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- EMDB-45855: The consensus map of ligation complex II in the NHEJ pathway -

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Basic information

Entry
Database: EMDB / ID: EMD-45855
TitleThe consensus map of ligation complex II in the NHEJ pathway
Map dataConsensus map of ligation complex II in the NHEJ complex
Sample
  • Complex: Ligation complex like in the NHEJ pathway
    • Protein or peptide: human Ku70
    • Protein or peptide: human Ku80
    • Protein or peptide: human XLF
    • Protein or peptide: human XRCC4
    • Protein or peptide: human ligase IV
    • Protein or peptide: human PAXX
    • DNA: DNA chain I
    • DNA: DNA chain J
    • DNA: DNA chain K
    • DNA: DNA chain L
KeywordsNHEJ / ligation / XLF / PAXX / DNA repair / Ligase IV / DNA BINDING PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.0 Å
AuthorsLi J / Liu L / Gellert M / Yang W
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK) United States
CitationJournal: To Be Published
Title: The ligation complex II in the NHEJ pathway
Authors: Li J / Liu L / Gellert M / Yang W
History
DepositionJul 21, 2024-
Header (metadata) releaseApr 23, 2025-
Map releaseApr 23, 2025-
UpdateApr 23, 2025-
Current statusApr 23, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_45855.png

Downloads & links

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Map

FileDownload / File: emd_45855.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationConsensus map of ligation complex II in the NHEJ complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 512 pix.
= 426.496 Å		0.83 Å/pix.
x 512 pix.
= 426.496 Å		0.83 Å/pix.
x 512 pix.
= 426.496 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.833 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-0.2016854 - 0.80205804
Average (Standard dev.)-0.0005477393 (±0.024921367)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 426.496 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_45855_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half 1 map

Fileemd_45855_half_map_1.map
Annotationhalf 1 map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half 2 map

Fileemd_45855_half_map_2.map
Annotationhalf 2 map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Ligation complex like in the NHEJ pathway

EntireName: Ligation complex like in the NHEJ pathway
Components
  • Complex: Ligation complex like in the NHEJ pathway
    • Protein or peptide: human Ku70
    • Protein or peptide: human Ku80
    • Protein or peptide: human XLF
    • Protein or peptide: human XRCC4
    • Protein or peptide: human ligase IV
    • Protein or peptide: human PAXX
    • DNA: DNA chain I
    • DNA: DNA chain J
    • DNA: DNA chain K
    • DNA: DNA chain L

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Supramolecule #1: Ligation complex like in the NHEJ pathway

SupramoleculeName: Ligation complex like in the NHEJ pathway / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 854 KDa

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Macromolecule #1: human Ku70

MacromoleculeName: human Ku70 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GPVMSGWESY YKTEGDEEAE EEQEENLEAS GDYKYSGRDS LIFLVDASKA MFESQSEDEL TPF DMSIQC IQSVYISKII SSDRDLLAVV FYGTEKDKNS VNFKNIYVLQ ELDNPGAKRI LELD QFKGQ QGQKRFQDMM GHGSDYSLSE VLWVCANLFS DVQFKMSHKR ...String:
GPVMSGWESY YKTEGDEEAE EEQEENLEAS GDYKYSGRDS LIFLVDASKA MFESQSEDEL TPF DMSIQC IQSVYISKII SSDRDLLAVV FYGTEKDKNS VNFKNIYVLQ ELDNPGAKRI LELD QFKGQ QGQKRFQDMM GHGSDYSLSE VLWVCANLFS DVQFKMSHKR IMLFTNEDNP HGNDS AKAS RARTKAGDLR DTGIFLDLMH LKKPGGFDIS LFYRDIISIA EDEDLRVHFE ESSKLE DLL RKVRAKETRK RALSRLKLKL NKDIVISVGI YNLVQKALKP PPIKLYRETN EPVKTKT RT FNTSTGGLLL PSDTKRSQIY GSRQIILEKE ETEELKRFDD PGLMLMGFKP LVLLKKHH Y LRPSLFVYPE ESLVIGSSTL FSALLIKCLE KEVAALCRYT PRRNIPPYFV ALVPQEEEL DDQKIQVTPP GFQLVFLPFA DDKRKMPFTE KIMATPEQVG KMKAIVEKLR FTYRSDSFEN PVLQQHFRN LEALALDLME PEQAVDLTLP KVEAMNKRLG SLVDEFKELV YPPDYNPEGK V TKRKHDNE GSGSKRPKVE YSEEELKTHI SKGTLGKFTV PMLKEACRAY GLKSGLKKQE LL EALTKHF QD

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Macromolecule #2: human Ku80

MacromoleculeName: human Ku80 / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MVRSGNKAAV VLCMDVGFTM SNSIPGIESP FEQAKKVITM FVQRQVFAEN KDEIALVLFG TDGTDNPLS GGDQYQNITV HRHLMLPDFD LLEDIESKIQ PGSQQADFLD ALIVSMDVIQ H ETIGKKFE KRHIEIFTDL SSRFSKSQLD IIIHSLKKCD ISLQFFLPFS ...String:
MVRSGNKAAV VLCMDVGFTM SNSIPGIESP FEQAKKVITM FVQRQVFAEN KDEIALVLFG TDGTDNPLS GGDQYQNITV HRHLMLPDFD LLEDIESKIQ PGSQQADFLD ALIVSMDVIQ H ETIGKKFE KRHIEIFTDL SSRFSKSQLD IIIHSLKKCD ISLQFFLPFS LGKEDGSGDR GD GPFRLGG HGPSFPLKGI TEQQKEGLEI VKMVMISLEG EDGLDEIYSF SESLRKLCVF KKI ERHSIH WPCRLTIGSN LSIRIAAYKS ILQERVKKTW TVVDAKTLKK EDIQKETVYC LNDD DETEV LKEDIIQGFR YGSDIVPFSK VDEEQMKYKS EGKCFSVLGF CKSSQVQRRF FMGNQ VLKV FAARDDEAAA VALSSLIHAL DDLDMVAIVR YAYDKRANPQ VGVAFPHIKH NYECLV YVQ LPFMEDLRQY MFSSLKNSKK YAPTEAQLNA VDALIDSMSL AKKDEKTDTL EDLFPTT KI PNPRFQRLFQ CLLHRALHPR EPLPPIQQHI WNMLNPPAEV TTKSQIPLSK IKTLFPLI E AKKKDQVTAQ EIFQDNHEDG PTAKKLKTEQ GGAHFSVSSL AEGSVTSVGS VNPAENFRV LVKQKKASFE EASNQLINHI EQFLDTNETP YFMKSIDCIR AFREEAIKFS EEQRFNNFLK ALQEKVEIK QLNHFWEIVV QDGITLITKE EASGSSVTAE EAKKFLAPKD KPSGDTAAVF E EGGDVDDL LDMI

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Macromolecule #3: human XLF

MacromoleculeName: human XLF / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GPVMEELEQG LLMQPWAWLQ LAENSLLAKV FITKQGYALL VSDLQQVWHE QVDTSVVSQR AKE LNKRLT APPAAFLCHL DNLLRPLLKD AAHPSEATFS CDCVADALIL RVRSELSGLP FYWN FHCML ASPSLVSQHL IRPLMGMSLA LQCQVRELAT LLHMKDLEIQ ...String:
GPVMEELEQG LLMQPWAWLQ LAENSLLAKV FITKQGYALL VSDLQQVWHE QVDTSVVSQR AKE LNKRLT APPAAFLCHL DNLLRPLLKD AAHPSEATFS CDCVADALIL RVRSELSGLP FYWN FHCML ASPSLVSQHL IRPLMGMSLA LQCQVRELAT LLHMKDLEIQ DYQESGATLI RDRLK TEPF EENSFLEQFM IEKLPEACSI GDGKPFVMNL QDLYMAVTTQ EVQVGQKHQG AGDPHT SNS ASLQGIDSQC VNQPEQLVSS APTLSAPEKE STGTSGPLQR PQLSKVKRKK PRGLFS

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Macromolecule #4: human XRCC4

MacromoleculeName: human XRCC4 / type: protein_or_peptide / ID: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MERKISRIHL VSEPSITHFL QVSWEKTLES GFVITLTDGH SAWTGTVSES EISQEADDMA MEKGKYVGE LRKALLSGAG PADVYTFNFS KESCYFFFEK NLKDVSFRLG SFNLEKVENP A EVIRELIC YCLDTIAENQ AKNEHLQKEN ERLLRDWNDV QGRFEKCVSA ...String:
MERKISRIHL VSEPSITHFL QVSWEKTLES GFVITLTDGH SAWTGTVSES EISQEADDMA MEKGKYVGE LRKALLSGAG PADVYTFNFS KESCYFFFEK NLKDVSFRLG SFNLEKVENP A EVIRELIC YCLDTIAENQ AKNEHLQKEN ERLLRDWNDV QGRFEKCVSA KEALETDLYK RF ILVLNEK KTKIRSLHNK LLNAAQEREK DIKQEGETAI CSEMTADRDP VYDESTDEES ENQ TDLSGL ASAAVSKDDS IISSLDVTDI APSRKRRQRM QRNLGTEPKM APQENQLQEK ENSR PDSSL PETSKKEHIS AENMSLETLR NSSPEDLFDE I

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Macromolecule #5: human ligase IV

MacromoleculeName: human ligase IV / type: protein_or_peptide / ID: 5 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GPVMAASQTS QTVASHVPFA DLCSTLERIQ KSKGRAEKIR HFREFLDSWR KFHDALHKNH KDV TDSFYP AMRLILPQLE RERMAYGIKE TMLAKLYIEL LNLPRDGKDA LKLLNYRTPT GTHG DAGDF AMIAYFVLKP RCLQKGSLTI QQVNDLLDSI ASNNSAKRKD ...String:
GPVMAASQTS QTVASHVPFA DLCSTLERIQ KSKGRAEKIR HFREFLDSWR KFHDALHKNH KDV TDSFYP AMRLILPQLE RERMAYGIKE TMLAKLYIEL LNLPRDGKDA LKLLNYRTPT GTHG DAGDF AMIAYFVLKP RCLQKGSLTI QQVNDLLDSI ASNNSAKRKD LIKKSLLQLI TQSSA LEQK WLIRMIIKDL KLGVSQQTIF SVFHNDAAEL HNVTTDLEKV CRQLHDPSVG LSDISI TLF SAFKPMLAAI ADIEHIEKDM KHQSFYIETK LDGERMQMHK DGDVYKYFSR NGYNYTD QF GASPTEGSLT PFIHNAFKAD IQICILDGEM MAYNPNTQTF MQKGTKFDIK RMVEDSDL Q TCYCVFDVLM VNNKKLGHET LRKRYEILSS IFTPIPGRIE IVQKTQAHTK NEVIDALNE AIDKREEGIM VKQPLSIYKP DKRGEGWLKI KPEYVSGLMD ELDILIVGGY WGKGSRGGMM SHFLCAVAE KPPPGEKPSV FHTLSRVGSG CTMKELYDLG LKLAKYWKPF HRKAPPSSIL C GTEKPEVY IEPCNSVIVQ IKAAEIVPSD MYKTGCTLRF PRIEKIRDDK EWHECMTLDD LE QLRGKAS GKLASKHLYI GGDDEPQEKK RKAAPKMKKV IGIIEHLKAP NLTNVNKISN IFE DVEFCV MSGTDSQPKP DLENRIAEFG GYIVQNPGPD TYCVIAGSEN IRVKNIILSN KHDV VKPAW LLECFKTKSF VPWQPRFMIH MCPSTKEHFA REYDCYGDSY FIDTDLNQLK EVFSG IKNS NEQTPEEMAS LIADLEYRYS WDCSPLSMFR RHTVYLDSYA VINDLSTKNE GTRLAI KAL ELRFHGAKVV SCLAEGVSHV IIGEDHSRVA DFKAFRRTFK RKFKILKESW VTDSIDK CE LQEENQYLI

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Macromolecule #6: human PAXX

MacromoleculeName: human PAXX / type: protein_or_peptide / ID: 6 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGSSHHHHHH SQDPMDPLSP PLCTLPPGPE PPRFVCYCEG EESGEGDRGG FNLYVTDAAE LWSTCFTPDS LAAL KARFG LSAAEDITPR FRAACEQQAV ALTLQEDRAS LTLSGGPSAL AFDLSKVPGP EAAPR LRAL TLGLAKRVWS LERRLAAAEE TAVSPRKSPR ...String:
MGSSHHHHHH SQDPMDPLSP PLCTLPPGPE PPRFVCYCEG EESGEGDRGG FNLYVTDAAE LWSTCFTPDS LAAL KARFG LSAAEDITPR FRAACEQQAV ALTLQEDRAS LTLSGGPSAL AFDLSKVPGP EAAPR LRAL TLGLAKRVWS LERRLAAAEE TAVSPRKSPR PAGPQLFLPD PDPQRGGPGP GVRRRC PGE SLINPGFKSK KPAGGVDFDE T

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Macromolecule #7: DNA chain I

MacromoleculeName: DNA chain I / type: dna / ID: 7 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
SequenceString:
CGCGCCCAGC TTTCCCAGCT AATAAACTAA AAACTATGCA TGCTCTACTG CTTCTGATCT AGTCGACT

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Macromolecule #8: DNA chain J

MacromoleculeName: DNA chain J / type: dna / ID: 8 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
SequenceString:
CGCGCCCAGC TTTCCCAGCT AATAAACTAA AAACATTCGT TCACGTGAGT TCCAGTACAA GTCTAGTC

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Macromolecule #9: DNA chain K

MacromoleculeName: DNA chain K / type: dna / ID: 9 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
SequenceString:
GACTAGATCA GAAGCAGTAG AGCATGCATA GTTTTTAGTT TATTGGGCGC G

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Macromolecule #10: DNA chain L

MacromoleculeName: DNA chain L / type: dna / ID: 10 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
SequenceString:
GACTTGTACT GGAACTCACG TGAACGAATG TTTTTAGTTT ATTGGGCGCG

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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

Concentration0.35 mg/mL
BufferpH: 7.9
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 54.4 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
EMDB ID:

23509

Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 133163
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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