2019-12-18
REL
PDBe
PDBe
PDBe
2019-04-02
2019-05-22
2019-06-12
2019-12-18
Swiss National Science Foundation
CRSII3_160734/1
Switzerland
European Commission
667951
European Union
666068
Japan Society for the Promotion of Science
JP18H05534
Japan
European Commission
705354
Japan Agency for Medical Research and Development (AMED)
JP18am0101076
Japan
Japan Society for the Promotion of Science
JP16H06307
Japan
Cryo-EM structure of NCP-THF2(+1)-UV-DDB class A
Matsumoto S
Cavadini S
Bunker RD
Thoma NH
Matsumoto S
Cavadini S
Bunker RD
Grand RS
Potenza A
Rabl J
Yamamoto J
Schenk AD
Schubeler D
Iwai S
Sugasawa K
Kurumizaka H
Thoma NH
DNA damage detection in nucleosomes involves DNA register shifting.
Nature
UK
571
79
84
2019
31142837
doi:10.1038/s41586-019-1259-3
1476-4687
0006
NATUAS
EMD-4764
associated EM volume
Cryo-EM structure of NCP-THF2(+1)-UV-DDB class A
6r90
FULLOVERLAP
UV-DDB bound to a THF2 containing nucleosome class A
UV-DDB bound to a THF2 containing nucleosome class A
0
1
2
3
4
5
6
7
8
0.199
Histone H3.1, Histone H2A, Histone H2B
1
1
3
4
Homo sapiens
Escherichia coli BL21(DE3)
Histone H4
1
2
Homo sapiens
Escherichia coli
DNA
1
5
6
Homo sapiens
synthetic construct
DNA damage-binding protein 1(2), DNA damage-binding protein 2
1
7
8
Homo sapiens
Trichoplusia ni
Histone H3.1
Homo sapiens
0.015719445
2
Escherichia coli BL21(DE3)
LEVO
GSHMARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQ
DFKTDLRFQSSAVMALQEACEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA
Histone H4
Homo sapiens
0.011676703
2
Escherichia coli
LEVO
GSHMSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHA
KRKTVTAMDVVYALKRQGRTLYGFGG
Histone H2A type 1-B/E
Homo sapiens
0.014447825
2
Escherichia coli BL21(DE3)
LEVO
GSHMSGRGKQGGKARAKAKTRSSRAGLQFPVGRVHRLLRKGNYSERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKT
RIIPRHLQLAIRNDEELNKLLGRVTIAQGGVLPNIQAVLLPKKTESHHKAKGK
Histone H2B type 1-J
Homo sapiens
0.014217516
2
Escherichia coli BL21(DE3)
LEVO
GSHMPEPAKSAPAPKKGSKKAVTKAQKKDGKKRKRSRKESYSIYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGE
ASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSAK
Human alpha-satellite DNA (145-MER)
Homo sapiens
0.044756648
1
(DA)(DT)(DC)(DA)(DA)(DT)(DA)(DT)(DC)(DC)(DA)(DC)(DC)(DT)(DG)(DC)(DA)(DG)(DA)(DT)
(DT)(DC)(DT)(DA)(DC)(DC)(DA)(DA)(DA)(DA)(DG)(DT)(DG)(DT)(DA)(DT)(DT)(DT)(DG)(DG)
(DA)(DA)(DA)(DC)(DT)(DG)(DC)(DT)(DC)(DC)(DA)(DT)(DC)(DA)(DA)(DA)(DA)(DG)(DG)(DC)
(DA)(DT)(DG)(DT)(DT)(DC)(DA)(DG)(DC)(DT)(DG)(DG)(DT)(DT)(DC)(DA)(DG)(DC)(DT)(DG)
(DA)(DA)(DC)(DA)(DT)(DG)(DC)(DC)(DT)(DT)(DT)(DT)(DG)(DA)(DT)(DG)(DG)(DA)(DG)(DC)
(DA)(DG)(DT)(DT)(DT)(DC)(DC)(DA)(DA)(DA)(DT)(DA)(DC)(DA)(DC)(DT)(DT)(DT)(DT)(DG)
(DG)(DT)(DA)(DG)(DA)(DA)(DT)(DC)(DT)(DG)(DC)(DA)(DG)(DG)(DT)(DG)(DG)(DA)(DT)(DA)
(DT)(DT)(DG)(DA)(DT)
DNA
Human alpha-satellite DNA (145-MER) with abasic sites at positions 93-94
Homo sapiens
0.044452434
1
(DA)(DT)(DC)(DA)(DA)(DT)(DA)(DT)(DC)(DC)(DA)(DC)(DC)(DT)(DG)(DC)(DA)(DG)(DA)(DT)
(DT)(DC)(DT)(DA)(DC)(DC)(DA)(DA)(DA)(DA)(DG)(DT)(DG)(DT)(DA)(DT)(DT)(DT)(DG)(DG)
(DA)(DA)(DA)(DC)(DT)(DG)(DC)(DT)(DC)(DC)(DA)(DT)(DC)(DA)(DA)(DA)(DA)(DG)(DG)(DC)
(DA)(DT)(DG)(DT)(DT)(DC)(DA)(DG)(DC)(DT)(DG)(DA)(DA)(DC)(DC)(DA)(DG)(DC)(DT)(DG)
(DA)(DA)(DC)(DA)(DT)(DG)(DC)(DC)(DT)(DT)(DT)(DT)(3DR)(3DR)(DT)(DG)(DG)(DA)(DG)
(DC)(DA)(DG)(DT)(DT)(DT)(DC)(DC)(DA)(DA)(DA)(DT)(DA)(DC)(DA)(DC)(DT)(DT)(DT)(DT)
(DG)(DG)(DT)(DA)(DG)(DA)(DA)(DT)(DC)(DT)(DG)(DC)(DA)(DG)(DG)(DT)(DG)(DG)(DA)(DT)
(DA)(DT)(DT)(DG)(DA)(DT)
DNA
DNA damage-binding protein 1
Homo sapiens
0.129766305
1
Trichoplusia ni
LEVO
MASWSHPQFEKVDENLYFQGGGRMSYNYVVTAQKPTAVNGCVTGHFTSAEDLNLLIAKNTRLEIYVVTAEGLRPVKEVGM
YGKIAVMELFRPKGESKDLLFILTAKYNACILEYKQSGESIDIITRAHGNVQDRIGRPSETGIIGIIDPECRMIGLRLYD
GLFKVIPLDRDNKELKAFNIRLEELHVIDVKFLYGCQAPTICFVYQDPQGRHVKTYEVSLREKEFNKGPWKQENVEAEAS
MVIAVPEPFGGAIIIGQESITYHNGDKYLAIAPPIIKQSTIVCHNRVDPNGSRYLLGDMEGRLFMLLLEKEEQMDGTVTL
KDLRVELLGETSIAECLTYLDNGVVFVGSRLGDSQLVKLNVDSNEQGSYVVAMETFTNLGPIVDMCVVDLERQGQGQLVT
CSGAFKEGSLRIIRNGIGIHEHASIDLPGIKGLWPLRSDPNRETDDTLVLSFVGQTRVLMLNGEEVEETELMGFVDDQQT
FFCGNVAHQQLIQITSASVRLVSQEPKALVSEWKEPQAKNISVASCNSSQVVVAVGRALYYLQIHPQELRQISHTEMEHE
VACLDITPLGDSNGLSPLCAIGLWTDISARILKLPSFELLHKEMLGGEIIPRSILMTTFESSHYLLCALGDGALFYFGLN
IETGLLSDRKKVTLGTQPTVLRTFRSLSTTNVFACSDRPTVIYSSNHKLVFSNVNLKEVNYMCPLNSDGYPDSLALANNS
TLTIGTIDEIQKLHIRTVPLYESPRKICYQEVSQCFGVLSSRIEVQDTSGGTTALRPSASTQALSSSVSSSKLFSSSTAP
HETSFGEEVEVHNLLIIDQHTFEVLHAHQFLQNEYALSLVSCKLGKDPNTYFIVGTAMVYPEEAEPKQGRIVVFQYSDGK
LQTVAEKEVKGAVYSMVEFNGKLLASINSTVRLYEWTTEKELRTECNHYNNIMALYLKTKGDFILVGDLMRSVLLLAYKP
MEGNFEEIARDFNPNWMSAVEILDDDNFLGAENAFNLFVCQKDSAATTDEERQHLQEVGLFHLGEFVNVFCHGSLVMQNL
GETSTPTQGSVLFGTVNGMIGLVTSLSESWYNLLLDMQNRLNKVIKSVGKIEHSFWRSFHTERKTEPATGFIDGDLIESF
LDISRPKMQEVVANLQYDDGSGMKREATADDLIKVVEELTRIH
DNA damage-binding protein 2
Homo sapiens
0.050601844
1
Trichoplusia ni
LEVO
MASWSHPQFEKVDENLYFQGGGRMAPKKRPETQKTSEIVLRPRNKRSRSPLELEPEAKKLCAKGSGPSRRCDSDCLWVGL
AGPQILPPCRSIVRTLHQHKLGRASWPSVQQGLQQSFLHTLDSYRILQKAAPFDRRATSLAWHPTHPSTVAVGSKGGDIM
LWNFGIKDKPTFIKGIGAGGSITGLKFNPLNTNQFYASSMEGTTRLQDFKGNILRVFASSDTINIWFCSLDVSASSRMVV
TGDNVGNVILLNMDGKELWNLRMHKKKVTHVALNPCCDWFLATASVDQTVKIWDLRQVRGKASFLYSLPHRHPVNAACFS
PDGARLLTTDQKSEIRVYSASQWDCPLGLIPHPHRHFQHLTPIKAAWHPRYNLIVVGRYPDPNFKSCTPYELRTIDVFDG
NSGKMMCQLYDPESSGISSLNEFNPMGDTLASAMGYHILIWSQEEARTRK
singleParticle
particle
2
7.4
50.0
NaCl
Sodium chloride
50.0
HEPES
0.25
TCEP
ETHANE
85
277
LEICA EM GP
FEI TITAN KRIOS
SPOT SCAN
BRIGHT FIELD
FIELD EMISSION GUN
300
50.0
0.0
130000.0
FEI TITAN KRIOS AUTOGRID HOLDER
NITROGEN
GIF Quantum LS
20
GATAN K2 SUMMIT (4k x 4k)
COUNTING
1
6.0
40.0
1
Gctf
4.5
FSC 0.143 CUT-OFF
RELION
2
128763
OTHER
RELION
OTHER
RELION
4ZUX
I
4ZUX
J
5Y0C
A
5Y0C
B
5Y0C
C
5Y0C
D
5Y0C
E
5Y0C
F
5Y0C
G
5Y0C
H
4E54
B
3EI4
A
FLEXIBLE FIT
REAL