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- EMDB-71019: Consensus map of E. coli clamp loader DnaX-complex loading beta-c... -

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Basic information

Entry
Database: EMDB / ID: EMD-71019
TitleConsensus map of E. coli clamp loader DnaX-complex loading beta-clamp onto 10-nt gapped DNA in state 1 the DNA recognition state
Map dataconsensus map
Sample
  • Complex: E. coli clamp loading complex
    • Complex: beta clamp bound to loader DnaX-complex
      • Other: E. coli DnaX-complex loads beta-clamp onto 10-nt gapped DNA at state 1
    • Complex: 10-nt gapped DNA substrate
KeywordsE. Coli / DNA replication / DNA damage repair / clamp loading complex / clamp beta / clamp loader DnaX-complex / REPLICATION
Biological speciesEscherichia coli (E. coli) / DNA molecule (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.54 Å
AuthorsZheng F / Yao YN / Georgescu R / O'Donnell ME / Li H
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM131754 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM115809 United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: To Be Published
Title: The E. coli clamp loader sharply bends DNA to load beta-clamp onto small gaps
Authors: Zheng F / Yao YN / Georgescu R / Lyu M / O'Donnell ME / Li H
History
DepositionJun 4, 2025-
Header (metadata) releaseJun 10, 2026-
Map releaseJun 10, 2026-
UpdateJun 10, 2026-
Current statusJun 10, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_71019.png

Downloads & links

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Map

FileDownload / File: emd_71019.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationconsensus map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 320 pix.
= 264.96 Å		0.83 Å/pix.
x 320 pix.
= 264.96 Å		0.83 Å/pix.
x 320 pix.
= 264.96 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.828 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.06
Minimum - Maximum-0.60957813 - 1.0736433
Average (Standard dev.)-0.00012968696 (±0.019992974)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 264.96 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half map A

Fileemd_71019_half_map_1.map
Annotationhalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map B

Fileemd_71019_half_map_2.map
Annotationhalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : E. coli clamp loading complex

EntireName: E. coli clamp loading complex
Components
  • Complex: E. coli clamp loading complex
    • Complex: beta clamp bound to loader DnaX-complex
      • Other: E. coli DnaX-complex loads beta-clamp onto 10-nt gapped DNA at state 1
    • Complex: 10-nt gapped DNA substrate

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Supramolecule #1: E. coli clamp loading complex

SupramoleculeName: E. coli clamp loading complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#11

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Supramolecule #2: beta clamp bound to loader DnaX-complex

SupramoleculeName: beta clamp bound to loader DnaX-complex / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#7, #10
Source (natural)Organism: Escherichia coli (E. coli)

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Supramolecule #3: 10-nt gapped DNA substrate

SupramoleculeName: 10-nt gapped DNA substrate / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #8-#9, #11
Source (natural)Organism: DNA molecule (others)

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Macromolecule #1: E. coli DnaX-complex loads beta-clamp onto 10-nt gapped DNA at state 1

MacromoleculeName: E. coli DnaX-complex loads beta-clamp onto 10-nt gapped DNA at state 1
type: other / ID: 1
Details: E. coli DNA polymerase III complex including subunit delta--subunit tau*3--subunit delta'---Beta sliding clamp*2 and 10-nt gapped DNA
Classification: other
SequenceString: MIRLYPEQLR AQLNEGLRAA YLLLGNDPLL LQESQDAVRQ VAAAQGFEEH HTFSIDPNTD WNAIFSLCQA MSLFASRQTL LLLLPENGPN AAINEQLLTL TGLLHDDLLL IVRGNKLSKA QENAAWFTAL ANRSVQVTCQ TPEQAQLPRW VAARAKQLNL ELDDAANQVL ...String:
MIRLYPEQLR AQLNEGLRAA YLLLGNDPLL LQESQDAVRQ VAAAQGFEEH HTFSIDPNTD WNAIFSLCQA MSLFASRQTL LLLLPENGPN AAINEQLLTL TGLLHDDLLL IVRGNKLSKA QENAAWFTAL ANRSVQVTCQ TPEQAQLPRW VAARAKQLNL ELDDAANQVL CYCYEGNLLA LAQALERLSL LWPDGKLTLP RVEQAVNDAA HFTPFHWVDA LLMGKSKRAL HILQQLRLEG SEPVILLRTL QRELLLLVNL KRQSAHTPLR ALFDKHRVWQ NRRGMMGEAL NRLSQTQLRQ AVQLLTRTEL TLKQDYGQSV WAELEGLSLL LCHKPLADVF IDGMSYQVLA RKWRPQTFAD VVGQEHVLTA LANGLSLGRI HHAYLFSGTR GVGKTSIARL LAKGLNCETG ITATPCGVCD NCREIEQGRF VDLIEIDAAS RTKVEDTRDL LDNVQYAPAR GRFKVYLIDE VHMLSRHSFN ALLKTLEEPP EHVKFLLATT DPQKLPVTIL SRCLQFHLKA LDVEQIRHQL EHILNEEHIA HEPRALQLLA RAAEGSLRDA LSLTDQAIAS GDGQVSTQAV SAMLGTLDDD QALSLVEAMV EANGERVMAL INEAAARGIE WEALLVEMLG LLHRIAMVQL SPAALGNDMA AIELRMRELA RTIPPTDIQL YYQTLLIGRK ELPYAPDRRM GVEMTLLRAL AFHPRMPLPE PEVPRQSFAP VAPTAVMTPT QVPPQPQSAP QQAPTVPLPE TTSQVLAARQ QLQRVQGATK AKKSEPAAAT RARPVNNAAL ERLASVTDRV QARPVPSALE KAPAKKEAYR WKATTPVMQQ KEVVATPKAL KKALEHEKTP ELAAKLAAEA IERDPWAAQV SQLSLPKLVE QVALNAWKEE SDNAVCLHLR SSQRHLNNRG AQQKLAEALS MLKGSTVELT IVEDDNPAVR TPLEWRQAIY EEKLAQARES IIADNNIQTL RRFFDAELDE ESIRPIMSYQ VLARKWRPQT FADVVGQEHV LTALANGLSL GRIHHAYLFS GTRGVGKTSI ARLLAKGLNC ETGITATPCG VCDNCREIEQ GRFVDLIEID AASRTKVEDT RDLLDNVQYA PARGRFKVYL IDEVHMLSRH SFNALLKTLE EPPEHVKFLL ATTDPQKLPV TILSRCLQFH LKALDVEQIR HQLEHILNEE HIAHEPRALQ LLARAAEGSL RDALSLTDQA IASGDGQVST QAVSAMLGTL DDDQALSLVE AMVEANGERV MALINEAAAR GIEWEALLVE MLGLLHRIAM VQLSPAALGN DMAAIELRMR ELARTIPPTD IQLYYQTLLI GRKELPYAPD RRMGVEMTLL RALAFHPRMP LPEPEVPRQS FAPVAPTAVM TPTQVPPQPQ SAPQQAPTVP LPETTSQVLA ARQQLQRVQG ATKAKKSEPA AATRARPVNN AALERLASVT DRVQARPVPS ALEKAPAKKE AYRWKATTPV MQQKEVVATP KALKKALEHE KTPELAAKLA AEAIERDPWA AQVSQLSLPK LVEQVALNAW KEESDNAVCL HLRSSQRHLN NRGAQQKLAE ALSMLKGSTV ELTIVEDDNP AVRTPLEWRQ AIYEEKLAQA RESIIADNNI QTLRRFFDAE LDEESIRPIM SYQVLARKWR PQTFADVVGQ EHVLTALANG LSLGRIHHAY LFSGTRGVGK TSIARLLAKG LNCETGITAT PCGVCDNCRE IEQGRFVDLI EIDAASRTKV EDTRDLLDNV QYAPARGRFK VYLIDEVHML SRHSFNALLK TLEEPPEHVK FLLATTDPQK LPVTILSRCL QFHLKALDVE QIRHQLEHIL NEEHIAHEPR ALQLLARAAE GSLRDALSLT DQAIASGDGQ VSTQAVSAML GTLDDDQALS LVEAMVEANG ERVMALINEA AARGIEWEAL LVEMLGLLHR IAMVQLSPAA LGNDMAAIEL RMRELARTIP PTDIQLYYQT LLIGRKELPY APDRRMGVEM TLLRALAFHP RMPLPEPEVP RQSFAPVAPT AVMTPTQVPP QPQSAPQQAP TVPLPETTSQ VLAARQQLQR VQGATKAKKS EPAAATRARP VNNAALERLA SVTDRVQARP VPSALEKAPA KKEAYRWKAT TPVMQQKEVV ATPKALKKAL EHEKTPELAA KLAAEAIERD PWAAQVSQLS LPKLVEQVAL NAWKEESDNA VCLHLRSSQR HLNNRGAQQK LAEALSMLKG STVELTIVED DNPAVRTPLE WRQAIYEEKL AQARESIIAD NNIQTLRRFF DAELDEESIR PIMRWYPWLR PDFEKLVASY QAGRGHHALL IQALPGMGDD ALIYALSRYL LCQQPQGHKS CGHCRGCQLM QAGTHPDYYT LAPEKGKNTL GVDAVREVTE KLNEHARLGG AKVVWVTDAA LLTDAAANAL LKTLEEPPAE TWFFLATREP ERLLATLRSR CRLHYLAPPP EQYAVTWLSR EVTMSQDALL AALRLSAGSP GAALALFQGD NWQARETLCQ ALAYSVPSGD WYSLLAALNH EQAPARLHWL ATLLMDALKR HHGAAQVTNV DVPGLVAELA NHLSPSRLQA ILGDVCHIRE QLMSVTGINR ELLITDLLLR IEHYLQPGVV LPVPHLMKFT VEREHLLKPL QQVSGPLGGR PTLPILGNLL LQVADGTLSL TGTDLEMEMV ARVALVQPHE PGATTVPARK FFDICRGLPE GAEIAVQLEG ERMLVRSGRS RFSLSTLPAA DFPNLDDWQS EVEFTLPQAT MKRLIEATQF SMAHQDVRYY LNGMLFETEG EELRTVATDG HRLAVCSMPI GQSLPSHSVI VPRKGVIELM RMLDGGDNPL RVQIGSNNIR AHVGDFIFTS KLVDGRFPDY RRVLPKNPDK HLEAGCDLLK QAFARAAILS NEKFRGVRLY VSENQLKITA NNPEQEEAEE ILDVTYSGAE MEIGFNVSYV LDVLNALKCE NVRMMLTDSV SSVQIEDAAS QSAAYVVMPM RLMKFTVERE HLLKPLQQVS GPLGGRPTLP ILGNLLLQVA DGTLSLTGTD LEMEMVARVA LVQPHEPGAT TVPARKFFDI CRGLPEGAEI AVQLEGERML VRSGRSRFSL STLPAADFPN LDDWQSEVEF TLPQATMKRL IEATQFSMAH QDVRYYLNGM LFETEGEELR TVATDGHRLA VCSMPIGQSL PSHSVIVPRK GVIELMRMLD GGDNPLRVQI GSNNIRAHVG DFIFTSKLVD GRFPDYRRVL PKNPDKHLEA GCDLLKQAFA RAAILSNEKF RGVRLYVSEN QLKITANNPE QEEAEEILDV TYSGAEMEIG FNVSYVLDVL NALKCENVRM MLTDSVSSVQ IEDAASQSAA YVVMPMRL

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 49.6 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.6 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

1jr3


Details: PDB 1JR3, 3BEP and 3SXU
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.54 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 473295
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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