EMDB-45384: Cryo-EM structure of human SRCAP-nucleosome complex in the pre-en...

Basic information

Entry

Database: EMDB / ID: EMD-45384

• Title: Cryo-EM structure of human SRCAP-nucleosome complex in the pre-engaged state (composite structure)

Sample

• Complex: SRCAP-nucleosome complex
  • Complex: Endogenous human SRCAP complex
    • Protein or peptide: x 6 types
  • Protein or peptide: x 4 types
  • DNA: x 2 types
• Ligand: x 4 types

• Keywords: Chromatin Remodeler / Snf2 family ATPase / H2A.Z / GENE REGULATION

Function / homology

Function:

positive regulation of lymphoid progenitor cell differentiation / intestinal stem cell homeostasis / promoter-enhancer loop anchoring activity / telomerase RNA localization to Cajal body / regulation of DNA strand elongation / positive regulation of telomere maintenance in response to DNA damage / histone chaperone activity / establishment of protein localization to chromatin / R2TP complex / heart process / dynein axonemal particle / Swr1 complex / RPAP3/R2TP/prefoldin-like complex / Ino80 complex / muscle cell differentiation / regulation of double-strand break repair / box C/D snoRNP assembly / nucleolus organization / positive regulation of DNA damage response, signal transduction by p53 class mediator / protein folding chaperone complex / negative regulation of transcription by RNA polymerase I / regulation of chromosome organization / NuA4 histone acetyltransferase complex / histone acetyltransferase activity / positive regulation of transcription by RNA polymerase I / regulation of DNA replication / TFIID-class transcription factor complex binding / regulation of embryonic development / MLL1 complex / somatic stem cell population maintenance / Telomere Extension By Telomerase / positive regulation of transcription initiation by RNA polymerase II / positive regulation of double-strand break repair via homologous recombination / regulation of DNA repair / RNA polymerase II core promoter sequence-specific DNA binding / DNA helicase activity / calcium ion homeostasis / nucleosome binding / Deposition of new CENPA-containing nucleosomes at the centromere / TBP-class protein binding / telomere maintenance / transcription initiation-coupled chromatin remodeling / positive regulation of DNA repair / helicase activity / cellular response to estradiol stimulus / Formation of the beta-catenin:TCF transactivating complex / negative regulation of canonical Wnt signaling pathway / euchromatin / DNA Damage Recognition in GG-NER / beta-catenin binding / ADP binding / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / chromatin DNA binding / nuclear matrix / transcription corepressor activity / structural constituent of chromatin / cellular response to UV / UCH proteinases / positive regulation of canonical Wnt signaling pathway / nucleosome / unfolded protein binding / heterochromatin formation / protein folding / nucleosome assembly / HATs acetylate histones / ATPase binding / regulation of apoptotic process / DNA recombination / spermatogenesis / DNA helicase / histone binding / forked DNA-dependent helicase activity / single-stranded 3'-5' DNA helicase activity / four-way junction helicase activity / double-stranded DNA helicase activity / cytoskeleton / transcription coactivator activity / regulation of cell cycle / protein stabilization / Ub-specific processing proteases / nuclear speck / nuclear body / ciliary basal body / cadherin binding / chromatin remodeling / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein heterodimerization activity / ribonucleoprotein complex / cell division / DNA repair / centrosome / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / nucleolus / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / Golgi apparatus / protein homodimerization activity / positive regulation of transcription by RNA polymerase II

Domain/homology:

HIT zinc finger / Vps71/ZNHIT1 / Zinc finger HIT-type profile. / Zinc finger, HIT-type / Vps72/YL1, N-terminal / YL1 nuclear protein / : / Vps72/YL1, C-terminal / YL1 nuclear protein C-terminal domain / YL1 nuclear protein C-terminal domain / domain in helicases and associated with SANT domains / DNA binding domain with preference for A/T rich regions / RuvB-like / RuvB-like, AAA-lid domain / RuvBL1/2, DNA/RNA binding domain / TIP49 P-loop domain / TIP49 AAA-lid domain / TIP49, P-loop domain / AT hook, DNA-binding motif / HSA domain / Helicase/SANT-associated domain / HSA domain profile. / : / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / Actin / Actin family / Actin / : / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A conserved site / Histone H2A signature. / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone H2A / Histone 2A / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Helicase conserved C-terminal domain / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / ATPase, nucleotide binding domain / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase

Component:

Zinc finger HIT domain-containing protein 1 / Histone H2B 1.1 / Histone H2A type 1 / Histone H4 / Histone H3.2 / Vacuolar protein sorting-associated protein 72 homolog / Helicase SRCAP / Actin-related protein 6 / RuvB-like 2 / RuvB-like 1

• Biological species: Homo sapiens (human) / Xenopus laevis (African clawed frog) / synthetic construct (others)
• Method: single particle reconstruction / cryo EM / Resolution: 4.04 Å
• Authors: Louder RK / Park G

Funding support

United States, 1 items

Organization	Grant number	Country
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)		United States

• Citation: Journal: To Be Published; Title: Structural divergence of H2A.Z-associated human chromatin remodelers SRCAP and TIP60; Authors: Park G / Patel AB / Wu C / Louder RK

History

Deposition	Jun 17, 2024	-
Header (metadata) release	Jun 18, 2025	-
Map release	Jun 18, 2025	-
Update	Jun 18, 2025	-
Current status	Jun 18, 2025	Processing site: RCSB / Status: Released

Map

• File: Download / File: emd_45384.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
• Voxel size: X=Y=Z: 1.025 Å

Density

Contour Level	By AUTHOR: 0.1
Minimum - Maximum	-0.04959834 - 1.8999971
Average (Standard dev.)	0.0014715712 (±0.026706617)

• Symmetry: Space group: 1

Details

EMDB XML:

Map geometry	Axis order X Y Z Origin 0 0 0 Dimensions 384 384 384 Spacing 384 384 384
Cell	A=B=C: 393.59998 Å α=β=γ: 90.0 °

Supplemental data

Sample components

Entire : SRCAP-nucleosome complex

• Entire: Name: SRCAP-nucleosome complex

Components

• Complex: SRCAP-nucleosome complex
  • Complex: Endogenous human SRCAP complex
    • Protein or peptide: Helicase SRCAP
    • Protein or peptide: Vacuolar protein sorting-associated protein 72 homolog
    • Protein or peptide: Actin-related protein 6
    • Protein or peptide: Zinc finger HIT domain-containing protein 1
    • Protein or peptide: RuvB-like 1
    • Protein or peptide: RuvB-like 2
  • Protein or peptide: Histone H2A type 1
  • Protein or peptide: Histone H2B 1.1
  • Protein or peptide: Histone H3.2
  • Protein or peptide: Histone H4
  • DNA: DNA (285-MER)
  • DNA: DNA (285-MER)
• Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
• Ligand: MAGNESIUM ION
• Ligand: ZINC ION
• Ligand: ADENOSINE-5'-DIPHOSPHATE

Supramolecule #1: SRCAP-nucleosome complex

• Supramolecule: Name: SRCAP-nucleosome complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#12; Details: Endogenous purified SRCAP in bound to 106N32 nucleosome
• Source (natural): Organism: Homo sapiens (human) / Strain: K-562 / Organ: BLOOD / Tissue: BONE MARROW / Organelle: NUCLEUS / Location in cell: NUCLEOPLASM

Supramolecule #2: Endogenous human SRCAP complex

• Supramolecule: Name: Endogenous human SRCAP complex / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#6
• Source (natural): Organism: Homo sapiens (human) / Strain: K-562 / Organ: BLOOD / Tissue: BONE MARROW / Organelle: NUCLEUS / Location in cell: NUCLEOPLASM

Macromolecule #1: Helicase SRCAP

• Macromolecule: Name: Helicase SRCAP / type: protein_or_peptide / ID: 1 / 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 weight: Theoretical: 343.91525 KDa

Sequence

String:

MQSSPSPAHP QLPVLQTQMV SDGMTGSNPV SPASSSSPAS SGAGGISPQH IAQDSSLDGP PGPPDGATVP LEGFSLSQAA DLANKGPKW EKSHAEIAEQ AKHEAEIETR IAELRKEGFW SLKRLPKVPE PPRPKGHWDY LCEEMQWLSA DFAQERRWKR G VARKVVRM VIRHHEEQRQ KEERARREEQ AKLRRIASTM AKDVRQFWSN VEKVVQFKQQ SRLEEKRKKA LDLHLDFIVG QT EKYSDLL SQSLNQPLTS SKAGSSPCLG SSSAASSPPP PASRLDDEDG DFQPQEDEEE DDEETIEVEE QQEGNDAEAQ RRE IELLRR EGELPLEELL RSLPPQLLEG PSSPSQTPSS HDSDTRDGPE EGAEEEPPQV LEIKPPPSAV TQRNKQPWHP DEDD EEFTA NEEEAEDEED TIAAEEQLEG EVDHAMELSE LAREGELSME ELLQQYAGAY APGSGSSEDE DEDEVDANSS DCEPE GPVE AEEPPQEDSS SQSDSVEDRS EDEEDEHSEE EETSGSSASE ESESEESEDA QSQSQADEEE EDDDFGVEYL LARDEE QSE ADAGSGPPTP GPTTLGPKKE ITDIAAAAES LQPKGYTLAT TQVKTPIPLL LRGQLREYQH IGLDWLVTMY EKKLNGI LA DEMGLGKTIQ TISLLAHLAC EKGNWGPHLI IVPTSVMLNW EMELKRWCPS FKILTYYGAQ KERKLKRQGW TKPNAFHV C ITSYKLVLQD HQAFRRKNWR YLILDEAQNI KNFKSQRWQS LLNFNSQRRL LLTGTPLQNS LMELWSLMHF LMPHVFQSH REFKEWFSNP LTGMIEGSQE YNEGLVKRLH KVLRPFLLRR VKVDVEKQMP KKYEHVIRCR LSKRQRCLYD DFMAQTTTKE TLATGHFMS VINILMQLRK VCNHPNLFDP RPVTSPFITP GICFSTASLV LRATDVHPLQ RIDMGRFDLI GLEGRVSRYE A DTFLPRHR LSRRVLLEVA TAPDPPPRPK PVKMKVNRML QPVPKQEGRT VVVVNNPRAP LGPVPVRPPP GPELSAQPTP GP VPQVLPA SLMVSASPAG PPLIPASRPP GPVLLPPLQP NSGSLPQVLP SPLGVLSGTS RPPTPTLSLK PTPPAPVRLS PAP PPGSSS LLKPLTVPPG YTFPPAAATT TSTTTATATT TAVPAPTPAP QRLILSPDMQ ARLPSGEVVS IGQLASLAQR PVAN AGGSK PLTFQIQGNK LTLTGAQVRQ LAVGQPRPLQ RNVVHLVSAG GQHHLISQPA HVALIQAVAP TPGPTPVSVL PSSTP STTP APTGLSLPLA ANQVPPTMVN NTGVVKIVVR QAPRDGLTPV PPLAPAPRPP SSGLPAVLNP RPTLTPGRLP TPTLGT ARA PMPTPTLVRP LLKLVHSPSP EVSASAPGAA PLTISSPLHV PSSLPGPASS PMPIPNSSPL ASPVSSTVSV PLSSSLP IS VPTTLPAPAS APLTIPISAP LTVSASGPAL LTSVTPPLAP VVPAAPGPPS LAPSGASPSA SALTLGLATA PSLSSSQT P GHPLLLAPTS SHVPGLNSTV APACSPVLVP ASALASPFPS APNPAPAQAS LLAPASSASQ ALATPLAPMA APQTAILAP SPAPPLAPLP VLAPSPGAAP VLASSQTPVP VMAPSSTPGT SLASASPVPA PTPVLAPSST QTMLPAPVPS PLPSPASTQT LALAPALAP TLGGSSPSQT LSLGTGNPQG PFPTQTLSLT PASSLVPTPA QTLSLAPGPP LGPTQTLSLA PAPPLAPASP V GPAPAHTL TLAPASSSAS LLAPASVQTL TLSPAPVPTL GPAAAQTLAL APASTQSPAS QASSLVVSAS GAAPLPVTMV SR LPVSKDE PDTLTLRSGP PSPPSTATSF GGPRPRRQPP PPPRSPFYLD SLEEKRKRQR SERLERIFQL SEAHGALAPV YGT EVLDFC TLPQPVASPI GPRSPGPSHP TFWTYTEAAH RAVLFPQQRL DQLSEIIERF IFVMPPVEAP PPSLHACHPP PWLA PRQAA FQEQLASELW PRARPLHRIV CNMRTQFPDL RLIQYDCGKL QTLAVLLRQL KAEGHRVLIF TQMTRMLDVL EQFLT YHGH LYLRLDGSTR VEQRQALMER FNADKRIFCF ILSTRSGGVG VNLTGADTVV FYDSDWNPTM DAQAQDRCHR IGQTRD VHI YRLISERTVE ENILKKANQK RMLGDMAIEG GNFTTAYFKQ QTIRELFDMP LEEPSSSSVP SAPEEEEETV ASKQTHI LE QALCRAEDEE DIRAATQAKA EQVAELAEFN ENDGFPAGEG EEAGRPGAED EEMSRAEQEI AALVEQLTPI ERYAMKFL E ASLEEVSREE LKQAEEQVEA ARKDLDQAKE EVFRLPQEEE EGPGAGDESS CGTGGGTHRR SKKAKAPERP GTRVSERLR GARAETQGAN HTPVISAHQT RSTTTPPRCS PARERVPRPA PRPRPTPASA PAAIPALVPV PVSAPVPISA PNPITILPVH ILPSPPPPS QIPPCSSPAC TPPPACTPPP AHTPPPAQTC LVTPSSPLLL GPPSVPISAS VTNLPLGLRP EAELCAQALA S PESLELAS VASSETSSLS LVPPKDLLPV AVEILPVSEK NLSLTPSAPS LTLEAGSIPN GQEQEAPDSA EGTTLTVLPE GE ELPLCVS ESNGLELPPS AASDEPLQEP LEADRTSEEL TEAKTPTSSP EKPQELVTAE VAAPSTSSSA TSSPEGPSPA RPP RRRTSA DVEIRGQGTG RPGQPPGPKV LRKLPGRLVT VVEEKELVRR RRQQRGAAST LVPGVSETSA SPGSPSVRSM SGPE SSPPI GGPCEAAPSS SLPTPPQQPF IARRHIELGV TGGGSPENGD GALLAITPPA VKRRRGRPPK KNRSPADAGR GVDEA PSST LKGKTNGADP VPGPETLIVA DPVLEPQLIP GPQPLGPQPV HRPNPLLSPV EKRRRGRPPK ARDLPIPGTI SSAGDG NSE SRTQPPPHPS PLTPLPPLLV CPTATVANTV TTVTISTSPP KRKRGRPPKN PPSPRPSQLP VLDRDSTSVL ESCGLGR RR QPQGQGESEG SSSDEDGSRP LTRLARLRLE AEGMRGRKSG GSMVVAVIQD DLDLADSGPG GLELTPPVVS LTPKLRST R LRPGSLVPPL ETEKLPRKRA GAPVGGSPGL AKRGRLQPPS PLGPEGSVEE SEAEASGEEE EGDGTPRRRP GPRRLVGTT NQGDQRILRS SAPPSLAGPA VSHRGRKAKT

UniProtKB: Helicase SRCAP

Macromolecule #2: Vacuolar protein sorting-associated protein 72 homolog

• Macromolecule: Name: Vacuolar protein sorting-associated protein 72 homolog; type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 40.658363 KDa

Sequence

String:

MSLAGGRAPR KTAGNRLSGL LEAEEEDEFY QTTYGGFTEE SGDDEYQGDQ SDTEDEVDSD FDIDEGDEPS SDGEAEEPRR KRRVVTKAY KEPLKSLRPR KVNTPAGSSQ KAREEKALLP LELQDDGSDS RKSMRQSTAE HTRQTFLRVQ ERQGQSRRRK G PHCERPLT QEELLREAKI TEELNLRSLE TYERLEADKK KQVHKKRKCP GPIITYHSVT VPLVGEPGPK EENVDIEGLD PA PSVSALT PHAGTGPVNP PARCSRTFIT FSDDATFEEW FPQGRPPKVP VREVCPVTHR PALYRDPVTD IPYATARAFK IIR EAYKKY ITAHGLPPTA SALGPGPPPP EPLPGSGPRA LRQKIVIK

UniProtKB: Vacuolar protein sorting-associated protein 72 homolog

Macromolecule #3: Actin-related protein 6

• Macromolecule: Name: Actin-related protein 6 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 45.857902 KDa

Sequence

String:

MTTLVLDNGA YNAKIGYSHE NVSVIPNCQF RSKTARLKTF TANQIDEIKD PSGLFYILPF QKGYLVNWDV QRQVWDYLFG KEMYQVDFL DTNIIITEPY FNFTSIQESM NEILFEEYQF QAVLRVNAGA LSAHRYFRDN PSELCCIIVD SGYSFTHIVP Y CRSKKKKE AIIRINVGGK LLTNHLKEII SYRQLHVMDE THVINQVKED VCYVSQDFYR DMDIAKLKGE ENTVMIDYVL PD FSTIKKG FCKPREEMVL SGKYKSGEQI LRLANERFAV PEILFNPSDI GIQEMGIPEA IVYSIQNLPE EMQPHFFKNI VLT GGNSLF PGFRDRVYSE VRCLTPTDYD VSVVLPENPI TYAWEGGKLI SENDDFEDMV VTREDYEENG HSVCEEKFDI

UniProtKB: Actin-related protein 6

Macromolecule #4: Zinc finger HIT domain-containing protein 1

• Macromolecule: Name: Zinc finger HIT domain-containing protein 1 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 17.567023 KDa

Sequence

String:

MVEKKTSVRS QDPGQRRVLD RAARQRRINR QLEALENDNF QDDPHAGLPQ LGKRLPQFDD DADTGKKKKK TRGDHFKLRF RKNFQALLE EQNLSVAEGP NYLTACAGPP SRPQRPFCAV CGFPSPYTCV SCGARYCTVR CLGTHQETRC LKWTV

UniProtKB: Zinc finger HIT domain-containing protein 1

Macromolecule #5: RuvB-like 1

• Macromolecule: Name: RuvB-like 1 / type: protein_or_peptide / ID: 5 / Number of copies: 3 / Enantiomer: LEVO / EC number: DNA helicase
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 50.296914 KDa

Sequence

String:

MKIEEVKSTT KTQRIASHSH VKGLGLDESG LAKQAASGLV GQENAREACG VIVELIKSKK MAGRAVLLAG PPGTGKTALA LAIAQELGS KVPFCPMVGS EVYSTEIKKT EVLMENFRRA IGLRIKETKE VYEGEVTELT PCETENPMGG YGKTISHVII G LKTAKGTK QLKLDPSIFE SLQKERVEAG DVIYIEANSG AVKRQGRCDT YATEFDLEAE EYVPLPKGDV HKKKEIIQDV TL HDLDVAN ARPQGGQDIL SMMGQLMKPK KTEITDKLRG EINKVVNKYI DQGIAELVPG VLFVDEVHML DIECFTYLHR ALE SSIAPI VIFASNRGNC VIRGTEDITS PHGIPLDLLD RVMIIRTMLY TPQEMKQIIK IRAQTEGINI SEEALNHLGE IGTK TTLRY SVQLLTPANL LAKINGKDSI EKEHVEEISE LFYDAKSSAK ILADQQDKYM K

UniProtKB: RuvB-like 1

Macromolecule #6: RuvB-like 2

• Macromolecule: Name: RuvB-like 2 / type: protein_or_peptide / ID: 6 / Number of copies: 3 / Enantiomer: LEVO / EC number: DNA helicase
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 51.222465 KDa

Sequence

String:

MATVTATTKV PEIRDVTRIE RIGAHSHIRG LGLDDALEPR QASQGMVGQL AARRAAGVVL EMIREGKIAG RAVLIAGQPG TGKTAIAMG MAQALGPDTP FTAIAGSEIF SLEMSKTEAL TQAFRRSIGV RIKEETEIIE GEVVEIQIDR PATGTGSKVG K LTLKTTEM ETIYDLGTKM IESLTKDKVQ AGDVITIDKA TGKISKLGRS FTRARDYDAM GSQTKFVQCP DGELQKRKEV VH TVSLHEI DVINSRTQGF LALFSGDTGE IKSEVREQIN AKVAEWREEG KAEIIPGVLF IDEVHMLDIE SFSFLNRALE SDM APVLIM ATNRGITRIR GTSYQSPHGI PIDLLDRLLI VSTTPYSEKD TKQILRIRCE EEDVEMSEDA YTVLTRIGLE TSLR YAIQL ITAASLVCRK RKGTEVQVDD IKRVYSLFLD ESRSTQYMKE YQDAFLFNEL KGETMDTS

UniProtKB: RuvB-like 2

Macromolecule #7: Histone H2A type 1

• Macromolecule: Name: Histone H2A type 1 / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO
• Source (natural): Organism: Xenopus laevis (African clawed frog)
• Molecular weight: Theoretical: 13.907163 KDa
• Recombinant expression: Organism: Escherichia coli (E. coli)

Sequence

String:

SGRGKQGGKT RAKAKTRSSR AGLQFPVGRV HRLLRKGNYA ERVGAGAPVY LAAVLEYLTA EILELAGNAA RDNKKTRIIP RHLQLAVRN DEELNKLLGR VTIAQGGVLP NIQSVLLPKK TESSKSKSK

UniProtKB: Histone H2A type 1

Macromolecule #8: Histone H2B 1.1

• Macromolecule: Name: Histone H2B 1.1 / type: protein_or_peptide / ID: 8 / Number of copies: 2 / Enantiomer: LEVO
• Source (natural): Organism: Xenopus laevis (African clawed frog)
• Molecular weight: Theoretical: 13.848097 KDa
• Recombinant expression: Organism: Escherichia coli (E. coli)

Sequence

String:

PEPAKSAPAP KKGSKKAVTK TQKKDGKKRR KTRKESYAIY VYKVLKQVHP DTGISSKAMS IMNSFVNDVF ERIAGEASRL AHYNKRSTI TSREIQTAVR LLLPGELAKH AVSEGTKAVT KYTSAK

UniProtKB: Histone H2B 1.1

Macromolecule #9: Histone H3.2

• Macromolecule: Name: Histone H3.2 / type: protein_or_peptide / ID: 9 / Number of copies: 2 / Enantiomer: LEVO
• Source (natural): Organism: Xenopus laevis (African clawed frog)
• Molecular weight: Theoretical: 15.30393 KDa
• Recombinant expression: Organism: Escherichia coli (E. coli)

Sequence

String:

ARTKQTARKS TGGKAPRKQL ATKAARKSAP ATGGVKKPHR YRPGTVALRE IRRYQKSTEL LIRKLPFQRL VREIAQDFKT DLRFQSSAV MALQEASEAY LVALFEDTNL CAIHAKRVTI MPKDIQLARR IRGERA

UniProtKB: Histone H3.2

Macromolecule #10: Histone H4

• Macromolecule: Name: Histone H4 / type: protein_or_peptide / ID: 10 / Number of copies: 2 / Enantiomer: LEVO
• Source (natural): Organism: Xenopus laevis (African clawed frog)
• Molecular weight: Theoretical: 11.263231 KDa
• Recombinant expression: Organism: Escherichia coli (E. coli)

Sequence

String:

SGRGKGGKGL GKGGAKRHRK VLRDNIQGIT KPAIRRLARR GGVKRISGLI YEETRGVLKV FLENVIRDAV TYTEHAKRKT VTAMDVVYA LKRQGRTLYG FGG

UniProtKB: Histone H4

Macromolecule #11: DNA (285-MER)

• Macromolecule: Name: DNA (285-MER) / type: dna / ID: 11 / Number of copies: 1 / Classification: DNA
• Source (natural): Organism: synthetic construct (others)
• Molecular weight: Theoretical: 87.851664 KDa

Sequence

String:

(DA)(DT)(DC)(DG)(DA)(DA)(DG)(DG)(DG)(DC) (DG)(DC)(DC)(DT)(DA)(DT)(DA)(DT)(DA)(DA) (DG)(DG)(DG)(DG)(DG)(DT)(DG)(DG)(DG) (DG)(DG)(DC)(DG)(DC)(DG)(DT)(DT)(DC)(DG) (DT) (DC)(DC)(DT)(DC)(DC)(DC)(DT)(DC) (DT)(DC)(DC)(DT)(DC)(DG)(DC)(DG)(DG)(DC) (DG)(DC) (DG)(DA)(DG)(DT)(DT)(DT)(DC) (DA)(DG)(DG)(DC)(DA)(DG)(DC)(DG)(DC)(DT) (DG)(DC)(DG) (DT)(DC)(DC)(DT)(DG)(DC) (DT)(DG)(DC)(DG)(DC)(DA)(DC)(DG)(DT)(DG) (DG)(DG)(DA)(DA) (DG)(DC)(DC)(DC)(DT) (DG)(DC)(DT)(DG)(DG)(DA)(DG)(DA)(DA)(DT) (DC)(DC)(DC)(DG)(DG) (DT)(DG)(DC)(DG) (DC)(DA)(DG)(DG)(DC)(DC)(DG)(DC)(DT)(DC) (DA)(DA)(DT)(DT)(DG)(DG) (DT)(DC)(DG) (DT)(DA)(DG)(DA)(DC)(DA)(DG)(DC)(DT)(DC) (DT)(DA)(DG)(DC)(DA)(DC)(DC) (DG)(DC) (DT)(DT)(DA)(DA)(DA)(DC)(DG)(DC)(DA)(DG) (DC)(DT)(DA)(DC)(DG)(DC)(DG)(DC) (DT) (DG)(DT)(DC)(DC)(DC)(DC)(DC)(DG)(DC)(DG) (DT)(DT)(DT)(DT)(DA)(DA)(DC)(DC)(DG) (DC)(DC)(DA)(DA)(DG)(DG)(DG)(DG)(DA)(DT) (DT)(DA)(DC)(DT)(DC)(DC)(DC)(DT)(DA)(DG) (DT)(DC)(DT)(DC)(DC)(DA)(DG)(DG)(DC) (DA)(DG)(DC)(DT)(DG)(DT)(DC)(DA)(DG)(DA) (DT) (DA)(DT)(DG)(DT)(DA)(DC)(DA)(DT) (DC)(DC)(DT)(DG)(DT)(DG)(DA)(DT)(DC)(DC) (DC)(DC) (DG)(DG)(DG)(DT)(DA)(DC)(DC) (DG)(DA)(DG)(DC)(DT)(DC)(DG)(DA)(DA)(DT) (DT)(DC)(DA) (DC)(DT)(DG)(DG)(DC)

Macromolecule #12: DNA (285-MER)

• Macromolecule: Name: DNA (285-MER) / type: dna / ID: 12 / Number of copies: 1 / Classification: DNA
• Source (natural): Organism: synthetic construct (others)
• Molecular weight: Theoretical: 88.19093 KDa

Sequence

String:

(DG)(DC)(DC)(DA)(DG)(DT)(DG)(DA)(DA)(DT) (DT)(DC)(DG)(DA)(DG)(DC)(DT)(DC)(DG)(DG) (DT)(DA)(DC)(DC)(DC)(DG)(DG)(DG)(DG) (DA)(DT)(DC)(DA)(DC)(DA)(DG)(DG)(DA)(DT) (DG) (DT)(DA)(DC)(DA)(DT)(DA)(DT)(DC) (DT)(DG)(DA)(DC)(DA)(DG)(DC)(DT)(DG)(DC) (DC)(DT) (DG)(DG)(DA)(DG)(DA)(DC)(DT) (DA)(DG)(DG)(DG)(DA)(DG)(DT)(DA)(DA)(DT) (DC)(DC)(DC) (DC)(DT)(DT)(DG)(DG)(DC) (DG)(DG)(DT)(DT)(DA)(DA)(DA)(DA)(DC)(DG) (DC)(DG)(DG)(DG) (DG)(DG)(DA)(DC)(DA) (DG)(DC)(DG)(DC)(DG)(DT)(DA)(DG)(DC)(DT) (DG)(DC)(DG)(DT)(DT) (DT)(DA)(DA)(DG) (DC)(DG)(DG)(DT)(DG)(DC)(DT)(DA)(DG)(DA) (DG)(DC)(DT)(DG)(DT)(DC) (DT)(DA)(DC) (DG)(DA)(DC)(DC)(DA)(DA)(DT)(DT)(DG)(DA) (DG)(DC)(DG)(DG)(DC)(DC)(DT) (DG)(DC) (DG)(DC)(DA)(DC)(DC)(DG)(DG)(DG)(DA)(DT) (DT)(DC)(DT)(DC)(DC)(DA)(DG)(DC) (DA) (DG)(DG)(DG)(DC)(DT)(DT)(DC)(DC)(DC)(DA) (DC)(DG)(DT)(DG)(DC)(DG)(DC)(DA)(DG) (DC)(DA)(DG)(DG)(DA)(DC)(DG)(DC)(DA)(DG) (DC)(DG)(DC)(DT)(DG)(DC)(DC)(DT)(DG)(DA) (DA)(DA)(DC)(DT)(DC)(DG)(DC)(DG)(DC) (DC)(DG)(DC)(DG)(DA)(DG)(DG)(DA)(DG)(DA) (DG) (DG)(DG)(DA)(DG)(DG)(DA)(DC)(DG) (DA)(DA)(DC)(DG)(DC)(DG)(DC)(DC)(DC)(DC) (DC)(DA) (DC)(DC)(DC)(DC)(DC)(DT)(DT) (DA)(DT)(DA)(DT)(DA)(DG)(DG)(DC)(DG)(DC) (DC)(DC)(DT) (DT)(DC)(DG)(DA)(DT)

Macromolecule #13: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER

• Macromolecule: Name: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / type: ligand / ID: 13 / Number of copies: 1 / Formula: AGS
• Molecular weight: Theoretical: 523.247 Da

Chemical component information

ChemComp-AGS:
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-gamma-S, energy-carrying molecule analogue*YM

Macromolecule #14: MAGNESIUM ION

• Macromolecule: Name: MAGNESIUM ION / type: ligand / ID: 14 / Number of copies: 4 / Formula: MG
• Molecular weight: Theoretical: 24.305 Da

Macromolecule #15: ZINC ION

• Macromolecule: Name: ZINC ION / type: ligand / ID: 15 / Number of copies: 2 / Formula: ZN
• Molecular weight: Theoretical: 65.409 Da

Macromolecule #16: ADENOSINE-5'-DIPHOSPHATE

• Macromolecule: Name: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 16 / Number of copies: 6 / Formula: ADP
• Molecular weight: Theoretical: 427.201 Da

Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

Experimental details

Structure determination

• Method: cryo EM
• Processing: single particle reconstruction
• Aggregation state: particle

Sample preparation

• Buffer: pH: 7.6
• Vitrification: Cryogen name: ETHANE

Electron microscopy

• Microscope: FEI TITAN KRIOS
• Image recording: Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Ų
• Electron beam: Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
• Electron optics: Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.8 µm
• Experimental equipment: Model: Titan Krios / Image courtesy: FEI Company

Image processing

• CTF correction: Software - Name: Gctf / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
• Startup model: Type of model: OTHER / Details: Negative stain reconstruction
• Final reconstruction: Resolution.type: BY AUTHOR / Resolution: 4.04 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 28381
• Initial angle assignment: Type: MAXIMUM LIKELIHOOD / Software - Name: RELION
• Final angle assignment: Type: MAXIMUM LIKELIHOOD / Software - Name: RELION