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- EMDB-70960: NHEJ Short-range complex with Polymerase lambda -

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Basic information

Entry
Database: EMDB / ID: EMD-70960
TitleNHEJ Short-range complex with Polymerase lambda
Map data
Sample
  • Complex: NHEJ Short-range complex with Polymerase lambda
    • Protein or peptide: DNA ligase 4
    • Protein or peptide: Non-homologous end-joining factor 1
    • Protein or peptide: X-ray repair cross-complementing protein 6
    • Protein or peptide: X-ray repair cross-complementing protein 5
    • Protein or peptide: DNA polymerase lambda
    • Protein or peptide: DNA repair protein XRCC4
    • DNA: DNA (34-MER)
    • DNA: DNA (34-MER)
    • Protein or peptide: Protein PAXX
KeywordsDNA repair / NHEJ / Complex / Polymerase / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.23 Å
AuthorsVogt A / He Y
Funding support United States, 7 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM135651 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM144559 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5T32GM008382 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)P01CA092584 United States
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)1ZIC ES102645 United States
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)Z01 ES065070 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R24GM154185 United States
CitationJournal: To Be Published
Title: End Processing in NHEJ by Polymerase lambda and PNKP is coordinated during short-range synapsis
Authors: Vogt A / Kaminski AM / Pedersen LC / Naila T / Tomkinson AE / Lees-Miller SP / Kunkel TA / He Y
History
DepositionJun 3, 2025-
Header (metadata) releaseJul 1, 2026-
Map releaseJul 1, 2026-
UpdateJul 1, 2026-
Current statusJul 1, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_70960.png

Downloads & links

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Map

FileDownload / File: emd_70960.map.gz / Format: CCP4 / Size: 274.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 416 pix.
= 439.296 Å		1.06 Å/pix.
x 416 pix.
= 439.296 Å		1.06 Å/pix.
x 416 pix.
= 439.296 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.056 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.13
Minimum - Maximum0.0 - 19.506368999999999
Average (Standard dev.)0.0018320183 (±0.023318542)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions416416416
Spacing416416416
CellA=B=C: 439.296 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : NHEJ Short-range complex with Polymerase lambda

EntireName: NHEJ Short-range complex with Polymerase lambda
Components
  • Complex: NHEJ Short-range complex with Polymerase lambda
    • Protein or peptide: DNA ligase 4
    • Protein or peptide: Non-homologous end-joining factor 1
    • Protein or peptide: X-ray repair cross-complementing protein 6
    • Protein or peptide: X-ray repair cross-complementing protein 5
    • Protein or peptide: DNA polymerase lambda
    • Protein or peptide: DNA repair protein XRCC4
    • DNA: DNA (34-MER)
    • DNA: DNA (34-MER)
    • Protein or peptide: Protein PAXX

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Supramolecule #1: NHEJ Short-range complex with Polymerase lambda

SupramoleculeName: NHEJ Short-range complex with Polymerase lambda / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#9

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Macromolecule #1: DNA ligase 4

MacromoleculeName: DNA ligase 4 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: DNA ligase (ATP)
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 104.124953 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAASQTSQTV ASHVPFADLC STLERIQKSK GRAEKIRHFR EFLDSWRKFH DALHKNHKDV TDSFYPAMRL ILPQLERERM AYGIKETML AKLYIELLNL PRDGKDALKL LNYRTPTGTH GDAGDFAMIA YFVLKPRCLQ KGSLTIQQVN DLLDSIASNN S AKRKDLIK ...String:
MAASQTSQTV ASHVPFADLC STLERIQKSK GRAEKIRHFR EFLDSWRKFH DALHKNHKDV TDSFYPAMRL ILPQLERERM AYGIKETML AKLYIELLNL PRDGKDALKL LNYRTPTGTH GDAGDFAMIA YFVLKPRCLQ KGSLTIQQVN DLLDSIASNN S AKRKDLIK KSLLQLITQS SALEQKWLIR MIIKDLKLGV SQQTIFSVFH NDAAELHNVT TDLEKVCRQL HDPSVGLSDI SI TLFSAFK PMLAAIADIE HIEKDMKHQS FYIETKLDGE RMQMHKDGDV YKYFSRNGYN YTDQFGASPT EGSLTPFIHN AFK ADIQIC ILDGEMMAYN PNTQTFMQKG TKFDIKRMVE DSDLQTCYCV FDVLMVNNKK LGHETLRKRY EILSSIFTPI PGRI EIVQK TQAHTKNEVI DALNEAIDKR EEGIMVKQPL SIYKPDKRGE GWLKIKPEYV SGLMDELDIL IVGGYWGKGS RGGMM SHFL CAVAEKPPPG EKPSVFHTLS RVGSGCTMKE LYDLGLKLAK YWKPFHRKAP PSSILCGTEK PEVYIEPCNS VIVQIK AAE IVPSDMYKTG CTLRFPRIEK IRDDKEWHEC MTLDDLEQLR GKASGKLASK HLYIGGDDEP QEKKRKAAPK MKKVIGI IE HLKAPNLTNV NKISNIFEDV EFCVMSGTDS QPKPDLENRI AEFGGYIVQN PGPDTYCVIA GSENIRVKNI ILSNKHDV V KPAWLLECFK TKSFVPWQPR FMIHMCPSTK EHFAREYDCY GDSYFIDTDL NQLKEVFSGI KNSNEQTPEE MASLIADLE YRYSWDCSPL SMFRRHTVYL DSYAVINDLS TKNEGTRLAI KALELRFHGA KVVSCLAEGV SHVIIGEDHS RVADFKAFRR TFKRKFKIL KESWVTDSID KCELQEENQY LI

UniProtKB: DNA ligase 4

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Macromolecule #2: Non-homologous end-joining factor 1

MacromoleculeName: Non-homologous end-joining factor 1 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 33.372234 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MEELEQGLLM QPWAWLQLAE NSLLAKVFIT KQGYALLVSD LQQVWHEQVD TSVVSQRAKE LNKRLTAPPA AFLCHLDNLL RPLLKDAAH PSEATFSCDC VADALILRVR SELSGLPFYW NFHCMLASPS LVSQHLIRPL MGMSLALQCQ VRELATLLHM K DLEIQDYQ ...String:
MEELEQGLLM QPWAWLQLAE NSLLAKVFIT KQGYALLVSD LQQVWHEQVD TSVVSQRAKE LNKRLTAPPA AFLCHLDNLL RPLLKDAAH PSEATFSCDC VADALILRVR SELSGLPFYW NFHCMLASPS LVSQHLIRPL MGMSLALQCQ VRELATLLHM K DLEIQDYQ ESGATLIRDR LKTEPFEENS FLEQFMIEKL PEACSIGDGK PFVMNLQDLY MAVTTQEVQV GQKHQGAGDP HT SNSASLQ GIDSQCVNQP EQLVSSAPTL SAPEKESTGT SGPLQRPQLS KVKRKKPRGL FS

UniProtKB: Non-homologous end-joining factor 1

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Macromolecule #3: X-ray repair cross-complementing protein 6

MacromoleculeName: X-ray repair cross-complementing protein 6 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
EC number: Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 68.872875 KDa
Recombinant expressionOrganism: unidentified baculovirus
SequenceString: MSGWESYYKT EGDEEAEEEQ EENLEASGDY KYSGRDSLIF LVDASKAMFE SQSEDELTPF DMSIQCIQSV YISKIISSDR DLLAVVFYG TEKDKNSVNF KNIYVLQELD NPGAKRILEL DQFKGQQGQK RFQDMMGHGS DYSLSEVLWV CANLFSDVQF K MSHKRIML ...String:
MSGWESYYKT EGDEEAEEEQ EENLEASGDY KYSGRDSLIF LVDASKAMFE SQSEDELTPF DMSIQCIQSV YISKIISSDR DLLAVVFYG TEKDKNSVNF KNIYVLQELD NPGAKRILEL DQFKGQQGQK RFQDMMGHGS DYSLSEVLWV CANLFSDVQF K MSHKRIML FTNEDNPHGN DSAKASRART KAGDLRDTGI FLDLMHLKKP GGFDISLFYR DIISIAEDED LRVHFEESSK LE DLLRKVR AKETRKRALS RLKLKLNKDI VISVGIYNLV QKALKPPPIK LYRETNEPVK TKTRTFNTST GGLLLPSDTK RSQ IYGSRQ IILEKEETEE LKRFDDPGLM LMGFKPLVLL KKHHYLRPSL FVYPEESLVI GSSTLFSALL IKCLEKEVAA LCRY TPRRN IPPYFVALVP QEEELDDQKI QVTPPGFQLV FLPFADDKRK MPFTEKIMAT PEQVGKMKAI VEKLRFTYRS DSFEN PVLQ QHFRNLEALA LDLMEPEQAV DLTLPKVEAM NKRLGSLVDE FKELVYPPDY NPEGKVTKRK HDNEGSGSKR PKVEYS EEE LKTHISKGTL GKFTVPMLKE ACRAYGLKSG LKKQELL

UniProtKB: DNA repair protein Ku70

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Macromolecule #4: X-ray repair cross-complementing protein 5

MacromoleculeName: X-ray repair cross-complementing protein 5 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 82.812438 KDa
Recombinant expressionOrganism: unidentified baculovirus
SequenceString: MVRSGNKAAV VLCMDVGFTM SNSIPGIESP FEQAKKVITM FVQRQVFAEN KDEIALVLFG TDGTDNPLSG GDQYQNITVH RHLMLPDFD LLEDIESKIQ PGSQQADFLD ALIVSMDVIQ HETIGKKFEK RHIEIFTDLS SRFSKSQLDI IIHSLKKCDI S LQFFLPFS ...String:
MVRSGNKAAV VLCMDVGFTM SNSIPGIESP FEQAKKVITM FVQRQVFAEN KDEIALVLFG TDGTDNPLSG GDQYQNITVH RHLMLPDFD LLEDIESKIQ PGSQQADFLD ALIVSMDVIQ HETIGKKFEK RHIEIFTDLS SRFSKSQLDI IIHSLKKCDI S LQFFLPFS LGKEDGSGDR GDGPFRLGGH GPSFPLKGIT EQQKEGLEIV KMVMISLEGE DGLDEIYSFS ESLRKLCVFK KI ERHSIHW PCRLTIGSNL SIRIAAYKSI LQERVKKTWT VVDAKTLKKE DIQKETVYCL NDDDETEVLK EDIIQGFRYG SDI VPFSKV DEEQMKYKSE GKCFSVLGFC KSSQVQRRFF MGNQVLKVFA ARDDEAAAVA LSSLIHALDD LDMVAIVRYA YDKR ANPQV GVAFPHIKHN YECLVYVQLP FMEDLRQYMF SSLKNSKKYA PTEAQLNAVD ALIDSMSLAK KDEKTDTLED LFPTT KIPN PRFQRLFQCL LHRALHPREP LPPIQQHIWN MLNPPAEVTT KSQIPLSKIK TLFPLIEAKK KDQVTAQEIF QDNHED GPT AKKLKTEQGG AHFSVSSLAE GSVTSVGSVN PAENFRVLVK QKKASFEEAS NQLINHIEQF LDTNETPYFM KSIDCIR AF REEAIKFSEE QRFNNFLKAL QEKVEIKQLN HFWEIVVQDG ITLITKEEAS GSSVTAEEAK KFLAPKDKPS GDTAAVFE E GGDVDDLLDM I

UniProtKB: DNA repair protein Ku80

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Macromolecule #5: DNA polymerase lambda

MacromoleculeName: DNA polymerase lambda / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO / EC number: DNA-directed DNA polymerase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 63.571238 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MDPRGILKAF PKRQKIHADA SSKVLAKIPR REEGEEAEEW LSSLRAHVVR TGIGRARAEL FEKQIVQHGG QLCPAQGPGV THIVVDEGM DYERALRLLR LPQLPPGAQL VKSAWLSLCL QERRLVDVAG FSIFIPSRYL DHPQPSKAEQ DASIPPGTHE A LLQTALSP ...String:
MDPRGILKAF PKRQKIHADA SSKVLAKIPR REEGEEAEEW LSSLRAHVVR TGIGRARAEL FEKQIVQHGG QLCPAQGPGV THIVVDEGM DYERALRLLR LPQLPPGAQL VKSAWLSLCL QERRLVDVAG FSIFIPSRYL DHPQPSKAEQ DASIPPGTHE A LLQTALSP PPPPTRPVSP PQKAKEAPNT QAQPISDDEA SDGEETQVSA ADLEALISGH YPTSLEGDCE PSPAPAVLDK WV CAQPSSQ KATNHNLHIT EKLEVLAKAY SVQGDKWRAL GYAKAINALK SFHKPVTSYQ EACSIPGIGK RMAEKIIEIL ESG HLRKLD HISESVPVLE LFSNIWGAGT KTAQMWYQQG FRSLEDIRSQ ASLTTQQAIG LKHYSDFLER MPREEATEIE QTVQ KAAQA FNSGLLCVAC GSYRRGKATC GDVDVLITHP DGRSHRGIFS RLLDSLRQEG FLTDDLVSQE ENGQQQKYLG VCRLP GPGR RHRRLDIIVV PYSEFACALL YFTGSAHFNR SMRALAKTKG MSLSEHALST AVVRNTHGCK VGPGRVLPTP TEKDVF RLL GLPYREPAER DW

UniProtKB: DNA polymerase lambda

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Macromolecule #6: DNA repair protein XRCC4

MacromoleculeName: DNA repair protein XRCC4 / type: protein_or_peptide / ID: 6 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 38.337703 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MERKISRIHL VSEPSITHFL QVSWEKTLES GFVITLTDGH SAWTGTVSES EISQEADDMA MEKGKYVGEL RKALLSGAGP ADVYTFNFS KESCYFFFEK NLKDVSFRLG SFNLEKVENP AEVIRELICY CLDTIAENQA KNEHLQKENE RLLRDWNDVQ G RFEKCVSA ...String:
MERKISRIHL VSEPSITHFL QVSWEKTLES GFVITLTDGH SAWTGTVSES EISQEADDMA MEKGKYVGEL RKALLSGAGP ADVYTFNFS KESCYFFFEK NLKDVSFRLG SFNLEKVENP AEVIRELICY CLDTIAENQA KNEHLQKENE RLLRDWNDVQ G RFEKCVSA KEALETDLYK RFILVLNEKK TKIRSLHNKL LNAAQEREKD IKQEGETAIC SEMTADRDPV YDESTDEESE NQ TDLSGLA SAAVSKDDSI ISSLDVTDIA PSRKRRQRMQ RNLGTEPKMA PQENQLQEKE NSRPDSSLPE TSKKEHISAE NMS LETLRN SSPEDLFDEI

UniProtKB: DNA repair protein XRCC4

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Macromolecule #9: Protein PAXX

MacromoleculeName: Protein PAXX / type: protein_or_peptide / ID: 9 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 21.663498 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MDPLSPPLCT LPPGPEPPRF VCYCEGEESG EGDRGGFNLY VTDAAELWST CFTPDSLAAL KARFGLSAAE DITPRFRAAC EQQAVALTL QEDRASLTLS GGPSALAFDL SKVPGPEAAP RLRALTLGLA KRVWSLERRL AAAEETAVSP RKSPRPAGPQ L FLPDPDPQ ...String:
MDPLSPPLCT LPPGPEPPRF VCYCEGEESG EGDRGGFNLY VTDAAELWST CFTPDSLAAL KARFGLSAAE DITPRFRAAC EQQAVALTL QEDRASLTLS GGPSALAFDL SKVPGPEAAP RLRALTLGLA KRVWSLERRL AAAEETAVSP RKSPRPAGPQ L FLPDPDPQ RGGPGPGVRR RCPGESLINP GFKSKKPAGG VDFDET

UniProtKB: Protein PAXX

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Macromolecule #7: DNA (34-MER)

MacromoleculeName: DNA (34-MER) / type: dna / ID: 7 / Number of copies: 2 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 10.567767 KDa
SequenceString:
(DG)(DT)(DT)(DG)(DT)(DC)(DT)(DG)(DG)(DA) (DG)(DT)(DC)(DT)(DC)(DT)(DG)(DT)(DG)(DG) (DC)(DA)(DA)(DT)(DC)(DG)(DA)(DT)(DG) (DA)(DT)(DG)(DT)(DG)

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Macromolecule #8: DNA (34-MER)

MacromoleculeName: DNA (34-MER) / type: dna / ID: 8 / Number of copies: 2 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 10.374722 KDa
SequenceString:
(DA)(DC)(DA)(DT)(DC)(DA)(DT)(DC)(DG)(DA) (DT)(DT)(DG)(DC)(DC)(DA)(DC)(DA)(DG)(DA) (DG)(DA)(DC)(DT)(DC)(DC)(DA)(DG)(DA) (DC)(DA)(DA)(DC)(DA)

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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: 7.9
Component:
ConcentrationFormulaName
50.0 mMKClPotassium Chloride
10.0 mMHEPES
5.0 percentglycerol
1.0 mMDTT
0.01 percentNP-40
5.0 mMMgCl2Magnesium Chloride
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 400 / Support film - Material: GRAPHENE OXIDE / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 10 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV
DetailsSample stabilized by GraFix

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Number grids imaged: 1 / Average exposure time: 3.61 sec. / Average electron dose: 66.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1506486
CTF correctionSoftware - Name: cryoSPARC (ver. 4.6.2) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7lsy

Final reconstructionNumber classes used: 1 / Resolution.type: BY AUTHOR / Resolution: 7.23 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.6.2) / Number images used: 179057
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.6.2)
Final angle assignmentType: MAXIMUM LIKELIHOOD

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