BMRB Entry 30576

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR30576
MolProbity Validation Chart

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Title:
Structure of Asf1-H3:H4-Rtt109-Vps75 histone chaperone-lysine acetyltransferase complex with the histone substrate.
Deposition date:
2019-02-22
Original release date:
2019-07-26
Authors:
Danilenko, N.; Carlomagno, T.; Kirkpatrick, J.
Citation:

Citation: Danilenko, Nataliya; Lercher, Lukas; Kirkpatrick, John; Gabel, Frank; Codutti, Luca; Carlomagno, Teresa. "Histone chaperone exploits intrinsic disorder to switch acetylation specificity"  Nat. Commun. 10, 3435-3435 (2019).
PubMed: 31387991

Assembly members:

Assembly members:
entity_1, polymer, 264 residues, 30656.084 Da.
entity_2, polymer, 442 residues, 50765.434 Da.
entity_3, polymer, 279 residues, 31585.139 Da.
entity_4, polymer, 136 residues, 15421.101 Da.
entity_5, polymer, 103 residues, 11394.426 Da.

Natural source:

Natural source:   Common Name: baker's yeast   Taxonomy ID: 559292   Superkingdom: Eukaryota   Kingdom: Fungi   Genus/species: Saccharomyces cerevisiae

Experimental source:

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: MMSDQENENEHAKAFLGLAK CEEEVDAIEREVELYRLNKM KPVYEKRDAYIDEIAEFWKI VLSQHVSFANYIRASDFKYI DTIDKIKVEWLALESEMYDT RDFSITFHFHGIEGDFKEQQ VTKVFQIKKGKDDQEDGILT SEPVPIEWPQSYDSINPDLI KDKRSPEGKKKYRQGMKTIF GWFRWTGLKPGKEFPHGDSL ASLFSEEIYPFCVKYYAEAQ RDLEDEEGESGLSADGDSED DDGSLGEVDLPLSDEEPSSK KRKV
entity_2: GMDPNSMSLNDFLSSVLPVS EQFEYLSLQSIPLETHAVVT PNKDDKRVPKSTIKTQHFFS LFHQGKVFFSLEVYVYVTLW DEADAERLIFVSKADTNGYC NTRVSVRDITKIILEFILSI DPNYYLQKVKPAIRSYKKIS PELISAASTPARTLRILARR LKQSGSTVLKEIESPRFQQD LYLSFTCPREILTKICLFTR PASQYLFPDSSKNSKKHILN GEELMKWWGFILDRLLIECF QNDTQAKLRIPGEDPARVRS YLRGMKYPLWQVGDIFTSKE NSLAVYNIPLFPDDPKARFI HQLAEEDRLLKVSLSSFWIE LQERQEFKLSVTSSVMGISG YSLATPSLFPSSADVIVPKS RKQFRAIKKYITGEEYDTEE GAIEAFTNIRDFLLLRMATN LQSLTGKREHRERNQPVPAS NINTLAITMLKPRKKAKALP KT
entity_3: SSIVSLLGIKVLNNPAKFTD PYEFEITFECLESLKHDLEW KLTYVGSSRSLDHDQELDSI LVGPVPVGVNKFVFSADPPS AELIPASELVSVTVILLSCS YDGREFVRVGYYVNNEYDEE ELRENPPAKVQVDHIVRNIL AEKPRVTRFNIVWDNENEGD LYPPEQPGVDDEEEEDDEEE DDDEDDEDDEDDDQEDGEGE AEEAAEEEEEEEEKTEDNET NLEEEEEDIENSDGDEEEGE EEVGSVDKNEDGNDKKRRKI EGGSTDIESTPKDAARSTN
entity_4: MARTKQTARKSTGGKAPRKQ LATKAARKSAPATGGVKKPH RYRPGTVALREIRRYQKSTE LLIRKLPFQRLVREIAQDFK TDLRFQSSAVMALQEASEAY LVGLFEDTNLCAIHAKRVTI MPKDIQLARRIRGERA
entity_5: MSGRGKGGKGLGKGGAKRHR KVLRDNIQGITKPAIRRLAR RGGVKRISGLIYEETRGVLK VFLENVIRDAVTYTEHAKRK TVTAMDVVYALKRQGRTLYG FGG

Data sets:
Data typeCount
13C chemical shifts92
1H chemical shifts276

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
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Assembly:

Entity Assembly IDEntity NameEntity ID
1entity_1, 11
2entity_1, 21
3entity_22
4entity_33
5entity_44
6entity_55

Entities:

Entity 1, entity_1, 1 264 residues - 30656.084 Da.

1   METMETSERASPGLNGLUASNGLUASNGLU
2   HISALALYSALAPHELEUGLYLEUALALYS
3   CYSGLUGLUGLUVALASPALAILEGLUARG
4   GLUVALGLULEUTYRARGLEUASNLYSMET
5   LYSPROVALTYRGLULYSARGASPALATYR
6   ILEASPGLUILEALAGLUPHETRPLYSILE
7   VALLEUSERGLNHISVALSERPHEALAASN
8   TYRILEARGALASERASPPHELYSTYRILE
9   ASPTHRILEASPLYSILELYSVALGLUTRP
10   LEUALALEUGLUSERGLUMETTYRASPTHR
11   ARGASPPHESERILETHRPHEHISPHEHIS
12   GLYILEGLUGLYASPPHELYSGLUGLNGLN
13   VALTHRLYSVALPHEGLNILELYSLYSGLY
14   LYSASPASPGLNGLUASPGLYILELEUTHR
15   SERGLUPROVALPROILEGLUTRPPROGLN
16   SERTYRASPSERILEASNPROASPLEUILE
17   LYSASPLYSARGSERPROGLUGLYLYSLYS
18   LYSTYRARGGLNGLYMETLYSTHRILEPHE
19   GLYTRPPHEARGTRPTHRGLYLEULYSPRO
20   GLYLYSGLUPHEPROHISGLYASPSERLEU
21   ALASERLEUPHESERGLUGLUILETYRPRO
22   PHECYSVALLYSTYRTYRALAGLUALAGLN
23   ARGASPLEUGLUASPGLUGLUGLYGLUSER
24   GLYLEUSERALAASPGLYASPSERGLUASP
25   ASPASPGLYSERLEUGLYGLUVALASPLEU
26   PROLEUSERASPGLUGLUPROSERSERLYS
27   LYSARGLYSVAL

Entity 2, entity_2 442 residues - 50765.434 Da.

1   GLYMETASPPROASNSERMETSERLEUASN
2   ASPPHELEUSERSERVALLEUPROVALSER
3   GLUGLNPHEGLUTYRLEUSERLEUGLNSER
4   ILEPROLEUGLUTHRHISALAVALVALTHR
5   PROASNLYSASPASPLYSARGVALPROLYS
6   SERTHRILELYSTHRGLNHISPHEPHESER
7   LEUPHEHISGLNGLYLYSVALPHEPHESER
8   LEUGLUVALTYRVALTYRVALTHRLEUTRP
9   ASPGLUALAASPALAGLUARGLEUILEPHE
10   VALSERLYSALAASPTHRASNGLYTYRCYS
11   ASNTHRARGVALSERVALARGASPILETHR
12   LYSILEILELEUGLUPHEILELEUSERILE
13   ASPPROASNTYRTYRLEUGLNLYSVALLYS
14   PROALAILEARGSERTYRLYSLYSILESER
15   PROGLULEUILESERALAALASERTHRPRO
16   ALAARGTHRLEUARGILELEUALAARGARG
17   LEULYSGLNSERGLYSERTHRVALLEULYS
18   GLUILEGLUSERPROARGPHEGLNGLNASP
19   LEUTYRLEUSERPHETHRCYSPROARGGLU
20   ILELEUTHRLYSILECYSLEUPHETHRARG
21   PROALASERGLNTYRLEUPHEPROASPSER
22   SERLYSASNSERLYSLYSHISILELEUASN
23   GLYGLUGLULEUMETLYSTRPTRPGLYPHE
24   ILELEUASPARGLEULEUILEGLUCYSPHE
25   GLNASNASPTHRGLNALALYSLEUARGILE
26   PROGLYGLUASPPROALAARGVALARGSER
27   TYRLEUARGGLYMETLYSTYRPROLEUTRP
28   GLNVALGLYASPILEPHETHRSERLYSGLU
29   ASNSERLEUALAVALTYRASNILEPROLEU
30   PHEPROASPASPPROLYSALAARGPHEILE
31   HISGLNLEUALAGLUGLUASPARGLEULEU
32   LYSVALSERLEUSERSERPHETRPILEGLU
33   LEUGLNGLUARGGLNGLUPHELYSLEUSER
34   VALTHRSERSERVALMETGLYILESERGLY
35   TYRSERLEUALATHRPROSERLEUPHEPRO
36   SERSERALAASPVALILEVALPROLYSSER
37   ARGLYSGLNPHEARGALAILELYSLYSTYR
38   ILETHRGLYGLUGLUTYRASPTHRGLUGLU
39   GLYALAILEGLUALAPHETHRASNILEARG
40   ASPPHELEULEULEUARGMETALATHRASN
41   LEUGLNSERLEUTHRGLYLYSARGGLUHIS
42   ARGGLUARGASNGLNPROVALPROALASER
43   ASNILEASNTHRLEUALAILETHRMETLEU
44   LYSPROARGLYSLYSALALYSALALEUPRO
45   LYSTHR

Entity 3, entity_3 279 residues - 31585.139 Da.

1   SERSERILEVALSERLEULEUGLYILELYS
2   VALLEUASNASNPROALALYSPHETHRASP
3   PROTYRGLUPHEGLUILETHRPHEGLUCYS
4   LEUGLUSERLEULYSHISASPLEUGLUTRP
5   LYSLEUTHRTYRVALGLYSERSERARGSER
6   LEUASPHISASPGLNGLULEUASPSERILE
7   LEUVALGLYPROVALPROVALGLYVALASN
8   LYSPHEVALPHESERALAASPPROPROSER
9   ALAGLULEUILEPROALASERGLULEUVAL
10   SERVALTHRVALILELEULEUSERCYSSER
11   TYRASPGLYARGGLUPHEVALARGVALGLY
12   TYRTYRVALASNASNGLUTYRASPGLUGLU
13   GLULEUARGGLUASNPROPROALALYSVAL
14   GLNVALASPHISILEVALARGASNILELEU
15   ALAGLULYSPROARGVALTHRARGPHEASN
16   ILEVALTRPASPASNGLUASNGLUGLYASP
17   LEUTYRPROPROGLUGLNPROGLYVALASP
18   ASPGLUGLUGLUGLUASPASPGLUGLUGLU
19   ASPASPASPGLUASPASPGLUASPASPGLU
20   ASPASPASPGLNGLUASPGLYGLUGLYGLU
21   ALAGLUGLUALAALAGLUGLUGLUGLUGLU
22   GLUGLUGLULYSTHRGLUASPASNGLUTHR
23   ASNLEUGLUGLUGLUGLUGLUASPILEGLU
24   ASNSERASPGLYASPGLUGLUGLUGLYGLU
25   GLUGLUVALGLYSERVALASPLYSASNGLU
26   ASPGLYASNASPLYSLYSARGARGLYSILE
27   GLUGLYGLYSERTHRASPILEGLUSERTHR
28   PROLYSASPALAALAARGSERTHRASN

Entity 4, entity_4 136 residues - 15421.101 Da.

1   METALAARGTHRLYSGLNTHRALAARGLYS
2   SERTHRGLYGLYLYSALAPROARGLYSGLN
3   LEUALATHRLYSALAALAARGLYSSERALA
4   PROALATHRGLYGLYVALLYSLYSPROHIS
5   ARGTYRARGPROGLYTHRVALALALEUARG
6   GLUILEARGARGTYRGLNLYSSERTHRGLU
7   LEULEUILEARGLYSLEUPROPHEGLNARG
8   LEUVALARGGLUILEALAGLNASPPHELYS
9   THRASPLEUARGPHEGLNSERSERALAVAL
10   METALALEUGLNGLUALASERGLUALATYR
11   LEUVALGLYLEUPHEGLUASPTHRASNLEU
12   CYSALAILEHISALALYSARGVALTHRILE
13   METPROLYSASPILEGLNLEUALAARGARG
14   ILEARGGLYGLUARGALA

Entity 5, entity_5 103 residues - 11394.426 Da.

1   METSERGLYARGGLYLYSGLYGLYLYSGLY
2   LEUGLYLYSGLYGLYALALYSARGHISARG
3   LYSVALLEUARGASPASNILEGLNGLYILE
4   THRLYSPROALAILEARGARGLEUALAARG
5   ARGGLYGLYVALLYSARGILESERGLYLEU
6   ILETYRGLUGLUTHRARGGLYVALLEULYS
7   VALPHELEUGLUASNVALILEARGASPALA
8   VALTHRTYRTHRGLUHISALALYSARGLYS
9   THRVALTHRALAMETASPVALVALTYRALA
10   LEULYSARGGLNGLYARGTHRLEUTYRGLY
11   PHEGLYGLY

Samples:

sample_1: Vps75 (dimer), ILV methyl labelled, perdeuterated, 70 uM; Rtt109 70 uM; Asf1 70 uM; H3 70 uM; H4 70 uM

sample_2: Vps75 (dimer), ILV methyl labelled, perdeuterated, 70 uM; Rtt109 70 uM; Asf1 70 uM; H4 70 uM; H3(110A,63C) mutant with a cysteine coupled to a paramagnetic tag 70 uM

sample_3: Vps75 (dimer), ILV methyl labelled, perdeuterated, 90 uM; Rtt109 90 uM; Asf1 90 uM; H4 90 uM; H3(110A,76C) mutant with a cysteine coupled to a paramagnetic tag 90 uM

sample_4: Vps75 (dimer), ILV methyl labelled, perdeuterated, 30 uM; Rtt109 30 uM; Asf1 30 uM; H3 30 uM; H4(30C) mutant with a cysteine coupled to a paramagnetic tag 30 uM

sample_5: Vps75 (dimer), ILV methyl labelled, perdeuterated, 70 uM; Rtt109 70 uM; Asf1 70 uM; H3 70 uM; H4(82C) mutant with a cysteine coupled to a paramagnetic tag 70 uM

sample_6: Vps75 (dimer), ILV methyl labelled, perdeuterated, 80 uM; Rtt109 80 uM; Asf1 80 uM; H3 80 uM; H4(45C) mutant with a cysteine coupled to a paramagnetic tag 80 uM

sample_7: Vps75 (dimer), ILV methyl labelled, perdeuterated, 30 uM; Rtt109 30 uM; Asf1 30 uM; H3 30 uM; H4(93C) mutant with a cysteine coupled to a paramagnetic tag 30 uM

sample_conditions_1: ionic strength: 150 mM; pH: 6.5; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-13C HSQCsample_1isotropicsample_conditions_1
2D 1H-13C HSQCsample_2isotropicsample_conditions_1
2D 1H-13C HSQCsample_3isotropicsample_conditions_1
2D 1H-13C HSQCsample_4isotropicsample_conditions_1
2D 1H-13C HSQCsample_5isotropicsample_conditions_1
2D 1H-13C HSQCsample_6isotropicsample_conditions_1
2D 1H-13C HSQCsample_7isotropicsample_conditions_1

Software:

CcpNMR, CCPN - data analysis

HADDOCK, Bonvin - structure calculation

NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

TOPSPIN, Bruker Biospin - processing

AMBER, Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, and Kollman - refinement

FuDA, D. Flemming Hansen - data analysis

NMR spectrometers:

  • Bruker AvanceIII 850 MHz