[English] 日本語
Yorodumi
- EMDB-51267: RNAP-TopoI complex on duplex scaffold with visible TOPRIM loop -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-51267
TitleRNAP-TopoI complex on duplex scaffold with visible TOPRIM loop
Map dataRNAP-TopoI complex on duplex scaffold with visible TOPRIM loop - composite deepemhanced map
Sample
  • Complex: RNAP-TopoI complex on duplex scaffold
    • Complex: DNA-directed RNA polymerase elongation complex
      • Protein or peptide: DNA-directed RNA polymerase subunit alpha
      • 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
      • DNA: non-template DNA strand
      • RNA: RNA
      • DNA: template DNA strand
    • Complex: DNA topoisomerase 1
      • Protein or peptide: DNA topoisomerase 1
KeywordsRNA polymerase / topoisomerase / DNA topology / TRANSCRIPTION
Function / homology
Function and homology information


RNA topoisomerase activity / DNA topoisomerase activity / DNA topoisomerase / DNA topoisomerase type I (single strand cut, ATP-independent) activity / RNA polymerase complex / submerged biofilm formation / cellular response to cell envelope stress / regulation of DNA-templated transcription initiation / DNA topological change / bacterial-type flagellum assembly ...RNA topoisomerase activity / DNA topoisomerase activity / DNA topoisomerase / DNA topoisomerase type I (single strand cut, ATP-independent) activity / RNA polymerase complex / submerged biofilm formation / cellular response to cell envelope stress / regulation of DNA-templated transcription initiation / DNA topological change / bacterial-type flagellum assembly / bacterial-type RNA polymerase core enzyme binding / cytosolic DNA-directed RNA polymerase complex / bacterial-type flagellum-dependent cell motility / nitrate assimilation / regulation of DNA-templated transcription elongation / transcription elongation factor complex / transcription antitermination / cell motility / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed RNA polymerase / DNA-directed RNA polymerase activity / chromosome / response to heat / protein-containing complex assembly / intracellular iron ion homeostasis / protein dimerization activity / response to antibiotic / magnesium ion binding / DNA binding / zinc ion binding / membrane / cytoplasm / cytosol
Similarity search - Function
DNA topoisomerase I, zinc ribbon-like, bacterial-type / : / Topoisomerase I zinc-ribbon-like / Topoisomerase I, zinc finger / DNA topoisomerase, type IA, zn finger / Topoisomerase DNA binding C4 zinc finger / DNA topoisomerase I, bacterial-type / DNA topoisomerase I, type IA / DNA topoisomerase 1, TOPRIM domain / DNA topoisomerase, type IA ...DNA topoisomerase I, zinc ribbon-like, bacterial-type / : / Topoisomerase I zinc-ribbon-like / Topoisomerase I, zinc finger / DNA topoisomerase, type IA, zn finger / Topoisomerase DNA binding C4 zinc finger / DNA topoisomerase I, bacterial-type / DNA topoisomerase I, type IA / DNA topoisomerase 1, TOPRIM domain / DNA topoisomerase, type IA / DNA topoisomerase, type IA, central region, subdomain 2 / DNA topoisomerase, type IA, active site / Topoisomerase (Topo) IA-type active site signature. / Topoisomerase (Topo) IA-type catalytic domain profile. / DNA topoisomerase, type IA, domain 2 / DNA topoisomerase, type IA, DNA-binding domain / DNA topoisomerase, type IA, central / DNA topoisomerase, type IA, central region, subdomain 1 / DNA topoisomerase, type IA, central region, subdomain 3 / DNA topoisomerase, type IA, core domain / DNA topoisomerase / Bacterial DNA topoisomeraes I ATP-binding domain / Bacterial DNA topoisomerase I DNA-binding domain / TOPRIM / Toprim domain / Toprim domain profile. / TOPRIM domain / 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 Rpb1, domain 1 / RNA polymerase Rpb1, domain 1 / RNA polymerase, beta subunit, protrusion / RNA polymerase beta subunit / 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, N-terminal / RNA polymerase Rpb2, domain 2 / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase Rpb2, domain 2 / 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
Similarity search - Domain/homology
DNA topoisomerase 1 / DNA-directed RNA polymerase subunit alpha / DNA-directed RNA polymerase subunit omega / DNA-directed RNA polymerase subunit beta' / DNA-directed RNA polymerase subunit beta
Similarity search - Component
Biological speciesEscherichia coli (E. coli) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsVidmar V / Weixlbaumer A / Lamour V
Funding support France, 2 items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-21-CE11-0040-01 France
Agence Nationale de la Recherche (ANR)ANR-10-INBS-05 France
CitationJournal: To Be Published
Title: DNA topoisomerase I acts as supercoiling sensor for transcription elongation in E. coli
Authors: Vidmar V / Borde C / Bruno L / Takacs M / Batisse C / Saint-Andre C / Zhu C / Espeli O / Lamour V / Weixlbaumer A
History
DepositionAug 5, 2024-
Header (metadata) releaseNov 5, 2025-
Map releaseNov 5, 2025-
UpdateNov 5, 2025-
Current statusNov 5, 2025Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_51267.png

Downloads & links

-
Map

FileDownload / File: emd_51267.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationRNAP-TopoI complex on duplex scaffold with visible TOPRIM loop - composite deepemhanced map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
0.84 Å/pix.
x 360 pix.
= 302.04 Å		0.84 Å/pix.
x 360 pix.
= 302.04 Å		0.84 Å/pix.
x 360 pix.
= 302.04 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.839 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-1.843942 - 72.434240000000003
Average (Standard dev.)0.017514812 (±1.1803807)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 302.04 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Sample components

+
Entire : RNAP-TopoI complex on duplex scaffold

EntireName: RNAP-TopoI complex on duplex scaffold
Components
  • Complex: RNAP-TopoI complex on duplex scaffold
    • Complex: DNA-directed RNA polymerase elongation complex
      • Protein or peptide: DNA-directed RNA polymerase subunit alpha
      • 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
      • DNA: non-template DNA strand
      • RNA: RNA
      • DNA: template DNA strand
    • Complex: DNA topoisomerase 1
      • Protein or peptide: DNA topoisomerase 1

+
Supramolecule #1: RNAP-TopoI complex on duplex scaffold

SupramoleculeName: RNAP-TopoI complex on duplex scaffold / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#9
Molecular weightTheoretical: 100 KDa

+
Supramolecule #2: DNA-directed RNA polymerase elongation complex

SupramoleculeName: DNA-directed RNA polymerase elongation complex / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#5, #7-#9
Source (natural)Organism: Escherichia coli (E. coli)

+
Supramolecule #3: DNA topoisomerase 1

SupramoleculeName: DNA topoisomerase 1 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #6
Source (natural)Organism: Escherichia coli (E. coli)

+
Macromolecule #1: DNA-directed RNA polymerase subunit alpha

MacromoleculeName: DNA-directed RNA polymerase subunit alpha / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Escherichia coli (E. coli)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MQGSVTEFLK PRLVDIEQVS STHAKVTLEP LERGFGHTLG NALRRILLSS MPGCAVTEVE IDGVLHEYST KEGVQEDILE ILLNLKGLAV RVQGKDEVIL TLNKSGIGPV TAADITHDGD VEIVKPQHVI CHLTDENASI SMRIKVQRGR GYVPASTRIH SEEDERPIGR ...String:
MQGSVTEFLK PRLVDIEQVS STHAKVTLEP LERGFGHTLG NALRRILLSS MPGCAVTEVE IDGVLHEYST KEGVQEDILE ILLNLKGLAV RVQGKDEVIL TLNKSGIGPV TAADITHDGD VEIVKPQHVI CHLTDENASI SMRIKVQRGR GYVPASTRIH SEEDERPIGR LLVDACYSPV ERIAYNVEAA RVEQRTDLDK LVIEMETNGT IDPEEAIRRA ATILAEQLEA FVDLRDVRQP EVKEEKPEFD PILLRPVDDL ELTVRSANCL KAEAIHYIGD LVQRTEVELL KTPNLGKKSL TEIKDVLASR GLSLGMRLEN WPPASIADE

UniProtKB: DNA-directed RNA polymerase subunit alpha

+
Macromolecule #2: DNA-directed RNA polymerase subunit alpha

MacromoleculeName: DNA-directed RNA polymerase subunit alpha / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Escherichia coli (E. coli)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MQGSVTEFLK PRLVDIEQVS STHAKVTLEP LERGFGHTLG NALRRILLSS MPGCAVTEVE IDGVLHEYST KEGVQEDILE ILLNLKGLAV RVQGKDEVIL TLNKSGIGPV TAADITHDGD VEIVKPQHVI CHLTDENASI SMRIKVQRGR GYVPASTRIH SEEDERPIGR ...String:
MQGSVTEFLK PRLVDIEQVS STHAKVTLEP LERGFGHTLG NALRRILLSS MPGCAVTEVE IDGVLHEYST KEGVQEDILE ILLNLKGLAV RVQGKDEVIL TLNKSGIGPV TAADITHDGD VEIVKPQHVI CHLTDENASI SMRIKVQRGR GYVPASTRIH SEEDERPIGR LLVDACYSPV ERIAYNVEAA RVEQRTDLDK LVIEMETNGT IDPEEAIRRA ATILAEQLEA FVDLRDVRQP EVKEEKPEFD PILLRPVDDL ELTVRSANCL KAEAIHYIGD LVQRTEVELL KTPNLGKKSL TEIKDVLASR GLSLGMRLEN WPPASIADE

UniProtKB: DNA-directed RNA polymerase subunit alpha

+
Macromolecule #3: DNA-directed RNA polymerase subunit beta

MacromoleculeName: DNA-directed RNA polymerase subunit beta / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Escherichia coli (E. coli)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MVYSYTEKKR IRKDFGKRPQ VLDVPYLLSI QLDSFQKFIE QDPEGQYGLE AAFRSVFPIQ SYSGNSELQY VSYRLGEPVF DVQECQIRGV TYSAPLRVKL RLVIYEREAP EGTVKDIKEQ EVYMGEIPLM TDNGTFVING TERVIVSQLH RSPGVFFDSD KGKTHSSGKV ...String:
MVYSYTEKKR IRKDFGKRPQ VLDVPYLLSI QLDSFQKFIE QDPEGQYGLE AAFRSVFPIQ SYSGNSELQY VSYRLGEPVF DVQECQIRGV TYSAPLRVKL RLVIYEREAP EGTVKDIKEQ EVYMGEIPLM TDNGTFVING TERVIVSQLH RSPGVFFDSD KGKTHSSGKV LYNARIIPYR GSWLDFEFDP KDNLFVRIDR RRKLPATIIL RALNYTTEQI LDLFFEKVIF EIRDNKLQME LVPERLRGET ASFDIEANGK VYVEKGRRIT ARHIRQLEKD DVKLIEVPVE YIAGKVVAKD YIDESTGELI CAANMELSLD LLAKLSQSGH KRIETLFTND LDHGPYISET LRVDPTNDRL SALVEIYRMM RPGEPPTREA AESLFENLFF SEDRYDLSAV GRMKFNRSLL REEIEGSGIL SKDDIIDVMK KLIDIRNGKG EVDDIDHLGN RRIRSVGEMA ENQFRVGLVR VERAVKERLS LGDLDTLMPQ DMINAKPISA AVKEFFGSSQ LSQFMDQNNP LSEITHKRRI SALGPGGLTR ERAGFEVRDV HPTHYGRVCP IETPEGPNIG LINSLSVYAQ TNEYGFLETP YRKVTDGVVT DEIHYLSAIE EGNYVIAQAN SNLDEEGHFV EDLVTCRSKG ESSLFSRDQV DYMDVSTQQV VSVGASLIPF LEHDDANRAL MGANMQRQAV PTLRADKPLV GTGMERAVAV DSGVTAVAKR GGVVQYVDAS RIVIKVNEDE MYPGEAGIDI YNLTKYTRSN QNTCINQMPC VSLGEPVERG DVLADGPSTD LGELALGQNM RVAFMPWNGY NFEDSILVSE RVVQEDRFTT IHIQELACVS RDTKLGPEEI TADIPNVGEA ALSKLDESGI VYIGAEVTGG DILVGKVTPK GETQLTPEEK LLRAIFGEKA SDVKDSSLRV PNGVSGTVID VQVFTRDGVE KDKRALEIEE MQLKQAKKDL SEELQILEAG LFSRIRAVLV AGGVEAEKLD KLPRDRWLEL GLTDEEKQNQ LEQLAEQYDE LKHEFEKKLE AKRRKITQGD DLAPGVLKIV KVYLAVKRRI QPGDKMAGRH GNKGVISKIN PIEDMPYDEN GTPVDIVLNP LGVPSRMNIG QILETHLGMA AKGIGDKINA MLKQQQEVAK LREFIQRAYD LGADVRQKVD LSTFSDEEVM RLAENLRKGM PIATPVFDGA KEAEIKELLK LGDLPTSGQI RLYDGRTGEQ FERPVTVGYM YMLKLNHLVD DKMHARSTGS YSLVTQQPLG GKAQFGGQRF GEMEVWALEA YGAAYTLQEM LTVKSDDVNG RTKMYKNIVD GNHQMEPGMP ESFNVLLKEI RSLGINIELE DE

UniProtKB: DNA-directed RNA polymerase subunit beta

+
Macromolecule #4: DNA-directed RNA polymerase subunit beta'

MacromoleculeName: DNA-directed RNA polymerase subunit beta' / type: protein_or_peptide / ID: 4 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Escherichia coli (E. coli)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKDLLKFLKA QTKTEEFDAI KIALASPDMI RSWSFGEVKK PETINYRTFK PERDGLFCAR IFGPVKDYEC LCGKYKRLKH RGVICEKCGV EVTQTKVRRE RMGHIELASP TAHIWFLKSL PSRIGLLLDM PLRDIERVLY FESYVVIEGG MTNLERQQIL TEEQYLDALE ...String:
MKDLLKFLKA QTKTEEFDAI KIALASPDMI RSWSFGEVKK PETINYRTFK PERDGLFCAR IFGPVKDYEC LCGKYKRLKH RGVICEKCGV EVTQTKVRRE RMGHIELASP TAHIWFLKSL PSRIGLLLDM PLRDIERVLY FESYVVIEGG MTNLERQQIL TEEQYLDALE EFGDEFDAKM GAEAIQALLK SMDLEQECEQ LREELNETNS ETKRKKLTKR IKLLEAFVQS GNKPEWMILT VLPVLPPDLR PLVPLDGGRF ATSDLNDLYR RVINRNNRLK RLLDLAAPDI IVRNEKRMLQ EAVDALLDNG RRGRAITGSN KRPLKSLADM IKGKQGRFRQ NLLGKRVDYS GRSVITVGPY LRLHQCGLPK KMALELFKPF IYGKLELRGL ATTIKAAKKM VEREEAVVWD ILDEVIREHP VLLNRAPTLH RLGIQAFEPV LIEGKAIQLH PLVCAAYNAD FDGDQMAVHV PLTLEAQLEA RALMMSTNNI LSPANGEPII VPSQDVVLGL YYMTRDCVNA KGEGMVLTGP KEAERLYRSG LASLHARVKV RITEYEKDAN GELVAKTSLK DTTVGRAILW MIVPKGLPYS IVNQALGKKA ISKMLNTCYR ILGLKPTVIF ADQIMYTGFA YAARSGASVG IDDMVIPEKK HEIISEAEAE VAEIQEQFQS GLVTAGERYN KVIDIWAAAN DRVSKAMMDN LQTETVINRD GQEEKQVSFN SIYMMADSGA RGSAAQIRQL AGMRGLMAKP DGSIIETPIT ANFREGLNVL QYFISTHGAR KGLADTALKT ANSGYLTRRL VDVAQDLVVT EDDCGTHEGI MMTPVIEGGD VKEPLRDRVL GRVTAEDVLK PGTADILVPR NTLLHEQWCD LLEENSVDAV KVRSVVSCDT DFGVCAHCYG RDLARGHIIN KGEAIGVIAA QSIGEPGTQL TMRTFHIGGA ASRAAAESSI QVKNKGSIKL SNVKSVVNSS GKLVITSRNT ELKLIDEFGR TKESYKVPYG AVLAKGDGEQ VAGGETVANW DPHTMPVITE VSGFVRFTDM IDGQTITRQT DELTGLSSLV VLDSAERTAG GKDLRPALKI VDAQGNDVLI PGTDMPAQYF LPGKAIVQLE DGVQISSGDT LARIPQESGG TKDITGGLPR VADLFEARRP KEPAILAEIS GIVSFGKETK GKRRLVITPV DGSDPYEEMI PKWRQLNVFE GERVERGDVI SDGPEAPHDI LRLRGVHAVT RYIVNEVQDV YRLQGVKIND KHIEVIVRQM LRKATIVNAG SSDFLEGEQV EYSRVKIANR ELEANGKVGA TYSRDLLGIT KASLATESFI SAASFQETTR VLTEAAVAGK RDELRGLKEN VIVGRLIPAG TGYAYHQDRM RRRAAGEAPA APQVTAEDAS ASLAELLNAG LGGSDNELEL EVLFQ

UniProtKB: DNA-directed RNA polymerase subunit beta'

+
Macromolecule #5: DNA-directed RNA polymerase subunit omega

MacromoleculeName: DNA-directed RNA polymerase subunit omega / type: protein_or_peptide / ID: 5 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Escherichia coli (E. coli)
SequenceString:
MARVTVQDAV EKIGNRFDLV LVAARRARQM QVGGKDPLVP EENDKTTVIA LREIEEGLIN NQILDVRERQ EQQEQEAAEL QAVTAIAEGR R

UniProtKB: DNA-directed RNA polymerase subunit omega

+
Macromolecule #6: DNA topoisomerase 1

MacromoleculeName: DNA topoisomerase 1 / type: protein_or_peptide / ID: 6 / Details: N-terminal TwinStrep tag / Enantiomer: LEVO / EC number: DNA topoisomerase
Source (natural)Organism: Escherichia coli (E. coli)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GPWSHPQFEK GGGSGGGSGG SAWSHPQFEK HMGKALVIVE SPAKAKTINK YLGSDYVVKS SVGHIRDLPT SGSAAKKSAD STSTKTAKKP KKDERGALVN RMGVDPWHNW EAHYEVLPGK EKVVSELKQL AEKADHIYLA TDLDREGEAI AWHLREVIGG DDARYSRVVF ...String:
GPWSHPQFEK GGGSGGGSGG SAWSHPQFEK HMGKALVIVE SPAKAKTINK YLGSDYVVKS SVGHIRDLPT SGSAAKKSAD STSTKTAKKP KKDERGALVN RMGVDPWHNW EAHYEVLPGK EKVVSELKQL AEKADHIYLA TDLDREGEAI AWHLREVIGG DDARYSRVVF NEITKNAIRQ AFNKPGELNI DRVNAQQARR FMDRVVGYMV SPLLWKKIAR GLSAGRVQSV AVRLVVERER EIKAFVPEEF WEVDASTTTP SGEALALQVT HQNDKPFRPV NKEQTQAAVS LLEKARYSVL EREDKPTTSK PGAPFITSTL QQAASTRLGF GVKKTMMMAQ RLYEAGYITY MRTDSTNLSQ DAVNMVRGYI SDNFGKKYLP ESPNQYASKE NSQEAHEAIR PSDVNVMAES LKDMEADAQK LYQLIWRQFV ACQMTPAKYD STTLTVGAGD FRLKARGRIL RFDGWTKVMP ALRKGDEDRI LPAVNKGDAL TLVELTPAQH FTKPPARFSE ASLVKELEKR GIGRPSTYAS IISTIQDRGY VRVENRRFYA EKMGEIVTDR LEENFRELMN YDFTAQMENS LDQVANHEAE WKAVLDHFFS DFTQQLDKAE KDPEEGGMRP NQMVLTSIDC PTCGRKMGIR TASTGVFLGC SGYALPPKER CKTTINLVPE NEVLNVLEGE DAETNALRAK RRCPKCGTAM DSYLIDPKRK LHVCGNNPTC DGYEIEEGEF RIKGYDGPIV ECEKCGSEMH LKMGRFGKYM ACTNEECKNT RKILRNGEVA PPKEDPVPLP ELPCEKSDAY FVLRDGAAGV FLAANTFPKS RETRAPLVEE LYRFRDRLPE KLRYLADAPQ QDPEGNKTMV RFSRKTKQQY VSSEKDGKAT GWSAFYVDGK WVEGKK

UniProtKB: DNA topoisomerase 1

+
Macromolecule #7: non-template DNA strand

MacromoleculeName: non-template DNA strand / type: dna / ID: 7 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
SequenceString:
GGTCAGTACG TCCTATCGAT CTTCGGAAGA GATTCAGAG

+
Macromolecule #9: template DNA strand

MacromoleculeName: template DNA strand / type: dna / ID: 9 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
SequenceString:
CTCTGAATCT CTTCCGACGC GCCGCGGGAC GTACTGACC

+
Macromolecule #8: RNA

MacromoleculeName: RNA / type: rna / ID: 8
Source (natural)Organism: synthetic construct (others)
SequenceString:
GAGUCCGCGG CGCG

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration10 mg/mL
BufferpH: 7.5
Component:
ConcentrationName
10.0 mMHEPES/KOH
150.0 mMpotassium acetate
5.0 mMmagnesium acetate
0.01 mMzinc chloride
2.0 mMDTT
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Support film - Film thickness: 50 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 35 sec. / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 56.6 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 58571
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC

-
Atomic model buiding 1

Initial model
PDB IDChain

6alh

source_name: PDB, initial_model_type: experimental model

4rul

source_name: PDB, initial_model_type: experimental model
DetailsInitial rigid body fit was done in UCSF Chimera, followed by flexible fitting in Isolde. The entire model was further refined in Phenix and Coot.
RefinementSpace: REAL

+
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