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- EMDB-11215: Cryo-EM structure of DNA-PKcs:Ku80ct194 -

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Basic information

Entry
Database: EMDB / ID: EMD-11215
TitleCryo-EM structure of DNA-PKcs:Ku80ct194
Map data
Sample
  • Organelle or cellular component: DNA-PKcs in complex with Ku80 C-terminal domain
    • Organelle or cellular component: DNA-dependent protein kinase catalytic subunit,DNA-PKcs
      • Protein or peptide: DNA-dependent protein kinase catalytic subunit,DNA-PKcs
    • Organelle or cellular component: X-ray repair cross-complementing protein 5
      • Protein or peptide: X-ray repair cross-complementing protein 5
KeywordsKinase / DNA-PKcs / NHEJ / DNA-repair / DNA-PK / DNA BINDING PROTEIN / Ku80
Function / homology
Function and homology information


positive regulation of platelet formation / Ku70:Ku80 complex / negative regulation of t-circle formation / T cell receptor V(D)J recombination / DNA end binding / pro-B cell differentiation / small-subunit processome assembly / positive regulation of lymphocyte differentiation / DNA-dependent protein kinase activity / DNA-dependent protein kinase complex ...positive regulation of platelet formation / Ku70:Ku80 complex / negative regulation of t-circle formation / T cell receptor V(D)J recombination / DNA end binding / pro-B cell differentiation / small-subunit processome assembly / positive regulation of lymphocyte differentiation / DNA-dependent protein kinase activity / DNA-dependent protein kinase complex / histone H2AXS139 kinase activity / DNA-dependent protein kinase-DNA ligase 4 complex / immunoglobulin V(D)J recombination / nonhomologous end joining complex / immature B cell differentiation / regulation of smooth muscle cell proliferation / nuclear telomere cap complex / double-strand break repair via alternative nonhomologous end joining / regulation of epithelial cell proliferation / telomere capping / Cytosolic sensors of pathogen-associated DNA / IRF3-mediated induction of type I IFN / positive regulation of neurogenesis / regulation of hematopoietic stem cell differentiation / recombinational repair / regulation of telomere maintenance / protein localization to chromosome, telomeric region / U3 snoRNA binding / maturation of 5.8S rRNA / T cell lineage commitment / negative regulation of cGAS/STING signaling pathway / positive regulation of double-strand break repair via nonhomologous end joining / 2-LTR circle formation / B cell lineage commitment / telomeric DNA binding / hematopoietic stem cell proliferation / negative regulation of protein phosphorylation / positive regulation of protein kinase activity / site of DNA damage / peptidyl-threonine phosphorylation / hematopoietic stem cell differentiation / ATP-dependent activity, acting on DNA / ectopic germ cell programmed cell death / somitogenesis / telomere maintenance via telomerase / mitotic G1 DNA damage checkpoint signaling / neurogenesis / telomere maintenance / activation of innate immune response / DNA helicase activity / positive regulation of erythrocyte differentiation / positive regulation of translation / cellular response to leukemia inhibitory factor / response to gamma radiation / small-subunit processome / Nonhomologous End-Joining (NHEJ) / enzyme activator activity / cellular response to gamma radiation / protein-DNA complex / regulation of circadian rhythm / brain development / protein destabilization / peptidyl-serine phosphorylation / double-strand break repair via nonhomologous end joining / protein modification process / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / cellular response to insulin stimulus / intrinsic apoptotic signaling pathway in response to DNA damage / rhythmic process / T cell differentiation in thymus / double-strand break repair / E3 ubiquitin ligases ubiquitinate target proteins / heart development / double-stranded DNA binding / secretory granule lumen / DNA recombination / transcription regulator complex / damaged DNA binding / RNA polymerase II-specific DNA-binding transcription factor binding / chromosome, telomeric region / protein phosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / transcription cis-regulatory region binding / positive regulation of apoptotic process / ribonucleoprotein complex / protein domain specific binding / innate immune response / protein serine kinase activity / negative regulation of DNA-templated transcription / protein serine/threonine kinase activity / DNA damage response / ubiquitin protein ligase binding / Neutrophil degranulation / negative regulation of apoptotic process / chromatin / protein-containing complex binding / nucleolus / enzyme binding / positive regulation of transcription by RNA polymerase II
Similarity search - Function
DNA-dependent protein kinase catalytic subunit, CC3 / DNA-dependent protein kinase catalytic subunit, catalytic domain / DNA-dependent protein kinase catalytic subunit, CC5 / DNA-dependent protein kinase catalytic subunit, CC1/2 / DNA-PKcs, N-terminal / DNA-dependent protein kinase catalytic subunit, CC3 / DNA-PKcs, CC5 / DNA-PKcs, N-terminal / DNA-dependent protein kinase catalytic subunit, CC1/2 / NUC194 ...DNA-dependent protein kinase catalytic subunit, CC3 / DNA-dependent protein kinase catalytic subunit, catalytic domain / DNA-dependent protein kinase catalytic subunit, CC5 / DNA-dependent protein kinase catalytic subunit, CC1/2 / DNA-PKcs, N-terminal / DNA-dependent protein kinase catalytic subunit, CC3 / DNA-PKcs, CC5 / DNA-PKcs, N-terminal / DNA-dependent protein kinase catalytic subunit, CC1/2 / NUC194 / Ku, C-terminal / Ku, C-terminal domain superfamily / Ku C terminal domain like / Ku80 / Ku70/Ku80 C-terminal arm / Ku70/Ku80 C-terminal arm / Ku70/Ku80, N-terminal alpha/beta / Ku70/Ku80 N-terminal alpha/beta domain / Ku70/Ku80 beta-barrel domain / Ku70 and Ku80 are 70kDa and 80kDa subunits of the Lupus Ku autoantigen / Ku70/Ku80 beta-barrel domain / SPOC-like, C-terminal domain superfamily / : / FATC domain / PIK-related kinase, FAT / FAT domain / FATC / FATC domain / PIK-related kinase / FAT domain profile. / FATC domain profile. / Phosphatidylinositol 3- and 4-kinases signature 1. / Phosphatidylinositol 3/4-kinase, conserved site / Phosphatidylinositol 3- and 4-kinases signature 2. / Phosphatidylinositol 3-/4-kinase, catalytic domain superfamily / Phosphoinositide 3-kinase, catalytic domain / Phosphatidylinositol 3- and 4-kinase / Phosphatidylinositol 3- and 4-kinases catalytic domain profile. / Phosphatidylinositol 3-/4-kinase, catalytic domain / von Willebrand factor (vWF) type A domain / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily / Armadillo-like helical / Armadillo-type fold / Protein kinase-like domain superfamily
Similarity search - Domain/homology
X-ray repair cross-complementing protein 5 / DNA-dependent protein kinase catalytic subunit
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.93 Å
AuthorsChaplin AK / Hardwick SW
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Wellcome Trust200814/Z/16/Z United Kingdom
Citation
Journal: Nat Struct Mol Biol / Year: 2021
Title: Dimers of DNA-PK create a stage for DNA double-strand break repair.
Authors: Amanda K Chaplin / Steven W Hardwick / Shikang Liang / Antonia Kefala Stavridi / Ales Hnizda / Lee R Cooper / Taiana Maia De Oliveira / Dimitri Y Chirgadze / Tom L Blundell /
Abstract: DNA double-strand breaks are the most dangerous type of DNA damage and, if not repaired correctly, can lead to cancer. In humans, Ku70/80 recognizes DNA broken ends and recruits the DNA-dependent ...DNA double-strand breaks are the most dangerous type of DNA damage and, if not repaired correctly, can lead to cancer. In humans, Ku70/80 recognizes DNA broken ends and recruits the DNA-dependent protein kinase catalytic subunit (DNA-PKcs) to form DNA-dependent protein kinase holoenzyme (DNA-PK) in the process of non-homologous end joining (NHEJ). We present a 2.8-Å-resolution cryo-EM structure of DNA-PKcs, allowing precise amino acid sequence registration in regions uninterpreted in previous 4.3-Å X-ray maps. We also report a cryo-EM structure of DNA-PK at 3.5-Å resolution and reveal a dimer mediated by the Ku80 C terminus. Central to dimer formation is a domain swap of the conserved C-terminal helix of Ku80. Our results suggest a new mechanism for NHEJ utilizing a DNA-PK dimer to bring broken DNA ends together. Furthermore, drug inhibition of NHEJ in combination with chemo- and radiotherapy has proved successful, making these models central to structure-based drug targeting efforts.
#1: Journal: Nat.Struct.Mol.Biol. / Year: 2020
Title: Dimers of DNA-PK create a stage for DNA-double strand break repair
Authors: Chaplin AK / Hardwick SW / Liang S / Stavridi AK / Hnizda A / Cooper LR / De Oliveira TM / Chirgadze DY / Blundell TL
History
DepositionJun 21, 2020-
Header (metadata) releaseOct 21, 2020-
Map releaseOct 21, 2020-
UpdateMay 1, 2024-
Current statusMay 1, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.125
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.17
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6zh6
  • Surface level: 0.17
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11215.png

Downloads & links

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Map

FileDownload / File: emd_11215.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 320 pix.
= 336.64 Å		1.05 Å/pix.
x 320 pix.
= 336.64 Å		1.05 Å/pix.
x 320 pix.
= 336.64 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.052 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.125 / Movie #1: 0.125
Minimum - Maximum-0.13818944 - 0.50365704
Average (Standard dev.)0.0021313815 (±0.02395952)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 336.64 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0521.0521.052
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z336.640336.640336.640
α/β/γ90.00090.00090.000
start NX/NY/NZ9482110
NX/NY/NZ11313776
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.1380.5040.002

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Supplemental data

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Additional map: Resolve cryoEM density modified map at 3.79 angstrom resolution

Fileemd_11215_additional_1.map
AnnotationResolve cryoEM density modified map at 3.79 angstrom resolution
Projections & Slices
AxesZYX

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Half map: #2

Fileemd_11215_half_map_1.map
Projections & Slices
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Histogram (log scale)

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Half map: #1

Fileemd_11215_half_map_2.map
Projections & Slices
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Sample components

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Entire : DNA-PKcs in complex with Ku80 C-terminal domain

EntireName: DNA-PKcs in complex with Ku80 C-terminal domain
Components
  • Organelle or cellular component: DNA-PKcs in complex with Ku80 C-terminal domain
    • Organelle or cellular component: DNA-dependent protein kinase catalytic subunit,DNA-PKcs
      • Protein or peptide: DNA-dependent protein kinase catalytic subunit,DNA-PKcs
    • Organelle or cellular component: X-ray repair cross-complementing protein 5
      • Protein or peptide: X-ray repair cross-complementing protein 5

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Supramolecule #1: DNA-PKcs in complex with Ku80 C-terminal domain

SupramoleculeName: DNA-PKcs in complex with Ku80 C-terminal domain / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Molecular weightTheoretical: 480 KDa

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Supramolecule #2: DNA-dependent protein kinase catalytic subunit,DNA-PKcs

SupramoleculeName: DNA-dependent protein kinase catalytic subunit,DNA-PKcs
type: organelle_or_cellular_component / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: X-ray repair cross-complementing protein 5

SupramoleculeName: X-ray repair cross-complementing protein 5 / type: organelle_or_cellular_component / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: DNA-dependent protein kinase catalytic subunit,DNA-PKcs

MacromoleculeName: DNA-dependent protein kinase catalytic subunit,DNA-PKcs
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: non-specific serine/threonine protein kinase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 472.056281 KDa
SequenceString: MAGSGAGVRC SLLRLQETLS AADRCGAALA GHQLIRGLGQ ECVLSSSPAV LALQTSLVFS RDFGLLVFVR KSLNSIEFRE CREEILKFL CIFLEKMGQK IAPYSVEIKN TCTSVYTKDR AAKCKIPALD LLIKLLQTFR SSRLMDEFKI GELFSKFYGE L ALKKKIPD ...String:
MAGSGAGVRC SLLRLQETLS AADRCGAALA GHQLIRGLGQ ECVLSSSPAV LALQTSLVFS RDFGLLVFVR KSLNSIEFRE CREEILKFL CIFLEKMGQK IAPYSVEIKN TCTSVYTKDR AAKCKIPALD LLIKLLQTFR SSRLMDEFKI GELFSKFYGE L ALKKKIPD TVLEKVYELL GLLGEVHPSE MINNAENLFR AFLGELKTQM TSAVREPKLP VLAGCLKGLS SLLCNFTKSM EE DPQTSRE IFNFVLKAIR PQIDLKRYAV PSAGLRLFAL HASQFSTCLL DNYVSLFEVL LKWCAHTNVE LKKAALSALE SFL KQVSNM VAKNAEMHKN KLQYFMEQFY GIIRNVDSNN KELSIAIRGY GLFAGPCKVI NAKDVDFMYV ELIQRCKQMF LTQT DTGDD RVYQMPSFLQ SVASVLLYLD TVPEVYTPVL EHLVVMQIDS FPQYSPKMQL VCCRAIVKVF LALAAKGPVL RNCIS TVVH QGLIRICSKP VVLPKGPESE SEDHRASGEV RTGKWKVPTY KDYVDLFRHL LSSDQMMDSI LADEAFFSVN SSSESL NHL LYDEFVKSVL KIVEKLDLTL EIQTVGEQEN GDEAPGVWMI PTSDPAANLH PAKPKDFSAF INLVEFCREI LPEKQAE FF EPWVYSFSYE LILQSTRLPL ISGFYKLLSI TVRNAKKIKY FEGVSPKSLK HSPEDPEKYS CFALFVKFGK EVAVKMKQ Y KDELLASCLT FLLSLPHNII ELDVRAYVPA LQMAFKLGLS YTPLAEVGLN ALEEWSIYID RHVMQPYYKD ILPCLDGYL KTSALSDETK NNWEVSALSR AAQKGFNKVV LKHLKKTKNL SSNEAISLEE IRIRVVQMLG SLGGQINKNL LTVTSSDEMM KSYVAWDRE KRLSFAVPFR EMKPVIFLDV FLPRVTELAL TASDRQTKVA ACELLHSMVM FMLGKATQMP EGGQGAPPMY Q LYKRTFPV LLRLACDVDQ VTRQLYEPLV MQLIHWFTNN KKFESQDTVA LLEAILDGIV DPVDSTLRDF CGRCIREFLK WS IKQITPQ QQEKSPVNTK SLFKRLYSLA LHPNAFKRLG ASLAFNNIYR EFREEESLVE QFVFEALVIY MESLALAHAD EKS LGTIQQ CCDAIDHLCR IIEKKHVSLN KAKKRRLPRG FPPSASLCLL DLVKWLLAHC GRPQTECRHK SIELFYKFVP LLPG NRSPN LWLKDVLKEE GVSFLINTFE GGGCGQPSGI LAQPTLLYLR GPFSLQATLC WLDLLLAALE CYNTFIGERT VGALQ VLGT EAQSSLLKAV AFFLESIAMH DIIAAEKCFG TGAAGNRTSP QEGERYNYSK CTVVVRIMEF TTTLLNTSPE GWKLLK KDL CNTHLMRVLV QTLCEPASIG FNIGDVQVMA HLPDVCVNLM KALKMSPYKD ILETHLREKI TAQSIEELCA VNLYGPD AQ VDRSRLAAVV SACKQLHRAG LLHNILPSQS TDLHHSVGTE LLSLVYKGIA PGDERQCLPS LDLSCKQLAS GLLELAFA F GGLCERLVSL LLNPAVLSTA SLGSSQGSVI HFSHGEYFYS LFSETINTEL LKNLDLAVLE LMQSSVDNTK MVSAVLNGM LDQSFRERAN QKHQGLKLAT TILQHWKKCD SWWAKDSPLE TKMAVLALLA KILQIDSSVS FNTSHGSFPE VFTTYISLLA DTKLDLHLK GQAVTLLPFF TSLTGGSLEE LRRVLEQLIV AHFPMQSREF PPGTPRFNNY VDCMKKFLDA LELSQSPMLL E LMTEVLCR EQQHVMEELF QSSFRRIARR GSCVTQVGLL ESVYEMFRKD DPRLSFTRQS FVDRSLLTLL WHCSLDALRE FF STIVVDA IDVLKSRFTK LNESTFDTQI TKKMGYYKIL DVMYSRLPKD DVHAKESKIN QVFHGSCITE GNELTKTLIK LCY DAFTEN MAGENQLLER RRLYHCAAYN CAISVICCVF NELKFYQGFL FSEKPEKNLL IFENLIDLKR RYNFPVEVEV PMER KKKYI EIRKEAREAA NGDSDGPSYM SSLSYLADST LSEEMSQFDF STGVQSYSYS SQDPRPATGR FRRREQRDPT VHDDV LELE MDELNRHECM APLTALVKHM HRSLGPPQGE EDSVPRDLPS WMKFLHGKLG NPIVPLNIRL FLAKLVINTE EVFRPY AKH WLSPLLQLAA SENNGGEGIH YMVVEIVATI LSWTGLATPT GVPKDEVLAN RLLNFLMKHV FHPKRAVFRH NLEIIKT LV ECWKDCLSIP YRLIFEKFSG KDPNSKDNSV GIQLLGIVMA NDLPPYDPQC GIQSSEYFQA LVNNMSFVRY KEVYAAAA E VLGLILRYVM ERKNILEESL CELVAKQLKQ HQNTMEDKFI VCLNKVTKSF PPLADRFMNA VFFLLPKFHG VLKTLCLEV VLCRVEGMTE LYFQLKSKDF VQVMRHRDDE RQKVCLDIIY KMMPKLKPVE LRELLNPVVE FVSHPSTTCR EQMYNILMWI HDNYRDPES ETDNDSQEIF KLAKDVLIQG LIDENPGLQL IIRNFWSHET RLPSNTLDRL LALNSLYSPK IEVHFLSLAT N FLLEMTSM SPDYPNPMFE HPLSECEFQE YTIDSDWRFR STVLTPMFVE TQASQGTLQT RTQEGSLSAR WPVAGQIRAT QQ QHDFTLT QTADGRSSFD WLTGSSTDPL VDHTSPSSDS LLFAHKRSER LQRAPLKSVG PDFGKKRLGL PGDEVDNKVK GAA GRTDLL RLRRRFMRDQ EKLSLMYARK GVAEQKREKE IKSELKMKQD AQVVLYRSYR HGDLPDIQIK HSSLITPLQA VAQR DPIIA KQLFSSLFSG ILKEMDKFKT LSEKNNITQK LLQDFNRFLN TTFSFFPPFV SCIQDISCQH AALLSLDPAA VSAGC LASL QQPVGIRLLE EALLRLLPAE LPAKRVRGKA RLPPDVLRWV ELAKLYRSIG EYDVLRGIFT SEIGTKQITQ SALLAE ARS DYSEAAKQYD EALNKQDWVD GEPTEAEKDF WELASLDCYN HLAEWKSLEY CSTASIDSEN PPDLNKIWSE PFYQETY LP YMIRSKLKLL LQGEADQSLL TFIDKAMHGE LQKAILELHY SQELSLLYLL QDDVDRAKYY IQNGIQSFMQ NYSSIDVL L HQSRLTKLQS VQALTEIQEF ISFISKQGNL SSQVPLKRLL NTWTNRYPDA KMDPMNIWDD IITNRCFFLS KIEEKLTPL PEDNSMNVDQ DGDPSDRMEV QEQEEDISSL IRSCKFSMKM KMIDSARKQN NFSLAMKLLK ELHKESKTRD DWLVSWVQSY CRLSHCRSR SQGCSEQVLT VLKTVSLLDE NNVSSYLSKN ILAFRDQNIL LGTTYRIIAN ALSSEPACLA EIEEDKARRI L ELSGSSSE DSEKVIAGLY QRAFQHLSEA VQAAEEEAQP PSWSCGPAAG VIDAYMTLAD FCDQQLRKEE ENASVIDSAE LQ AYPALVV EKMLKALKLN SNEARLKFPR LLQIIERYPE ETLSLMTKEI SSVPCWQFIS WISHMVALLD KDQAVAVQHS VEE ITDNYP QAIVYPFIIS SESYSFKDTS TGHKNKEFVA RIKSKLDQGG VIQDFINALD QLSNPELLFK DWSNDVRAEL AKTP VNKKN IEKMYERMYA ALGDPKAPGL GAFRRKFIQT FGKEFDKHFG KGGSKLLRMK LSDFNDITNM LLLKMNKDSK PPGNL KECS PWMSDFKVEF LRNELEIPGQ YDGRGKPLPE YHVRIAGFDE RVTVMASLRR PKRIIIRGHD EREHPFLVKG GEDLRQ DQR VEQLFQVMNG ILAQDSACSQ RALQLRTYSV VPMTSRLGLI EWLENTVTLK DLLLNTMSQE EKAAYLSDPR APPCEYK DW LTKMSGKHDV GAYMLMYKGA NRTETVTSFR KRESKVPADL LKRAFVRMST SPEAFLALRS HFASSHALIC ISHWILGI G DRHLNNFMVA METGGVIGID FGHAFGSATQ FLPVPELMPF RLTRQFINLM LPMKETGLMY SIMVHALRAF RSDPGLLTN TMDVFVKEPS FDWKNFEQKM LKKGGSWIQE INVAEKNWYP RQKICYAKRK LAGANPAVIT CDELLLGHEK APAFRDYVAV ARGSKDHNI RAQEPESGLS EETQVKCLMD QATDPNILGR TWEGWEPWM(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)

UniProtKB: DNA-dependent protein kinase catalytic subunit

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Macromolecule #2: X-ray repair cross-complementing protein 5

MacromoleculeName: X-ray repair cross-complementing protein 5 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / 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: 21.454877 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: EAKKKDQVTA QEIFQDNHED GPTAKKLKTE QGGAHFSVSS LAEGSVTSVG SVNPAENFRV LVKQKKASFE EASNQLINHI EQFLDTNET PYFMKSIDCI RAFREEAIKF SEEQRFNNFL KALQEKVEIK QLNHFWEIVV QDGITLITKE EASGSSVTAE E AKKFLAPK ...String:
EAKKKDQVTA QEIFQDNHED GPTAKKLKTE QGGAHFSVSS LAEGSVTSVG SVNPAENFRV LVKQKKASFE EASNQLINHI EQFLDTNET PYFMKSIDCI RAFREEAIKF SEEQRFNNFL KALQEKVEIK QLNHFWEIVV QDGITLITKE EASGSSVTAE E AKKFLAPK DKPSGDTAAV FEEGGDVDDL LDMI

UniProtKB: X-ray repair cross-complementing protein 5

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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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 54.49 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 104374
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5luq

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.93 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 43995
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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