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- EMDB-49379: Human SRCAP-nucleosome complex in the pre-dissociation state of t... -

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Basic information

Entry
Database: EMDB / ID: EMD-49379
TitleHuman SRCAP-nucleosome complex in the pre-dissociation state of the H2A.Z histone exchange reaction (composite structure)
Map data
Sample
  • Complex: SRCAP-nucleosome complex
    • Complex: Endogenous human SRCAP complex
      • Protein or peptide: x 6 types
    • Protein or peptide: x 6 types
    • DNA: x 2 types
  • Ligand: x 4 types
KeywordsChromatin Remodeler / Snf2 family ATPase / H2A.Z / GENE REGULATION
Function / homology
Function and homology information


positive regulation of lymphoid progenitor cell differentiation / catalytic activity, acting on a protein / hematopoietic stem cell homeostasis / intestinal stem cell homeostasis / RPAP3/R2TP/prefoldin-like complex / promoter-enhancer loop anchoring activity / telomerase RNA localization to Cajal body / muscle cell differentiation / positive regulation of telomere maintenance in response to DNA damage / regulation of DNA strand elongation ...positive regulation of lymphoid progenitor cell differentiation / catalytic activity, acting on a protein / hematopoietic stem cell homeostasis / intestinal stem cell homeostasis / RPAP3/R2TP/prefoldin-like complex / promoter-enhancer loop anchoring activity / telomerase RNA localization to Cajal body / muscle cell differentiation / positive regulation of telomere maintenance in response to DNA damage / regulation of DNA strand elongation / histone chaperone activity / R2TP complex / dynein axonemal particle / Swr1 complex / establishment of protein localization to chromatin / heart process / Ino80 complex / negative regulation of transcription by RNA polymerase I / regulation of double-strand break repair / box C/D snoRNP assembly / ATP-dependent chromatin remodeler activity / nucleolus organization / positive regulation of DNA damage response, signal transduction by p53 class mediator / regulation of chromosome organization / positive regulation of transcription by RNA polymerase I / NuA4 histone acetyltransferase complex / MLL1 complex / regulation of DNA replication / TFIID-class transcription factor complex binding / protein folding chaperone complex / Telomere Extension By Telomerase / positive regulation of transcription initiation by RNA polymerase II / cAMP/PKA signal transduction / RNA polymerase II core promoter sequence-specific DNA binding / calcium ion homeostasis / positive regulation of double-strand break repair via homologous recombination / nucleosome binding / heterochromatin / Replacement of protamines by nucleosomes in the male pronucleus / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / regulation of embryonic development / telomere maintenance / Deposition of new CENPA-containing nucleosomes at the centromere / TBP-class protein binding / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / DNA helicase activity / transcription initiation-coupled chromatin remodeling / RNA Polymerase I Promoter Opening / Inhibition of DNA recombination at telomere / Assembly of the ORC complex at the origin of replication / Meiotic synapsis / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / DNA methylation / Condensation of Prophase Chromosomes / cellular response to estradiol stimulus / Chromatin modifications during the maternal to zygotic transition (MZT) / SIRT1 negatively regulates rRNA expression / HCMV Late Events / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / HDACs deacetylate histones / Transcriptional regulation by small RNAs / negative regulation of canonical Wnt signaling pathway / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / RNA Polymerase I Promoter Escape / Nonhomologous End-Joining (NHEJ) / euchromatin / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / chromatin DNA binding / ADP binding / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Negative Regulation of CDH1 Gene Transcription / NoRC negatively regulates rRNA expression / beta-catenin binding / G2/M DNA damage checkpoint / Formation of the beta-catenin:TCF transactivating complex / B-WICH complex positively regulates rRNA expression / DNA Damage/Telomere Stress Induced Senescence / Meiotic recombination / Pre-NOTCH Transcription and Translation / DNA Damage Recognition in GG-NER / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / Activation of anterior HOX genes in hindbrain development during early embryogenesis / histone deacetylase binding / Transcriptional regulation of granulopoiesis / nucleosomal DNA binding / nuclear matrix / innate immune response in mucosa / HCMV Early Events / cellular response to UV / positive regulation of canonical Wnt signaling pathway / : / structural constituent of chromatin / transcription corepressor activity / nucleosome
Similarity search - Function
Vps71/ZNHIT1 / HIT zinc finger / Zinc finger HIT-type profile. / Vps72/YL1, N-terminal / YL1 nuclear protein / Zinc finger, HIT-type / : / Vps72/YL1, C-terminal / YL1 nuclear protein C-terminal domain / YL1 nuclear protein C-terminal domain ...Vps71/ZNHIT1 / HIT zinc finger / Zinc finger HIT-type profile. / Vps72/YL1, N-terminal / YL1 nuclear protein / Zinc finger, HIT-type / : / Vps72/YL1, C-terminal / YL1 nuclear protein C-terminal domain / YL1 nuclear protein C-terminal domain / DNA binding domain with preference for A/T rich regions / AT hook, DNA-binding motif / 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 / domain in helicases and associated with SANT domains / 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 H2A conserved site / Histone H2A signature. / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone 2A / Histone H2A / 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. / ATPase, nucleotide binding domain / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / 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
Similarity search - Domain/homology
Zinc finger HIT domain-containing protein 1 / Histone H2B 1.1 / Histone H2A type 1 / Histone H2A.Z / Histone H4 / Histone H2B type 1-C/E/F/G/I / Histone H3.2 / Vacuolar protein sorting-associated protein 72 homolog / Chromatin remodeling protein SRCAP / Actin-related protein 6 ...Zinc finger HIT domain-containing protein 1 / Histone H2B 1.1 / Histone H2A type 1 / Histone H2A.Z / Histone H4 / Histone H2B type 1-C/E/F/G/I / Histone H3.2 / Vacuolar protein sorting-associated protein 72 homolog / Chromatin remodeling protein SRCAP / Actin-related protein 6 / RuvB-like 2 / RuvB-like 1
Similarity search - Component
Biological speciesHomo sapiens (human) / Xenopus laevis (African clawed frog) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsLouder RK / Park G
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Sci Adv / Year: 2026
Title: Structural mechanism of histone H2A.Z exchange by human SRCAP-CFDP1 holoenzyme.
Authors: Giho Park / Carl Wu / Robert K Louder /
Abstract: The conserved yeast SWR1 and human SRCAP chromatin remodeling complexes catalyze exchange of nucleosomal histone H2A for H2A.Z, but the underlying mechanism has remained obscure. Here, we show that ...The conserved yeast SWR1 and human SRCAP chromatin remodeling complexes catalyze exchange of nucleosomal histone H2A for H2A.Z, but the underlying mechanism has remained obscure. Here, we show that histone exchange by SRCAP requires the transient activator CFDP1 and resolve nine cryo-electron microscopy structures of the SRCAP-CFDP1 holoenzyme that define the stepwise exchange mechanism. CFDP1 recognizes the conformation of the fully engaged SRCAP-nucleosome complex through interactions with multiple subunits-including direct contact with the ATPase domain-and induces conformational transitions that drive extensive DNA unwrapping, eviction of the H2A-H2B dimer, and insertion of the H2A.Z-H2B dimer, all without necessarily requiring hydrolysis of bound ATP. Collectively, these findings provide unprecedented insight into the mechanism of activator- and nucleotide-driven histone exchange from nucleosomal H2A to H2A.Z.
History
DepositionFeb 21, 2025-
Header (metadata) releaseAug 12, 2026-
Map releaseAug 12, 2026-
UpdateAug 12, 2026-
Current statusAug 12, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49379.png

Downloads & links

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Map

FileDownload / File: emd_49379.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.03 Å/pix.
x 384 pix.
= 393.6 Å		1.03 Å/pix.
x 384 pix.
= 393.6 Å		1.03 Å/pix.
x 384 pix.
= 393.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.025 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.05529177 - 2.2540522
Average (Standard dev.)0.0018554439 (±0.031685766)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 393.59998 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : SRCAP-nucleosome complex

EntireName: 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.Z
    • Protein or peptide: Histone H2B type 1-C/E/F/G/I
    • 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

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Supramolecule #1: SRCAP-nucleosome complex

SupramoleculeName: SRCAP-nucleosome complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#14
Details: Endogenous purified SRCAP bound to 106N32 nucleosome
Source (natural)Organism: Homo sapiens (human) / Strain: K-562 / Organ: BLOOD / Tissue: BONE MARROW / Organelle: NUCLEUS / Location in cell: NUCLEOPLASM

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Supramolecule #2: Endogenous human SRCAP complex

SupramoleculeName: 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

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Macromolecule #1: Helicase SRCAP

MacromoleculeName: 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) / Organ: BLOOD / Tissue: BONE MARROW
Molecular weightTheoretical: 343.91525 KDa
SequenceString: MQSSPSPAHP QLPVLQTQMV SDGMTGSNPV SPASSSSPAS SGAGGISPQH IAQDSSLDGP PGPPDGATVP LEGFSLSQAA DLANKGPKW EKSHAEIAEQ AKHEAEIETR IAELRKEGFW SLKRLPKVPE PPRPKGHWDY LCEEMQWLSA DFAQERRWKR G VARKVVRM ...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: Chromatin remodeling protein SRCAP

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

MacromoleculeName: 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) / Organ: BLOOD / Tissue: BONE MARROW
Molecular weightTheoretical: 40.658363 KDa
SequenceString: MSLAGGRAPR KTAGNRLSGL LEAEEEDEFY QTTYGGFTEE SGDDEYQGDQ SDTEDEVDSD FDIDEGDEPS SDGEAEEPRR KRRVVTKAY KEPLKSLRPR KVNTPAGSSQ KAREEKALLP LELQDDGSDS RKSMRQSTAE HTRQTFLRVQ ERQGQSRRRK G PHCERPLT ...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

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Macromolecule #3: Actin-related protein 6

MacromoleculeName: Actin-related protein 6 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human) / Organ: BLOOD / Tissue: BONE MARROW
Molecular weightTheoretical: 45.857902 KDa
SequenceString: MTTLVLDNGA YNAKIGYSHE NVSVIPNCQF RSKTARLKTF TANQIDEIKD PSGLFYILPF QKGYLVNWDV QRQVWDYLFG KEMYQVDFL DTNIIITEPY FNFTSIQESM NEILFEEYQF QAVLRVNAGA LSAHRYFRDN PSELCCIIVD SGYSFTHIVP Y CRSKKKKE ...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

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

MacromoleculeName: 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) / Organ: BLOOD / Tissue: BONE MARROW
Molecular weightTheoretical: 17.567023 KDa
SequenceString:
MVEKKTSVRS QDPGQRRVLD RAARQRRINR QLEALENDNF QDDPHAGLPQ LGKRLPQFDD DADTGKKKKK TRGDHFKLRF RKNFQALLE EQNLSVAEGP NYLTACAGPP SRPQRPFCAV CGFPSPYTCV SCGARYCTVR CLGTHQETRC LKWTV

UniProtKB: Zinc finger HIT domain-containing protein 1

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Macromolecule #5: RuvB-like 1

MacromoleculeName: 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) / Organ: BLOOD / Tissue: BONE MARROW
Molecular weightTheoretical: 50.296914 KDa
SequenceString: MKIEEVKSTT KTQRIASHSH VKGLGLDESG LAKQAASGLV GQENAREACG VIVELIKSKK MAGRAVLLAG PPGTGKTALA LAIAQELGS KVPFCPMVGS EVYSTEIKKT EVLMENFRRA IGLRIKETKE VYEGEVTELT PCETENPMGG YGKTISHVII G LKTAKGTK ...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

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Macromolecule #6: RuvB-like 2

MacromoleculeName: 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) / Organ: BLOOD / Tissue: BONE MARROW
Molecular weightTheoretical: 51.222465 KDa
SequenceString: MATVTATTKV PEIRDVTRIE RIGAHSHIRG LGLDDALEPR QASQGMVGQL AARRAAGVVL EMIREGKIAG RAVLIAGQPG TGKTAIAMG MAQALGPDTP FTAIAGSEIF SLEMSKTEAL TQAFRRSIGV RIKEETEIIE GEVVEIQIDR PATGTGSKVG K LTLKTTEM ...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

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Macromolecule #7: Histone H2A.Z

MacromoleculeName: Histone H2A.Z / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.450601 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
AGGKAGKDSG KAKTKAVSRS QRAGLQFPVG RIHRHLKSRT TSHGRVGATA AVYSAAILEY LTAEVLELAG NASKDLKVKR ITPRHLQLA IRGDEELDSL IKATIAGGGV IPHIHKSLIG KKGQQKTV

UniProtKB: Histone H2A.Z

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Macromolecule #8: Histone H2B type 1-C/E/F/G/I

MacromoleculeName: Histone H2B type 1-C/E/F/G/I / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.806018 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
PEPAKSAPAP KKGSKKAVTK AQKKDGKKRK RSRKESYSVY VYKVLKQVHP DTGISSKAMG IMNSFVNDIF ERIAGEASRL AHYNKRSTI TSREIQTAVR LLLPGELAKH AVSEGTKAVT KYTSSK

UniProtKB: Histone H2B type 1-C/E/F/G/I

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Macromolecule #9: Histone H2A type 1

MacromoleculeName: Histone H2A type 1 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 13.907163 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
SGRGKQGGKT RAKAKTRSSR AGLQFPVGRV HRLLRKGNYA ERVGAGAPVY LAAVLEYLTA EILELAGNAA RDNKKTRIIP RHLQLAVRN DEELNKLLGR VTIAQGGVLP NIQSVLLPKK TESSKSKSK

UniProtKB: Histone H2A type 1

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Macromolecule #10: Histone H2B 1.1

MacromoleculeName: Histone H2B 1.1 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 13.848097 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
PEPAKSAPAP KKGSKKAVTK TQKKDGKKRR KTRKESYAIY VYKVLKQVHP DTGISSKAMS IMNSFVNDVF ERIAGEASRL AHYNKRSTI TSREIQTAVR LLLPGELAKH AVSEGTKAVT KYTSAK

UniProtKB: Histone H2B 1.1

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Macromolecule #11: Histone H3.2

MacromoleculeName: Histone H3.2 / type: protein_or_peptide / ID: 11 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 15.30393 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
ARTKQTARKS TGGKAPRKQL ATKAARKSAP ATGGVKKPHR YRPGTVALRE IRRYQKSTEL LIRKLPFQRL VREIAQDFKT DLRFQSSAV MALQEASEAY LVALFEDTNL CAIHAKRVTI MPKDIQLARR IRGERA

UniProtKB: Histone H3.2

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Macromolecule #12: Histone H4

MacromoleculeName: Histone H4 / type: protein_or_peptide / ID: 12 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 11.263231 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
SGRGKGGKGL GKGGAKRHRK VLRDNIQGIT KPAIRRLARR GGVKRISGLI YEETRGVLKV FLENVIRDAV TYTEHAKRKT VTAMDVVYA LKRQGRTLYG FGG

UniProtKB: Histone H4

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Macromolecule #13: DNA(285-MER)

MacromoleculeName: DNA(285-MER) / type: dna / ID: 13 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 87.851664 KDa
SequenceString: (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) ...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)

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Macromolecule #14: DNA(285-MER)

MacromoleculeName: DNA(285-MER) / type: dna / ID: 14 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 88.19093 KDa
SequenceString: (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) ...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)

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Macromolecule #15: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / type: ligand / ID: 15 / Number of copies: 2 / Formula: AGS
Molecular weightTheoretical: 523.247 Da
Chemical component information

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

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Macromolecule #16: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 16 / Number of copies: 5 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #17: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 17 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #18: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 18 / Number of copies: 6 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

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

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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: 7.6
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination 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

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: Negative stain reconstruction
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 24877
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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