[English] 日本語
Yorodumi
- EMDB-33761: The cryo-EM structure of C. crescentus GcrA-TACup -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-33761
TitleThe cryo-EM structure of C. crescentus GcrA-TACup
Map data
Sample
  • Complex: The cryo-EM structure of C. crescentus GcrA-TACup
    • Complex: DNA-directed RNA polymerase/GcrA/TACup
      • 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
      • Protein or peptide: Cell cycle regulatory protein GcrA
    • Complex: DNA
      • DNA: DNA (57-MER)-non template
      • DNA: DNA (57-MER)-template
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION
Keywordstranscription activator / TRANSCRIPTION
Function / homology
Function and homology information


sigma factor activity / DNA-directed RNA polymerase complex / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / 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 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / protein dimerization activity / DNA-templated transcription / magnesium ion binding / DNA binding / zinc ion binding / metal ion binding / cytoplasm
Similarity search - Function
GcrA cell cycle regulator / GcrA cell cycle regulator / 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 ...GcrA cell cycle regulator / GcrA cell cycle regulator / 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, 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 / 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, 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 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
DNA-directed RNA polymerase subunit beta' / Cell cycle regulatory protein GcrA / RNA polymerase sigma factor RpoD / DNA-directed RNA polymerase subunit beta / DNA-directed RNA polymerase subunit alpha / DNA-directed RNA polymerase subunit omega
Similarity search - Component
Biological speciesCaulobacter vibrioides NA1000 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsWu XX / Zhang Y
Funding support China, 2 items
OrganizationGrant numberCountry
Other governmentXDB29020000
National Natural Science Foundation of China (NSFC)31870047 China
CitationJournal: Nucleic Acids Res. / Year: 2023
Title: Cryo-EM structures of Caulobacter crescentus transcription activation complex with an essential cell cycle regulator GcrA
Authors: Wu XX / Zhang Y
History
DepositionJul 5, 2022-
Header (metadata) releaseJan 18, 2023-
Map releaseJan 18, 2023-
UpdateJul 3, 2024-
Current statusJul 3, 2024Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_33761.png

Downloads & links

-
Map

FileDownload / File: emd_33761.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.01 Å/pix.
x 300 pix.
= 304.2 Å		1.01 Å/pix.
x 300 pix.
= 304.2 Å		1.01 Å/pix.
x 300 pix.
= 304.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.014 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.008
Minimum - Maximum-0.032827456 - 0.06857348
Average (Standard dev.)0.00022669348 (±0.0020814238)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 304.2 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: #1

Fileemd_33761_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_33761_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_33761_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 GcrA-TACup

EntireName: The cryo-EM structure of C. crescentus GcrA-TACup
Components
  • Complex: The cryo-EM structure of C. crescentus GcrA-TACup
    • Complex: DNA-directed RNA polymerase/GcrA/TACup
      • 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
      • Protein or peptide: Cell cycle regulatory protein GcrA
    • Complex: DNA
      • DNA: DNA (57-MER)-non template
      • DNA: DNA (57-MER)-template
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION

+
Supramolecule #1: The cryo-EM structure of C. crescentus GcrA-TACup

SupramoleculeName: The cryo-EM structure of C. crescentus GcrA-TACup / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#8
Source (natural)Organism: Caulobacter vibrioides NA1000 (bacteria)

+
Supramolecule #2: DNA-directed RNA polymerase/GcrA/TACup

SupramoleculeName: DNA-directed RNA polymerase/GcrA/TACup / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#6

+
Supramolecule #3: DNA

SupramoleculeName: DNA / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #7-#8

+
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: NA1000
Molecular weightTheoretical: 37.315523 KDa
Recombinant expressionOrganism: Escherichia coli DH5[alpha] (bacteria)
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: NA1000
Molecular weightTheoretical: 151.085609 KDa
Recombinant expressionOrganism: Escherichia coli DH5[alpha] (bacteria)
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: NA1000
Molecular weightTheoretical: 154.467 KDa
Recombinant expressionOrganism: Escherichia coli DH5[alpha] (bacteria)
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: NA1000
Molecular weightTheoretical: 13.289844 KDa
Recombinant expressionOrganism: Escherichia coli DH5[alpha] (bacteria)
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: NA1000
Molecular weightTheoretical: 72.770172 KDa
Recombinant expressionOrganism: Escherichia coli DH5[alpha] (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 #6: Cell cycle regulatory protein GcrA

MacromoleculeName: Cell cycle regulatory protein GcrA / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Caulobacter vibrioides NA1000 (bacteria) / Strain: NA1000
Molecular weightTheoretical: 18.515287 KDa
Recombinant expressionOrganism: Escherichia coli DH5[alpha] (bacteria)
SequenceString:
MSWTDERVST LKKLWLDGLS ASQIAKQLGG VTRNAVIGKV HRLGLSGRAA PSQPARPAFK APRPARPAAQ AMPSAPRRVT PVEAPTSVP VAAAPAPLPA FRHEEPGSAT VLTLGAHMCK WPIGDPSSEG FTFCGRRSSE GPYCVEHARV AYQPQQTKKK S GGAELARS LRRYI

UniProtKB: Cell cycle regulatory protein GcrA

+
Macromolecule #7: DNA (57-MER)-non template

MacromoleculeName: DNA (57-MER)-non template / type: dna / ID: 7 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Caulobacter vibrioides NA1000 (bacteria)
Molecular weightTheoretical: 17.675373 KDa
SequenceString: (DA)(DA)(DA)(DA)(DA)(DA)(DA)(DG)(DA)(DG) (DT)(DT)(DG)(DA)(DC)(DA)(DC)(DC)(DC)(DG) (DG)(DG)(DC)(DG)(6MA)(DA)(DT)(DC)(DC) (DC)(DT)(DG)(DC)(DT)(DA)(DT)(DA)(DA)(DT) (DG)(DG)(DG)(DA)(DG)(DC)(DT) ...String:
(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DG)(DA)(DG) (DT)(DT)(DG)(DA)(DC)(DA)(DC)(DC)(DC)(DG) (DG)(DG)(DC)(DG)(6MA)(DA)(DT)(DC)(DC) (DC)(DT)(DG)(DC)(DT)(DA)(DT)(DA)(DA)(DT) (DG)(DG)(DG)(DA)(DG)(DC)(DT)(DG)(DT) (DC)(DA)(DC)(DG)(DG)(DA)(DT)(DG)(DC)

+
Macromolecule #8: DNA (57-MER)-template

MacromoleculeName: DNA (57-MER)-template / type: dna / ID: 8 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Caulobacter vibrioides NA1000 (bacteria)
Molecular weightTheoretical: 17.652293 KDa
SequenceString: (DG)(DC)(DA)(DT)(DC)(DC)(DG)(DT)(DG)(DA) (DG)(DT)(DC)(DG)(DA)(DG)(DG)(DG)(DT)(DA) (DA)(DT)(DA)(DA)(DG)(DC)(DA)(DG)(DG) (DG)(6MA)(DT)(DT)(DC)(DG)(DC)(DC)(DC)(DG) (DG)(DG)(DT)(DG)(DT)(DC)(DA) ...String:
(DG)(DC)(DA)(DT)(DC)(DC)(DG)(DT)(DG)(DA) (DG)(DT)(DC)(DG)(DA)(DG)(DG)(DG)(DT)(DA) (DA)(DT)(DA)(DA)(DG)(DC)(DA)(DG)(DG) (DG)(6MA)(DT)(DT)(DC)(DG)(DC)(DC)(DC)(DG) (DG)(DG)(DT)(DG)(DT)(DC)(DA)(DA)(DC) (DT)(DC)(DT)(DT)(DT)(DT)(DT)(DT)(DT)

+
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: 3 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
GridModel: C-flat-1.2/1.3 / Material: COPPER / Mesh: 400
VitrificationCryogen name: NITROGEN

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 62.4 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

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

6ca0

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 287227
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
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