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- EMDB-23511: DNA-PKcs, Ku, DNA and LigIV N-BRCT in the NHEJ Long-range synapti... -

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Basic information

Entry
Database: EMDB / ID: EMD-23511
TitleDNA-PKcs, Ku, DNA and LigIV N-BRCT in the NHEJ Long-range synaptic complex
Map dataDNAPK-BRCT in the Long-range synaptic complex
Sample
  • Complex: DNAPK complex and LigIV N-BRCT in the Long-range synaptic complex of NHEJ
    • Protein or peptide: XRCC6_HUMAN X-ray repair cross-complementing protein 6
    • Protein or peptide: XRCC5_HUMAN X-ray repair cross-complementing protein 5
    • Protein or peptide: PRKDC_HUMAN DNA-dependent protein kinase catalytic subunit
    • DNA: DNA (31-MER)
    • DNA: DNA (30-MER)
    • Protein or peptide: DNLI4_HUMAN DNA ligase 4
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsHe Y / Chen S
Funding support United States, 6 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)5T32GM008382 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U24GM129547 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)P01CA092584 United States
American Cancer SocietyIRG-15-173-21 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM047251 United States
CitationJournal: Nature / Year: 2021
Title: Structural basis of long-range to short-range synaptic transition in NHEJ.
Authors: Siyu Chen / Linda Lee / Tasmin Naila / Susan Fishbain / Annie Wang / Alan E Tomkinson / Susan P Lees-Miller / Yuan He /
Abstract: DNA double-strand breaks (DSBs) are a highly cytotoxic form of DNA damage and the incorrect repair of DSBs is linked to carcinogenesis. The conserved error-prone non-homologous end joining (NHEJ) ...DNA double-strand breaks (DSBs) are a highly cytotoxic form of DNA damage and the incorrect repair of DSBs is linked to carcinogenesis. The conserved error-prone non-homologous end joining (NHEJ) pathway has a key role in determining the effects of DSB-inducing agents that are used to treat cancer as well as the generation of the diversity in antibodies and T cell receptors. Here we applied single-particle cryo-electron microscopy to visualize two key DNA-protein complexes that are formed by human NHEJ factors. The Ku70/80 heterodimer (Ku), the catalytic subunit of the DNA-dependent protein kinase (DNA-PKcs), DNA ligase IV (LigIV), XRCC4 and XLF form a long-range synaptic complex, in which the DNA ends are held approximately 115 Å apart. Two DNA end-bound subcomplexes comprising Ku and DNA-PKcs are linked by interactions between the DNA-PKcs subunits and a scaffold comprising LigIV, XRCC4, XLF, XRCC4 and LigIV. The relative orientation of the DNA-PKcs molecules suggests a mechanism for autophosphorylation in trans, which leads to the dissociation of DNA-PKcs and the transition into the short-range synaptic complex. Within this complex, the Ku-bound DNA ends are aligned for processing and ligation by the XLF-anchored scaffold, and a single catalytic domain of LigIV is stably associated with a nick between the two Ku molecules, which suggests that the joining of both strands of a DSB involves both LigIV molecules.
History
DepositionFeb 18, 2021-
Header (metadata) releaseMay 5, 2021-
Map releaseMay 5, 2021-
UpdateMay 26, 2021-
Current statusMay 26, 2021Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_23511.png

Downloads & links

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Map

FileDownload / File: emd_23511.map.gz / Format: CCP4 / Size: 93 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationDNAPK-BRCT in the Long-range synaptic complex
Voxel sizeX=Y=Z: 1.1 Å
Density
Contour LevelBy AUTHOR: 0.05 / Movie #1: 0.05
Minimum - Maximum-0.014779263 - 2.0966735
Average (Standard dev.)0.0032768296 (±0.04199135)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-145-145-145
Dimensions290290290
Spacing290290290
CellA=B=C: 319.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.11.11.1
M x/y/z290290290
origin x/y/z0.0000.0000.000
length x/y/z319.000319.000319.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ360360360
MAP C/R/S123
start NC/NR/NS-145-145-145
NC/NR/NS290290290
D min/max/mean-0.0152.0970.003

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Supplemental data

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Sample components

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Entire : DNAPK complex and LigIV N-BRCT in the Long-range synaptic complex...

EntireName: DNAPK complex and LigIV N-BRCT in the Long-range synaptic complex of NHEJ
Components
  • Complex: DNAPK complex and LigIV N-BRCT in the Long-range synaptic complex of NHEJ
    • Protein or peptide: XRCC6_HUMAN X-ray repair cross-complementing protein 6
    • Protein or peptide: XRCC5_HUMAN X-ray repair cross-complementing protein 5
    • Protein or peptide: PRKDC_HUMAN DNA-dependent protein kinase catalytic subunit
    • DNA: DNA (31-MER)
    • DNA: DNA (30-MER)
    • Protein or peptide: DNLI4_HUMAN DNA ligase 4

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Supramolecule #1: DNAPK complex and LigIV N-BRCT in the Long-range synaptic complex...

SupramoleculeName: DNAPK complex and LigIV N-BRCT in the Long-range synaptic complex of NHEJ
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6 / Details: DNAPKcs, Ku, LigIV N-BRCT
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 630 KDa

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Macromolecule #1: XRCC6_HUMAN X-ray repair cross-complementing protein 6

MacromoleculeName: XRCC6_HUMAN X-ray repair cross-complementing protein 6
type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: unidentified baculovirus
SequenceString: MSGWESYYKT EGDEEAEEEQ EENLEASGDY KYSGRDSLIF LVDASKAMFE SQSEDELTPF DMSIQCIQS VYISKIISSD RDLLAVVFYG TEKDKNSVNF KNIYVLQELD NPGAKRILEL D QFKGQQGQ KRFQDMMGHG SDYSLSEVLW VCANLFSDVQ FKMSHKRIML ...String:
MSGWESYYKT EGDEEAEEEQ EENLEASGDY KYSGRDSLIF LVDASKAMFE SQSEDELTPF DMSIQCIQS VYISKIISSD RDLLAVVFYG TEKDKNSVNF KNIYVLQELD NPGAKRILEL D QFKGQQGQ KRFQDMMGHG SDYSLSEVLW VCANLFSDVQ FKMSHKRIML FTNEDNPHGN DS AKASRAR TKAGDLRDTG IFLDLMHLKK PGGFDISLFY RDIISIAEDE DLRVHFEESS KLE DLLRKV RAKETRKRAL SRLKLKLNKD IVISVGIYNL VQKALKPPPI KLYRETNEPV KTKT RTFNT STGGLLLPSD TKRSQIYGSR QIILEKEETE ELKRFDDPGL MLMGFKPLVL LKKHH YLRP SLFVYPEESL VIGSSTLFSA LLIKCLEKEV AALCRYTPRR NIPPYFVALV PQEEEL DDQ KIQVTPPGFQ LVFLPFADDK RKMPFTEKIM ATPEQVGKMK AIVEKLRFTY RSDSFEN PV LQQHFRNLEA LALDLMEPEQ AVDLTLPKVE AMNKRLGSLV DEFKELVYPP DYNPEGKV T KRKHDNEGSG SKRPKVEYSE EELKTHISKG TLGKFTVPML KEACRAYGLK SGLKKQELL EALTKHFQD

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Macromolecule #2: XRCC5_HUMAN X-ray repair cross-complementing protein 5

MacromoleculeName: XRCC5_HUMAN X-ray repair cross-complementing protein 5
type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: unidentified baculovirus
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: PRKDC_HUMAN DNA-dependent protein kinase catalytic subunit

MacromoleculeName: PRKDC_HUMAN DNA-dependent protein kinase catalytic subunit
type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: unidentified baculovirus
SequenceString: MAGSGAGVRC SLLRLQETLS AADRCGAALA GHQLIRGLGQ ECVLSSSPAV LALQTSLVFS RDFGLLVFV RKSLNSIEFR ECREEILKFL CIFLEKMGQK IAPYSVEIKN TCTSVYTKDR A AKCKIPAL DLLIKLLQTF RSSRLMDEFK IGELFSKFYG ELALKKKIPD ...String:
MAGSGAGVRC SLLRLQETLS AADRCGAALA GHQLIRGLGQ ECVLSSSPAV LALQTSLVFS RDFGLLVFV RKSLNSIEFR ECREEILKFL CIFLEKMGQK IAPYSVEIKN TCTSVYTKDR A AKCKIPAL DLLIKLLQTF RSSRLMDEFK IGELFSKFYG ELALKKKIPD TVLEKVYELL GL LGEVHPS EMINNAENLF RAFLGELKTQ MTSAVREPKL PVLAGCLKGL SSLLCNFTKS MEE DPQTSR EIFNFVLKAI RPQIDLKRYA VPSAGLRLFA LHASQFSTCL LDNYVSLFEV LLKW CAHTN VELKKAALSA LESFLKQVSN MVAKNAEMHK NKLQYFMEQF YGIIRNVDSN NKELS IAIR GYGLFAGPCK VINAKDVDFM YVELIQRCKQ MFLTQTDTGD DRVYQMPSFL QSVASV LLY LDTVPEVYTP VLEHLVVMQI DSFPQYSPKM QLVCCRAIVK VFLALAAKGP VLRNCIS TV VHQGLIRICS KPVVLPKGPE SESEDHRASG EVRTGKWKVP TYKDYVDLFR HLLSSDQM M DSILADEAFF SVNSSSESLN HLLYDEFVKS VLKIVEKLDL TLEIQTVGEQ ENGDEAPGV WMIPTSDPAA NLHPAKPKDF SAFINLVEFC REILPEKQAE FFEPWVYSFS YELILQSTRL PLISGFYKL LSITVRNAKK IKYFEGVSPK SLKHSPEDPE KYSCFALFVK FGKEVAVKMK Q YKDELLAS CLTFLLSLPH NIIELDVRAY VPALQMAFKL GLSYTPLAEV GLNALEEWSI YI DRHVMQP YYKDILPCLD GYLKTSALSD ETKNNWEVSA LSRAAQKGFN KVVLKHLKKT KNL SSNEAI SLEEIRIRVV QMLGSLGGQI NKNLLTVTSS DEMMKSYVAW DREKRLSFAV PFRE MKPVI FLDVFLPRVT ELALTASDRQ TKVAACELLH SMVMFMLGKA TQMPEGGQGA PPMYQ LYKR TFPVLLRLAC DVDQVTRQLY EPLVMQLIHW FTNNKKFESQ DTVALLEAIL DGIVDP VDS TLRDFCGRCI REFLKWSIKQ ITPQQQEKSP VNTKSLFKRL YSLALHPNAF KRLGASL AF NNIYREFREE ESLVEQFVFE ALVIYMESLA LAHADEKSLG TIQQCCDAID HLCRIIEK K HVSLNKAKKR RLPRGFPPSA SLCLLDLVKW LLAHCGRPQT ECRHKSIELF YKFVPLLPG NRSPNLWLKD VLKEEGVSFL INTFEGGGCG QPSGILAQPT LLYLRGPFSL QATLCWLDLL LAALECYNT FIGERTVGAL QVLGTEAQSS LLKAVAFFLE SIAMHDIIAA EKCFGTGAAG N RTSPQEGE RYNYSKCTVV VRIMEFTTTL LNTSPEGWKL LKKDLCNTHL MRVLVQTLCE PA SIGFNIG DVQVMAHLPD VCVNLMKALK MSPYKDILET HLREKITAQS IEELCAVNLY GPD AQVDRS RLAAVVSACK QLHRAGLLHN ILPSQSTDLH HSVGTELLSL VYKGIAPGDE RQCL PSLDL SCKQLASGLL ELAFAFGGLC ERLVSLLLNP AVLSTASLGS SQGSVIHFSH GEYFY SLFS ETINTELLKN LDLAVLELMQ SSVDNTKMVS AVLNGMLDQS FRERANQKHQ GLKLAT TIL QHWKKCDSWW AKDSPLETKM AVLALLAKIL QIDSSVSFNT SHGSFPEVFT TYISLLA DT KLDLHLKGQA VTLLPFFTSL TGGSLEELRR VLEQLIVAHF PMQSREFPPG TPRFNNYV D CMKKFLDALE LSQSPMLLEL MTEVLCREQQ HVMEELFQSS FRRIARRGSC VTQVGLLES VYEMFRKDDP RLSFTRQSFV DRSLLTLLWH CSLDALREFF STIVVDAIDV LKSRFTKLNE STFDTQITK KMGYYKILDV MYSRLPKDDV HAKESKINQV FHGSCITEGN ELTKTLIKLC Y DAFTENMA GENQLLERRR LYHCAAYNCA ISVICCVFNE LKFYQGFLFS EKPEKNLLIF EN LIDLKRR YNFPVEVEVP MERKKKYIEI RKEAREAANG DSDGPSYMSS LSYLADSTLS EEM SQFDFS TGVQSYSYSS QDPRPATGRF RRREQRDPTV HDDVLELEMD ELNRHECMAP LTAL VKHMH RSLGPPQGEE DSVPRDLPSW MKFLHGKLGN PIVPLNIRLF LAKLVINTEE VFRPY AKHW LSPLLQLAAS ENNGGEGIHY MVVEIVATIL SWTGLATPTG VPKDEVLANR LLNFLM KHV FHPKRAVFRH NLEIIKTLVE CWKDCLSIPY RLIFEKFSGK DPNSKDNSVG IQLLGIV MA NDLPPYDPQC GIQSSEYFQA LVNNMSFVRY KEVYAAAAEV LGLILRYVME RKNILEES L CELVAKQLKQ HQNTMEDKFI VCLNKVTKSF PPLADRFMNA VFFLLPKFHG VLKTLCLEV VLCRVEGMTE LYFQLKSKDF VQVMRHRDDE RQKVCLDIIY KMMPKLKPVE LRELLNPVVE FVSHPSTTC REQMYNILMW IHDNYRDPES ETDNDSQEIF KLAKDVLIQG LIDENPGLQL I IRNFWSHE TRLPSNTLDR LLALNSLYSP KIEVHFLSLA TNFLLEMTSM SPDYPNPMFE HP LSECEFQ EYTIDSDWRF RSTVLTPMFV ETQASQGTLQ TRTQEGSLSA RWPVAGQIRA TQQ QHDFTL TQTADGRSSF DWLTGSSTDP LVDHTSPSSD SLLFAHKRSE RLQRAPLKSV GPDF GKKRL GLPGDEVDNK VKGAAGRTDL LRLRRRFMRD QEKLSLMYAR KGVAEQKREK EIKSE LKMK QDAQVVLYRS YRHGDLPDIQ IKHSSLITPL QAVAQRDPII AKQLFSSLFS GILKEM DKF KTLSEKNNIT QKLLQDFNRF LNTTFSFFPP FVSCIQDISC QHAALLSLDP AAVSAGC LA SLQQPVGIRL LEEALLRLLP AELPAKRVRG KARLPPDVLR WVELAKLYRS IGEYDVLR G IFTSEIGTKQ ITQSALLAEA RSDYSEAAKQ YDEALNKQDW VDGEPTEAEK DFWELASLD CYNHLAEWKS LEYCSTASID SENPPDLNKI WSEPFYQETY LPYMIRSKLK LLLQGEADQS LLTFIDKAM HGELQKAILE LHYSQELSLL YLLQDDVDRA KYYIQNGIQS FMQNYSSIDV L LHQSRLTK LQSVQALTEI QEFISFISKQ GNLSSQVPLK RLLNTWTNRY PDAKMDPMNI WD DIITNRC FFLSKIEEKL TPLPEDNSMN VDQDGDPSDR MEVQEQEEDI SSLIRSCKFS MKM KMIDSA RKQNNFSLAM KLLKELHKES KTRDDWLVSW VQSYCRLSHC RSRSQGCSEQ VLTV LKTVS LLDENNVSSY LSKNILAFRD QNILLGTTYR IIANALSSEP ACLAEIEEDK ARRIL ELSG SSSEDSEKVI AGLYQRAFQH LSEAVQAAEE EAQPPSWSCG PAAGVIDAYM TLADFC DQQ LRKEEENASV IDSAELQAYP ALVVEKMLKA LKLNSNEARL KFPRLLQIIE RYPEETL SL MTKEISSVPC WQFISWISHM VALLDKDQAV AVQHSVEEIT DNYPQAIVYP FIISSESY S FKDTSTGHKN KEFVARIKSK LDQGGVIQDF INALDQLSNP ELLFKDWSND VRAELAKTP VNKKNIEKMY ERMYAALGDP KAPGLGAFRR KFIQTFGKEF DKHFGKGGSK LLRMKLSDFN DITNMLLLK MNKDSKPPGN LKECSPWMSD FKVEFLRNEL EIPGQYDGRG KPLPEYHVRI A GFDERVTV MASLRRPKRI IIRGHDEREH PFLVKGGEDL RQDQRVEQLF QVMNGILAQD SA CSQRALQ LRTYSVVPMT SRLGLIEWLE NTVTLKDLLL NTMSQEEKAA YLSDPRAPPC EYK DWLTKM SGKHDVGAYM LMYKGANRTE TVTSFRKRES KVPADLLKRA FVRMSTSPEA FLAL RSHFA SSHALICISH WILGIGDRHL NNFMVAMETG GVIGIDFGHA FGSATQFLPV PELMP FRLT RQFINLMLPM KETGLMYSIM VHALRAFRSD PGLLTNTMDV FVKEPSFDWK NFEQKM LKK GGSWIQEINV AEKNWYPRQK ICYAKRKLAG ANPAVITCDE LLLGHEKAPA FRDYVAV AR GSKDHNIRAQ EPESGLSEET QVKCLMDQAT DPNILGRTWE GWEPWM

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Macromolecule #6: DNLI4_HUMAN DNA ligase 4

MacromoleculeName: DNLI4_HUMAN DNA ligase 4 / type: protein_or_peptide / ID: 6 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: unidentified baculovirus
SequenceString:
SNIFEDVEFC VMSGTDSQPK PDLENRIAEF GGYIVQNPGP DTYCVIAGSE NIRVKNIILS NKHDV VKPA WLLECFKTKS FVPWQPRFMI HMCPSTKEHF AREYDCYGDS YFIDTDLNQL KEVFSGIKNS N

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Macromolecule #4: DNA (31-MER)

MacromoleculeName: DNA (31-MER) / type: dna / ID: 4 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
SequenceString:
(DT)(DC)(DT)(DA)(DA)(DG)(DA)(DA)(DC)(DT) (DC)(DT)(DG)(DA)(DT)(DG)(DT)(DC)(DA)(DG) (DT)(DA)(DG)(DA)(DT)(DT)(DA)(DC)(DA) (DC)(DT)

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Macromolecule #5: DNA (30-MER)

MacromoleculeName: DNA (30-MER) / type: dna / ID: 5 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
SequenceString:
(DG)(DT)(DG)(DT)(DA)(DA)(DT)(DC)(DT)(DA) (DC)(DT)(DG)(DA)(DC)(DA)(DT)(DC)(DA)(DG) (DA)(DG)(DT)(DT)(DC)(DT)(DT)(DA)(DG) (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:
ConcentrationNameFormula
10.0 mMHEPES
50.0 mMKCl
10.0 mMMgCl2
2.5 %glycerol
1.0 mMDTT
0.05 %NP-40
GridModel: Quantifoil R3.5/1 / Material: COPPER / Mesh: 400 / Support film - Material: GRAPHENE OXIDE / Support film - topology: CONTINUOUS / Support film - Film thickness: 200.0 nm / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 101.325 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeJEOL 3200FS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3710 pixel / Digitization - Dimensions - Height: 3838 pixel / Digitization - Frames/image: 1-30 / Number grids imaged: 4 / Number real images: 17114 / Average exposure time: 0.3 sec. / Average electron dose: 76.5 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: DARK FIELD / Cs: 2.7 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 30000
Sample stageSpecimen holder model: JEOL / Cooling holder cryogen: NITROGEN

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Image processing

Particle selectionNumber selected: 1119381
CTF correctionSoftware: (Name: Gctf (ver. 0.50), CTFFIND (ver. 4.1))
Startup modelType of model: INSILICO MODEL
In silico model: Negative staining map reconstructed ab-initio from Cryosparc
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 333166
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software: (Name: EMAN, cryoSPARC)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final 3D classificationNumber classes: 3 / Avg.num./class: 330000 / Software - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model(PDB ID:

6erh

,

1jey

,

5luq

,

5y3r

,

6zha

)
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Target criteria: Correlation coefficient

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