[English] 日本語
Yorodumi- SASDCW6: Chd1-12N12, chromatin remodeler--nucleosome complex, in 60% sucro... -
+Open data
-Basic information
Entry | Database: SASBDB / ID: SASDCW6 |
---|---|
Sample | Chd1-12N12, chromatin remodeler--nucleosome complex, in 60% sucrose with AMP-PNP
|
Biological species | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Xenopus laevis (African clawed frog) |
-Structure visualization
-Downloads & links
-Data source
SASBDB page | SASDCW6 |
---|
-Models
-Sample
Sample | Name: Chd1-12N12, chromatin remodeler--nucleosome complex, in 60% sucrose with AMP-PNP Specimen concentration: 1.88 mg/ml / Entity id: 768 / 769 / 770 / 771 / 772 / 773 |
---|---|
Buffer | Name: 10 mM Tris, 100 mM NaCl, 2 mM MgCl2, 0.1 mM EDTA, 1 mM DTT, 60% (w/v) sucrose, 0.5 mM AMP-PNP pH: 7.8 |
Entity #768 | Name: Chd1 / Type: protein / Description: Chromodomain-helicase-DNA-binding protein 1 / Formula weight: 133.115 / Num. of mol.: 2 Source: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) Sequence: GPQSTVKIPT RFSNRQNKTV NYNIDYSDDD LLESEDDYGS EEALSEENVH EASANPQPED FHGIDIVINH RLKTSLEEGK VLEKTVPDLN NCKENYEFLI KWTDESHLHN TWETYESIGQ VRGLKRLDNY CKQFIIEDQQ VRLDPYVTAE DIEIMDMERE RRLDEFEEFH ...Sequence: GPQSTVKIPT RFSNRQNKTV NYNIDYSDDD LLESEDDYGS EEALSEENVH EASANPQPED FHGIDIVINH RLKTSLEEGK VLEKTVPDLN NCKENYEFLI KWTDESHLHN TWETYESIGQ VRGLKRLDNY CKQFIIEDQQ VRLDPYVTAE DIEIMDMERE RRLDEFEEFH VPERIIDSQR ASLEDGTSQL QYLVKWRRLN YDEATWENAT DIVKLAPEQV KHFQNRENSK ILPQYSSNYT SQRPRFEKLS VQPPFIKGGE LRDFQLTGIN WMAFLWSKGD NGILADEMGL GKTVQTVAFI SWLIFARRQN GPHIIVVPLS TMPAWLDTFE KWAPDLNCIC YMGNQKSRDT IREYEFYTNP RAKGKKTMKF NVLLTTYEYI LKDRAELGSI KWQFMAVDEA HRLKNAESSL YESLNSFKVA NRMLITGTPL QNNIKELAAL VNFLMPGRFT IDQEIDFENQ DEEQEEYIHD LHRRIQPFIL RRLKKDVEKS LPSKTERILR VELSDVQTEY YKNILTKNYS ALTAGAKGGH FSLLNIMNEL KKASNHPYLF DNAEERVLQK FGDGKMTREN VLRGLIMSSG KMVLLDQLLT RLKKDGHRVL IFSQMVRMLD ILGDYLSIKG INFQRLDGTV PSAQRRISID HFNSPDSNDF VFLLSTRAGG LGINLMTADT VVIFDSDWNP QADLQAMARA HRIGQKNHVM VYRLVSKDTV EEEVLERARK KMILEYAIIS LGVTDGNKYT KKNEPNAGEL SAILKFGAGN MFTATDNQKK LEDLNLDDVL NHAEDHVTTP DLGESHLGGE EFLKQFEVTD YKADIDWDDI IPEEELKKLQ DEEQKRKDEE YVKEQLEMMN RRDNALKKIK NSVNGDGTAA NSDSDDDSTS RSSRRRARAN DMDSIGESEV RALYKAILKF GNLKEILDEL IADGTLPVKS FEKYGETYDE MMEAAKDCVH EEEKNRKEIL EKLEKHATAY RAKLKSGEIK AENQPKDNPL TRLSLKKREK KAVLFNFKGV KSLNAESLLS RVEDLKYLKN LINSNYKDDP LKFSLGNNTP KPVQNWSSNW TKEEDEKLLI GVFKYGYGSW TQIRDDPFLG ITDKIFLNEV HNPVAKKSAS SSDTTPTPSK KGKGITGSSK KVPGAIHLGR RVDYLLSFLR GGLNTKSPS |
Entity #769 | Name: DNA / Type: DNA Description: 169 bp DNA (145 bp Widom 601, flanked by 12bp DNA) Formula weight: 52.468 / Num. of mol.: 1 Sequence: CTTTCAGCTG ATATCGATGT ATATATCTGA CACGTGCCTG GAGACTAGGG AGTAATCCCC TTGGCGGTTA AAACGCGGGG GACAGCGCGT ACGTGCGTTT AAGCGGTGCT AGAGCTGTCT ACGACCAATT GAGCGGCCTC GGCACCGGGA TCTTGATATC AGCTGAAAG |
Entity #770 | Name: H2A / Type: protein / Description: Histone H2A type 1 / Formula weight: 13.966 / Num. of mol.: 1 / Source: Xenopus laevis Sequence: MSGRGKQGGK TRAKAKTRSS RAGLQFPVGR VHRLLRKGNY AERVGAGAPV YLAAVLEYLT AEILELAGNA ARDNKKTRII PRHLQLAVRN DEELNKLLGG VTIAQGGVLP NIQSVLLPKK TESAKSAKSK |
Entity #771 | Name: H2B / Type: protein / Description: Histone H2B 1.1 / Formula weight: 13.934 / Num. of mol.: 1 / Source: Xenopus laevis Sequence: MPEPAKSAPA PKKGSKKAVT KTQKKDGKKR RKSRKESYAI YVYKVLKQVH PDTGISSKAM SIMNSFVNDV FERIAGEASR LAHYNKRSTI TSREIQTAVR LLLPGELAKH AVSEGTKAVT KYTSAK |
Entity #772 | Name: H3 / Type: protein / Description: Histone H3.2 / Formula weight: 15.388 / Num. of mol.: 1 / Source: Xenopus laevis Sequence: MARTKQTARK STGGKAPRKQ LATKAARKSA PATGGVKKPH RYRPGTVALR EIRRYQKSTE LLIRKLPFQR LVREIAQDFK TDLRFQSSAV MALQEASEAY LVGLFEDTNL CAIHAKRVTI MPKDIQLARR IRGERA |
Entity #773 | Name: H4 / Type: protein / Description: Histone H4 / Formula weight: 11.367 / Num. of mol.: 1 / Source: Xenopus laevis Sequence: MSGRGKGGKG LGKGGAKRHR KVLRDNIQGI TKPAIRRLAR RGGVKRISGL IYEETRGVLK VFLENVIRDA VTYTEHAKRK TVTAMDVVYA LKRQGRTLYG FGG |
-Experimental information
Beam | Instrument name: Cornell High Energy Synchrotron Source (CHESS) G1 City: Ithaca, NY / 国: USA / Type of source: X-ray synchrotron / Wavelength: 0.1109 Å / Dist. spec. to detc.: 2.08 mm | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Detector | Name: Pilatus 200K / Type: Pilatus / Pixsize x: 172 mm | ||||||||||||||||||||||||
Scan | Title: Chd1-12N12, chromatin remodeler--nucleosome complex, in 60% sucrose with AMP-PNP Measurement date: Oct 24, 2015 / Storage temperature: 25 °C / Cell temperature: 25 °C / Exposure time: 10 sec. / Number of frames: 40 / Unit: 1/A /
| ||||||||||||||||||||||||
Result | Experimental MW: 105 kDa / Type of curve: single_conc Comments: 12N12 nucleosomes in the presence of the chromatin remodeler Chd1 in 60% sucrose and AMP-PNP. The complex formed contains two Chd1 proteins bound to each nucleosome. Due to contrast ...Comments: 12N12 nucleosomes in the presence of the chromatin remodeler Chd1 in 60% sucrose and AMP-PNP. The complex formed contains two Chd1 proteins bound to each nucleosome. Due to contrast matching between the solvent and histone proteins, the measured signal is dominated by the DNA component. The models were generated using 3D-DART and custom scripts written in Pymol. The percentage-weighting of each model in the ensemble ('XXXperc') is noted in the following model key/list that sequentially corresponds to models displayed in this entry ordered from top-to-bottom: -------------------------------------------------------------------------------------------------------- --------------SASDCW6_fit1_model1=Chd1_12N12_AMP_01_wrapped_25perc; --------------SASDCW6_fit1_model2=Chd1_12N12_AMP_02_wrapped_01perc; --------------SASDCW6_fit1_model3=Chd1_12N12_AMP_03_wrapped_01perc; --------------SASDCW6_fit1_model4=Chd1_12N12_AMP_04_extreme_02perc; --------------SASDCW6_fit1_model5=Chd1_12N12_AMP_05_extreme_01perc; --------------SASDCW6_fit1_model6=Chd1_12N12_AMP_06_inplane_01perc; --------------SASDCW6_fit1_model7=Chd1_12N12_AMP_07_inplane_11perc; --------------SASDCW6_fit1_model8=Chd1_12N12_AMP_08_inplane_08perc; --------------SASDCW6_fit1_model9=Chd1_12N12_AMP_09_inplane_03perc; --------------SASDCW6_fit1_model10=Chd1_12N12_AMP_10_inplane_12perc; --------------SASDCW6_fit1_model11=Chd1_12N12_AMP_11_inplane_01perc; --------------SASDCW6_fit1_model12=Chd1_12N12_AMP_12_inplane_03perc_dyadfliip; --------------SASDCW6_fit1_model13=Chd1_12N12_AMP_13_inplane_12perc_dyadflip; --------------SASDCW6_fit1_model14=Chd1_12N12_AMP_14_inplane_01perc_dyadflip; --------------SASDCW6_fit1_model15=Chd1_12N12_AMP_15_inplane_01perc_dyadflip; --------------SASDCW6_fit1_model16=Chd1_12N12_AMP_16_inplane_15perc; --------------SASDCW6_fit1_model17=Chd1_12N12_AMP_17_inplane_02perc.
|