVEILEP GDTGLIKGDH LDKPE FDKE QEKAIARGGR PAVTQPVLLG ITKASLQTKS FISAASFQET TRVLTEASVH GKTDTLEGLK ENVIVGRLIP AGTGSY LRS LQRVAAKRDE QLAQQREDAM EPLPAEIALS DAE

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: Caulobacter vibrioides NA1000 (bacteria) / Strain: ML2315 (BSL1)
Molecular weightTheoretical: 13.289844 KDa
SequenceString:
MARVTVEDCV EKVPNRFALV LLSAHRARGI SAGAALMVDR DNDKNPVVAL REIADDVIDH EGLKEHLIST LQRVDEHTEA EEEAETLAL LADPSHMQMS ELELVRALQS DRDGGQEERY

UniProtKB: DNA-directed RNA polymerase subunit omega

+
Macromolecule #5: RNA polymerase sigma factor RpoD

MacromoleculeName: RNA polymerase sigma factor RpoD / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Caulobacter vibrioides NA1000 (bacteria) / Strain: ML2315 (BSL1)
Molecular weightTheoretical: 72.770172 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MSNNSSAETE APETTGGDGP LLDLTDAGVK KFIKQAKARG YVTMDELNKV LPSEEVSPDA IEDTLAMLSE MGVNVVEAEE DAENAEGGE VATRDENTTV IASDKPAAYD RTDDPVRMYL REMGSVELLS REGEIAIAKR IEAGRDTMIR GLCESALTFE A IMVWREEL ...String:
MSNNSSAETE APETTGGDGP LLDLTDAGVK KFIKQAKARG YVTMDELNKV LPSEEVSPDA IEDTLAMLSE MGVNVVEAEE DAENAEGGE VATRDENTTV IASDKPAAYD RTDDPVRMYL REMGSVELLS REGEIAIAKR IEAGRDTMIR GLCESALTFE A IMVWREEL GTGRILLREV IDLEGTYAAI NGVAAQPAAE DDEGPAEPVD DEAGEAKAEG AEGEDEDDFD DGAGPTVSAM EG ELREGVM AILDAIASEF EAFRKLQDKL VGSRLKGEDL SDADRKAYEG LSATIIQHLK TLKLNNNRIE ALVEQLYAIN KRL IGLEGR LLRLADSYGI SRGEFLKAYF GSELNPTWSE QVKAMGVRWT KFVENDSQSV TDIRSEIAAL ATETGVPIDD YRRI VQTVQ KGEREARQAK KEMVEANLRL VISIAKKYTN RGLQFLDLIQ EGNIGLMKAV DKFEYRRGYK FSTYATWWIR QAITR SIAD QARTIRIPVH MIETINKIVR TSRQMLHEIG REPTPEELAE KLAMPLEKVR KVLKIAKEPI SLETPIGDEE DSHLGD FIE DKNAILPIDA AIQSNLRETT TRVLASLTPR EERVLRMRFG IGMNTDHTLE EVGQQFSVTR ERIRQIEAKA LRKLKHP SR SRKLRSFLDS

UniProtKB: RNA polymerase sigma factor RpoD

+
Macromolecule #8: WYL domain-containing protein

MacromoleculeName: WYL domain-containing protein / type: protein_or_peptide / ID: 8 / Details: DeoR-family transcriptional regulator / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Caulobacter vibrioides NA1000 (bacteria) / Strain: ML2315 (BSL1)
Molecular weightTheoretical: 36.212246 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MTGGMRHEKA TRLLDLARML AGSAEGLTLD EMAAALGVGR RTAERMRDAV WAAFPQMEAI DDPPTKRFRI PSGLDGVFQT PTAEELAAL RVAADSLRAS GADARASSLY ALEAKLLSAL RGSARRRVAP DVEALVQAET IAVHAGPRPY EDQAVLGAIR A AIKGLQAL ...String:
MTGGMRHEKA TRLLDLARML AGSAEGLTLD EMAAALGVGR RTAERMRDAV WAAFPQMEAI DDPPTKRFRI PSGLDGVFQT PTAEELAAL RVAADSLRAS GADARASSLY ALEAKLLSAL RGSARRRVAP DVEALVQAET IAVHAGPRPY EDQAVLGAIR A AIKGLQAL SFRYEGGSTP GRTREVTPLG VLFGRSNYLV ALEGKGGKPR SWRLDRMSDL KVLDKPAPPP QDFSLQAFAD ES FGIYHDE IQDVVLRIHK SRAEDALRWR FHATQQVTPE ADGSVLVTFR AGGMRELSWH LFTWGDAVEI VAPQVLKDMM VQE LREAGR AHGAW

UniProtKB: Uncharacterized protein

+
Macromolecule #6: DNA (66-MER)-non template

MacromoleculeName: DNA (66-MER)-non template / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Caulobacter vibrioides NA1000 (bacteria)
Molecular weightTheoretical: 30.196248 KDa
SequenceString: (DC)(DA)(DT)(DG)(DC)(DC)(DG)(DC)(DC)(DC) (DG)(DT)(DC)(DA)(DT)(DA)(DC)(DG)(DA)(DC) (DC)(DG)(DT)(DT)(DT)(DC)(DT)(DG)(DT) (DC)(DG)(DC)(DA)(DA)(DT)(DG)(DC)(DG)(DC) (DG) (DG)(DA)(DC)(DA)(DA)(DT) ...String:
(DC)(DA)(DT)(DG)(DC)(DC)(DG)(DC)(DC)(DC) (DG)(DT)(DC)(DA)(DT)(DA)(DC)(DG)(DA)(DC) (DC)(DG)(DT)(DT)(DT)(DC)(DT)(DG)(DT) (DC)(DG)(DC)(DA)(DA)(DT)(DG)(DC)(DG)(DC) (DG) (DG)(DA)(DC)(DA)(DA)(DT)(DC)(DT) (DT)(DC)(DC)(DA)(DT)(DC)(DA)(DT)(DC)(DG) (DC)(DC) (DC)(DC)(DT)(DG)(DG)(DA)(DG) (DA)(DA)(DC)(DC)(DC)(DA)(DA)(DG)(DG)(DA) (DC)(DC)(DT) (DT)(DC)(DG)(DA)(DT)(DG) (DA)(DC)(DC)(DC)(DG)(DC)(DT)(DT)(DC)(DG) (DC)(DC)(DT)

GENBANK: GENBANK: CP001340.1

+
Macromolecule #7: DNA (53-MER)-template

MacromoleculeName: DNA (53-MER)-template / type: dna / ID: 7 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Caulobacter vibrioides NA1000 (bacteria)
Molecular weightTheoretical: 30.89468 KDa
SequenceString: (DA)(DG)(DG)(DC)(DG)(DA)(DA)(DG)(DC)(DG) (DG)(DG)(DT)(DC)(DA)(DT)(DC)(DG)(DA)(DA) (DG)(DG)(DT)(DC)(DC)(DT)(DT)(DG)(DG) (DG)(DT)(DT)(DC)(DT)(DC)(DC)(DA)(DG)(DG) (DG) (DG)(DC)(DG)(DA)(DT)(DG) ...String:
(DA)(DG)(DG)(DC)(DG)(DA)(DA)(DG)(DC)(DG) (DG)(DG)(DT)(DC)(DA)(DT)(DC)(DG)(DA)(DA) (DG)(DG)(DT)(DC)(DC)(DT)(DT)(DG)(DG) (DG)(DT)(DT)(DC)(DT)(DC)(DC)(DA)(DG)(DG) (DG) (DG)(DC)(DG)(DA)(DT)(DG)(DA)(DT) (DG)(DG)(DA)(DA)(DG)(DA)(DT)(DT)(DG)(DT) (DC)(DC) (DG)(DC)(DG)(DC)(DA)(DT)(DT) (DG)(DC)(DG)(DA)(DC)(DA)(DG)(DA)(DA)(DA) (DC)(DG)(DG) (DT)(DC)(DG)(DT)(DA)(DT) (DG)(DA)(DC)(DG)(DG)(DG)(DC)(DG)(DG)(DC) (DA)(DT)(DG)

GENBANK: GENBANK: CP001340.1

+
Macromolecule #9: DNA (5'-D(P*GP*TP*C)-3')

MacromoleculeName: DNA (5'-D(P*GP*TP*C)-3') / type: dna / ID: 9 / Details: ssDNA / Number of copies: 2 / Classification: DNA
Source (natural)Organism: Caulobacter vibrioides NA1000 (bacteria)
Molecular weightTheoretical: 2.103408 KDa
SequenceString:
(DT)(DG)(DT)(DC)(DT)(DA)(DT)

+
Macromolecule #10: MAGNESIUM ION

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

+
Macromolecule #11: ZINC ION

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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration1.5 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
20.0 mMC4H11NO3Tris-HCl
5.0 mMMgCl2Magnesium Chloride
100.0 mMNaClSodium Chloride
1.0 mMC2H6OS1

Details: 20 mM Tris-cl, 5 mM MgCl2, 100 mM NaCl, 1 mM BME
GridModel: UltrAuFoil R1.2/1.3 / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Support film - Film thickness: 50 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 300 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 293.15 K / Instrument: LEICA EM GP
Details3 uM of the reconstituted complex

-
Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 58.7 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 81000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. 4.2.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: Ab-Initio Reconstruction
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5) / Number images used: 68485
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: cryoSPARC (ver. 4.2.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 5)
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelPDB ID:

7ye1


Chain - Source name: PDB / Chain - Initial model type: experimental model
Output model

PDB-9pfv:
The cryo-EM structure of C. crescentus DriD-ssDNA-RNAP-Sigma73-CCNA_03891/CCNA_01149 promoter transcription activation complex

+
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