EMDB-37988: Structure of nucleosome-bound SRCAP-C in the ADP-BeFx-bound state

Basic information

Entry

Database: EMDB / ID: EMD-37988

• Title: Structure of nucleosome-bound SRCAP-C in the ADP-BeFx-bound state
• Map data: Structure of nucleosome-bound SRCAP-C in the ADP-BeFx-bound state

Sample

• Complex: Structure of nucleosome-bound SRCAP-C in the ADP-BeFx-bound state
  • Protein or peptide: x 14 types
  • DNA: x 2 types
• Ligand: x 4 types

• Keywords: Remodeler / SRCAP / H2A.Z / DNA BINDING PROTEIN/DNA / DNA BINDING PROTEIN-DNA complex

Function / homology

Function:

positive regulation of lymphoid progenitor cell differentiation / histone H3K18ac reader activity / histone H3K27ac reader activity / promoter-enhancer loop anchoring activity / intestinal stem cell homeostasis / positive regulation of norepinephrine uptake / telomerase RNA localization to Cajal body / regulation of DNA strand elongation / hematopoietic stem cell homeostasis / positive regulation of telomere maintenance in response to DNA damage / histone chaperone activity / establishment of protein localization to chromatin / bBAF complex / cellular response to cytochalasin B / npBAF complex / R2TP complex / nBAF complex / brahma complex / heart process / dynein axonemal particle / neural retina development / regulation of transepithelial transport / GBAF complex / Formation of annular gap junctions / morphogenesis of a polarized epithelium / negative regulation of G0 to G1 transition / Formation of the dystrophin-glycoprotein complex (DGC) / structural constituent of postsynaptic actin cytoskeleton / Gap junction degradation / regulation of G0 to G1 transition / Folding of actin by CCT/TriC / Swr1 complex / Cell-extracellular matrix interactions / protein localization to adherens junction / dense body / RPAP3/R2TP/prefoldin-like complex / postsynaptic actin cytoskeleton / Tat protein binding / Activation of the TFAP2 (AP-2) family of transcription factors / Prefoldin mediated transfer of substrate to CCT/TriC / RSC-type complex / Ino80 complex / regulation of nucleotide-excision repair / muscle cell differentiation / regulation of double-strand break repair / blastocyst formation / RHOF GTPase cycle / nucleolus organization / Adherens junctions interactions / adherens junction assembly / apical protein localization / Sensory processing of sound by outer hair cells of the cochlea / positive regulation of DNA damage response, signal transduction by p53 class mediator / box C/D snoRNP assembly / Interaction between L1 and Ankyrins / SWI/SNF complex / tight junction / regulation of mitotic metaphase/anaphase transition / protein folding chaperone complex / Sensory processing of sound by inner hair cells of the cochlea / negative regulation of transcription by RNA polymerase I / positive regulation of T cell differentiation / apical junction complex / positive regulation of double-strand break repair / regulation of norepinephrine uptake / transporter regulator activity / maintenance of blood-brain barrier / spinal cord development / nitric-oxide synthase binding / cortical cytoskeleton / establishment or maintenance of cell polarity / regulation of chromosome organization / NuA4 histone acetyltransferase complex / positive regulation of stem cell population maintenance / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / positive regulation of transcription by RNA polymerase I / Regulation of MITF-M-dependent genes involved in pigmentation / Recycling pathway of L1 / brush border / TFIID-class transcription factor complex binding / regulation of G1/S transition of mitotic cell cycle / regulation of DNA replication / regulation of T cell proliferation / MLL1 complex / regulation of embryonic development / kinesin binding / Telomere Extension By Telomerase / negative regulation of cell differentiation / EPH-ephrin mediated repulsion of cells / somatic stem cell population maintenance / RHO GTPases Activate WASPs and WAVEs / regulation of synaptic vesicle endocytosis / positive regulation of myoblast differentiation / positive regulation of transcription initiation by RNA polymerase II / RHO GTPases activate IQGAPs / histone acetyltransferase activity / RNA polymerase II core promoter sequence-specific DNA binding / negative regulation of megakaryocyte differentiation / regulation of protein localization to plasma membrane / positive regulation of double-strand break repair via homologous recombination

Domain/homology:

DNA methyltransferase 1-associated 1 / DNA methyltransferase 1-associated protein 1 (DMAP1) / Vps71/ZNHIT1 / SWR1-complex protein 4/DNA methyltransferase 1-associated protein 1 / DAMP1, SANT/Myb-like domain / HIT zinc finger / SANT/Myb-like domain of DAMP1 / Zinc finger HIT-type profile. / YEATS / Vps72/YL1, N-terminal / YL1 nuclear protein / Zinc finger, HIT-type / : / : / YEATS superfamily / YEATS family / YEATS domain profile. / 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 / AT hook, DNA-binding motif / HSA domain / 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 / Helicase/SANT-associated domain / HSA domain profile. / : / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Actin / Actin family / Actin / : / Histone H2B signature. / Histone H2A conserved site / Histone H2A 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. / 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 / YEATS domain-containing protein 4 / Actin-like protein 6A / Actin, cytoplasmic 1 / Histone H4 / Histone H2B type 1-C/E/F/G/I / Histone H3.1 / Vacuolar protein sorting-associated protein 72 homolog / Helicase SRCAP / Histone H2A type 1-C / Actin-related protein 6 / DNA methyltransferase 1-associated protein 1 / RuvB-like 2 / RuvB-like 1

• Biological species: Homo sapiens (human)
• Method: single particle reconstruction / cryo EM / Resolution: 3.2 Å
• Authors: Yu J / Wang Q / Yu Z / Li W / Wang L / Xu Y

Funding support

China, 1 items

Organization	Grant number	Country
National Natural Science Foundation of China (NSFC)		China

• Citation: Journal: Cell Discov / Year: 2024; Title: Structural insights into histone exchange by human SRCAP complex.; Authors: Jiali Yu / Fengrui Sui / Feng Gu / Wanjun Li / Zishuo Yu / Qianmin Wang / Shuang He / Li Wang / Yanhui Xu / ; Abstract: Histone variant H2A.Z is found at promoters and regulates transcription. The ATP-dependent chromatin remodeler SRCAP complex (SRCAP-C) promotes the replacement of canonical histone H2A-H2B dimer with H2A.Z-H2B dimer. Here, we determined structures of human SRCAP-C bound to H2A-containing nucleosome at near-atomic resolution. The SRCAP subunit integrates a 6-subunit actin-related protein (ARP) module and an ATPase-containing motor module. The ATPase-associated ARP module encircles half of the nucleosome along the DNA and may restrain net DNA translocation, a unique feature of SRCAP-C. The motor module adopts distinct nucleosome binding modes in the apo (nucleotide-free), ADP-bound, and ADP-BeF-bound states, suggesting that ATPase-driven movement destabilizes H2A-H2B by unwrapping the entry DNA and pulls H2A-H2B out of nucleosome through the ZNHIT1 subunit. Structure-guided chromatin immunoprecipitation sequencing analysis confirmed the requirement of H2A-contacting ZNHIT1 in maintaining H2A.Z occupancy on the genome. Our study provides structural insights into the mechanism of H2A-H2A.Z exchange mediated by SRCAP-C.

History

Deposition	Nov 6, 2023	-
Header (metadata) release	Mar 6, 2024	-
Map release	Mar 6, 2024	-
Update	May 29, 2024	-
Current status	May 29, 2024	Processing site: PDBc / Status: Released

Map

• File: Download / File: emd_37988.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
• Annotation: Structure of nucleosome-bound SRCAP-C in the ADP-BeFx-bound state
• Voxel size: X=Y=Z: 1.334 Å

Density

Contour Level	By AUTHOR: 0.027
Minimum - Maximum	-0.11516745 - 0.24396116
Average (Standard dev.)	-0.00004873848 (±0.0056481846)

• Symmetry: Space group: 1

Details

EMDB XML:

Map geometry	Axis order X Y Z Origin 0 0 0 Dimensions 400 400 400 Spacing 400 400 400
Cell	A=B=C: 533.6 Å α=β=γ: 90.0 °

Supplemental data

Additional map: Structure of ARP module

• File: emd_37988_additional_1.map
• Annotation: Structure of ARP module

Additional map: Structure of nucleosome-bound ATPase in the ADP-BeFx -bound state

• File: emd_37988_additional_2.map
• Annotation: Structure of nucleosome-bound ATPase in the ADP-BeFx -bound state

Additional map: Structure of SRCAP-C-bound nucleosome in the ADP-BeFx -bound state

• File: emd_37988_additional_3.map
• Annotation: Structure of SRCAP-C-bound nucleosome in the ADP-BeFx -bound state

Additional map: Structure of nucleosome-bound SRCAP-C in the ADP-BeFx-bound state

• File: emd_37988_additional_4.map
• Annotation: Structure of nucleosome-bound SRCAP-C in the ADP-BeFx-bound state

Half map: Structure of nucleosome-bound SRCAP-C in the ADP-BeFx-bound state

• File: emd_37988_half_map_1.map
• Annotation: Structure of nucleosome-bound SRCAP-C in the ADP-BeFx-bound state

Half map: Structure of nucleosome-bound SRCAP-C in the ADP-BeFx-bound state

• File: emd_37988_half_map_2.map
• Annotation: Structure of nucleosome-bound SRCAP-C in the ADP-BeFx-bound state

Sample components

Entire : Structure of nucleosome-bound SRCAP-C in the ADP-BeFx-bound state

• Entire: Name: Structure of nucleosome-bound SRCAP-C in the ADP-BeFx-bound state

Components

• Complex: Structure of nucleosome-bound SRCAP-C in the ADP-BeFx-bound state
  • Protein or peptide: Histone H4
  • Protein or peptide: Helicase SRCAP
  • Protein or peptide: Vacuolar protein sorting-associated protein 72 homolog
  • 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: Actin, cytoplasmic 1
  • Protein or peptide: Actin-like protein 6A
  • Protein or peptide: YEATS domain-containing protein 4
  • Protein or peptide: Histone H2A type 1-C
  • Protein or peptide: Histone H2B type 1-C/E/F/G/I
  • Protein or peptide: Histone H3.1
  • Protein or peptide: Actin-related protein 6
  • Protein or peptide: DNA methyltransferase 1-associated protein 1
  • DNA: DNA (147-MER)
  • DNA: DNA (147-MER)
• Ligand: ADENOSINE-5'-DIPHOSPHATE
• Ligand: MAGNESIUM ION
• Ligand: BERYLLIUM TRIFLUORIDE ION
• Ligand: ADENOSINE-5'-TRIPHOSPHATE

Supramolecule #1: Structure of nucleosome-bound SRCAP-C in the ADP-BeFx-bound state

• Supramolecule: Name: Structure of nucleosome-bound SRCAP-C in the ADP-BeFx-bound state; type: complex / ID: 1 / Parent: 0 ; Macromolecule list: #4-#6, #8-#12, #14, #1-#3, #7, #13, #15-#16
• Source (natural): Organism: Homo sapiens (human)

Macromolecule #1: Histone H2A type 1-C

• Macromolecule: Name: Histone H2A type 1-C / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 14.135523 KDa
• Recombinant expression: Organism: Escherichia coli (E. coli)

Sequence

String:

MSGRGKQGGK ARAKAKSRSS RAGLQFPVGR VHRLLRKGNY AERVGAGAPV YLAAVLEYLT AEILELAGNA ARDNKKTRII PRHLQLAIR NDEELNKLLG RVTIAQGGVL PNIQAVLLPK KTESHHKAKG K

UniProtKB: Histone H2A type 1-C

Macromolecule #2: Histone H2B type 1-C/E/F/G/I

• Macromolecule: Name: Histone H2B type 1-C/E/F/G/I / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 13.937213 KDa
• Recombinant expression: Organism: Escherichia coli (E. coli)

Sequence

String:

MPEPAKSAPA PKKGSKKAVT KAQKKDGKKR KRSRKESYSV YVYKVLKQVH PDTGISSKAM GIMNSFVNDI FERIAGEASR LAHYNKRST ITSREIQTAV RLLLPGELAK HAVSEGTKAV TKYTSSK

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

Macromolecule #3: Histone H3.1

• Macromolecule: Name: Histone H3.1 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 15.437167 KDa
• Recombinant expression: Organism: Escherichia coli (E. coli)

Sequence

String:

MARTKQTARK STGGKAPRKQ LATKAARKSA PATGGVKKPH RYRPGTVALR EIRRYQKSTE LLIRKLPFQR LVREIAQDFK TDLRFQSSA VMALQEACEA YLVGLFEDTN LCAIHAKRVT IMPKDIQLAR RIRGERA

UniProtKB: Histone H3.1

Macromolecule #4: Histone H4

• Macromolecule: Name: Histone H4 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 11.394426 KDa
• Recombinant expression: Organism: Escherichia coli (E. coli)

Sequence

String:

MSGRGKGGKG LGKGGAKRHR KVLRDNIQGI TKPAIRRLAR RGGVKRISGL IYEETRGVLK VFLENVIRDA VTYTEHAKRK TVTAMDVVY ALKRQGRTLY GFGG

UniProtKB: Histone H4

Macromolecule #5: Helicase SRCAP

• Macromolecule: Name: Helicase SRCAP / type: protein_or_peptide / ID: 5 / 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
• Recombinant expression: Organism: Homo sapiens (human)

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 #6: Vacuolar protein sorting-associated protein 72 homolog

• Macromolecule: Name: Vacuolar protein sorting-associated protein 72 homolog; type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 40.658363 KDa
• Recombinant expression: Organism: Homo sapiens (human)

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 #7: Actin-related protein 6

• Macromolecule: Name: Actin-related protein 6 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 45.857902 KDa
• Recombinant expression: Organism: Homo sapiens (human)

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 #8: Zinc finger HIT domain-containing protein 1

• Macromolecule: Name: Zinc finger HIT domain-containing protein 1 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 17.567023 KDa
• Recombinant expression: Organism: Homo sapiens (human)

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 #9: RuvB-like 1

• Macromolecule: Name: RuvB-like 1 / type: protein_or_peptide / ID: 9 / Number of copies: 3 / Enantiomer: LEVO / EC number: DNA helicase
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 50.296914 KDa
• Recombinant expression: Organism: Homo sapiens (human)

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 #10: RuvB-like 2

• Macromolecule: Name: RuvB-like 2 / type: protein_or_peptide / ID: 10 / Number of copies: 3 / Enantiomer: LEVO / EC number: DNA helicase
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 51.222465 KDa
• Recombinant expression: Organism: Homo sapiens (human)

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 #11: Actin, cytoplasmic 1

• Macromolecule: Name: Actin, cytoplasmic 1 / type: protein_or_peptide / ID: 11 / Number of copies: 2 / 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: 41.78266 KDa
• Recombinant expression: Organism: Homo sapiens (human)

Sequence

String:

MDDDIAALVV DNGSGMCKAG FAGDDAPRAV FPSIVGRPRH QGVMVGMGQK DSYVGDEAQS KRGILTLKYP IEHGIVTNWD DMEKIWHHT FYNELRVAPE EHPVLLTEAP LNPKANREKM TQIMFETFNT PAMYVAIQAV LSLYASGRTT GIVMDSGDGV T HTVPIYEG YALPHAILRL DLAGRDLTDY LMKILTERGY SFTTTAEREI VRDIKEKLCY VALDFEQEMA TAASSSSLEK SY ELPDGQV ITIGNERFRC PEALFQPSFL GMESCGIHET TFNSIMKCDV DIRKDLYANT VLSGGTTMYP GIADRMQKEI TAL APSTMK IKIIAPPERK YSVWIGGSIL ASLSTFQQMW ISKQEYDESG PSIVHRKCF

UniProtKB: Actin, cytoplasmic 1

Macromolecule #12: Actin-like protein 6A

• Macromolecule: Name: Actin-like protein 6A / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 47.509812 KDa
• Recombinant expression: Organism: Homo sapiens (human)

Sequence

String:

MSGGVYGGDE VGALVFDIGS YTVRAGYAGE DCPKVDFPTA IGMVVERDDG STLMEIDGDK GKQGGPTYYI DTNALRVPRE NMEAISPLK NGMVEDWDSF QAILDHTYKM HVKSEASLHP VLMSEAPWNT RAKREKLTEL MFEHYNIPAF FLCKTAVLTA F ANGRSTGL ILDSGATHTT AIPVHDGYVL QQGIVKSPLA GDFITMQCRE LFQEMNIELV PPYMIASKEA VREGSPANWK RK EKLPQVT RSWHNYMCNC VIQDFQASVL QVSDSTYDEQ VAAQMPTVHY EFPNGYNCDF GAERLKIPEG LFDPSNVKGL SGN TMLGVS HVVTTSVGMC DIDIRPGLYG SVIVAGGNTL IQSFTDRLNR ELSQKTPPSM RLKLIANNTT VERRFSSWIG GSIL ASLGT FQQMWISKQE YEEGGKQCVE RKCP

UniProtKB: Actin-like protein 6A

Macromolecule #13: DNA methyltransferase 1-associated protein 1

• Macromolecule: Name: DNA methyltransferase 1-associated protein 1 / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 53.090699 KDa
• Recombinant expression: Organism: Homo sapiens (human)

Sequence

String:

MATGADVRDI LELGGPEGDA ASGTISKKDI INPDKKKSKK SSETLTFKRP EGMHREVYAL LYSDKKDAPP LLPSDTGQGY RTVKAKLGS KKVRPWKWMP FTNPARKDGA MFFHWRRAAE EGKDYPFARF NKTVQVPVYS EQEYQLYLHD DAWTKAETDH L FDLSRRFD LRFVVIHDRY DHQQFKKRSV EDLKERYYHI CAKLANVRAV PGTDLKIPVF DAGHERRRKE QLERLYNRTP EQ VAEEEYL LQELRKIEAR KKEREKRSQD LQKLITAADT TAEQRRTERK APKKKLPQKK EAEKPAVPET AGIKFPDFKS AGV TLRSQR MKLPSSVGQK KIKALEQMLL ELGVELSPTP TEELVHMFNE LRSDLVLLYE LKQACANCEY ELQMLRHRHE ALAR AGVLG GPATPASGPG PASAEPAVTE PGLGPDPKDT IIDVVGAPLT PNSRKRRESA SSSSSVKKAK KP

UniProtKB: DNA methyltransferase 1-associated protein 1

Macromolecule #14: YEATS domain-containing protein 4

• Macromolecule: Name: YEATS domain-containing protein 4 / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 26.541537 KDa
• Recombinant expression: Organism: Homo sapiens (human)

Sequence

String:

MFKRMAEFGP DSGGRVKGVT IVKPIVYGNV ARYFGKKREE DGHTHQWTVY VKPYRNEDMS AYVKKIQFKL HESYGNPLRV VTKPPYEIT ETGWGEFEII IKIFFIDPNE RPVTLYHLLK LFQSDTNAML GKKTVVSEFY DEMIFQDPTA MMQQLLTTSR Q LTLGAYKH ETEFAELEVK TREKLEAAKK KTSFEIAELK ERLKASRETI NCLKNEIRKL EEDDQAKDI

UniProtKB: YEATS domain-containing protein 4

Macromolecule #15: DNA (147-MER)

• Macromolecule: Name: DNA (147-MER) / type: dna / ID: 15 / Number of copies: 1 / Classification: DNA
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 45.64407 KDa

Sequence

String:

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

Macromolecule #16: DNA (147-MER)

• Macromolecule: Name: DNA (147-MER) / type: dna / ID: 16 / Number of copies: 1 / Classification: DNA
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 45.105727 KDa

Sequence

String:

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

Macromolecule #17: ADENOSINE-5'-DIPHOSPHATE

• Macromolecule: Name: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 17 / Number of copies: 7 / Formula: ADP
• Molecular weight: Theoretical: 427.201 Da

Chemical component information

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

Macromolecule #18: MAGNESIUM ION

• Macromolecule: Name: MAGNESIUM ION / type: ligand / ID: 18 / Number of copies: 1 / Formula: MG
• Molecular weight: Theoretical: 24.305 Da

Macromolecule #19: BERYLLIUM TRIFLUORIDE ION

• Macromolecule: Name: BERYLLIUM TRIFLUORIDE ION / type: ligand / ID: 19 / Number of copies: 1 / Formula: BEF
• Molecular weight: Theoretical: 66.007 Da

Chemical component information

ChemComp-BEF:
BERYLLIUM TRIFLUORIDE ION

Macromolecule #20: ADENOSINE-5'-TRIPHOSPHATE

• Macromolecule: Name: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 20 / Number of copies: 2 / Formula: ATP
• Molecular weight: Theoretical: 507.181 Da

Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

Experimental details

Structure determination

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

Sample preparation

• Buffer: pH: 8
• 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: 2.5 µm / Nominal defocus min: 1.5 µm
• Experimental equipment: Model: Titan Krios / Image courtesy: FEI Company

Image processing

Startup model

Type of model: PDB ENTRY
PDB model - PDB ID:

6igm

• Final reconstruction: Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 475617
• Initial angle assignment: Type: MAXIMUM LIKELIHOOD
• Final angle assignment: Type: MAXIMUM LIKELIHOOD