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- EMDB-40789: BAP1/ASXL1 bound to the H2AK119Ub Nucleosome -

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Basic information

Entry
Database: EMDB / ID: EMD-40789
TitleBAP1/ASXL1 bound to the H2AK119Ub Nucleosome
Map dataSharpened map DNA clamp BAP1/ASXL1-H2AK119Ub nucleosome complex
Sample
  • Complex: BAP1/ASXL1 bound to the H2AK119Ub Nucleosome
    • Protein or peptide: Histone H3.2
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2A type 1
    • Protein or peptide: Histone H2B 1.1
    • Other: DNA/RNA (187-MER)
    • Other: DNA/RNA (327-MER)
    • Protein or peptide: Ubiquitin carboxyl-terminal hydrolase BAP1
    • Protein or peptide: Polycomb group protein ASXL1Polycomb-group proteins
    • Protein or peptide: Ubiquitin
KeywordsDNA complex protein / hydrolase / structural protein / NUCLEAR PROTEIN-DNA-RNA complex
Function / homology
Function and homology information


thrombocyte differentiation / nucleate erythrocyte differentiation / negative regulation of peroxisome proliferator activated receptor signaling pathway / PR-DUB complex / leukocyte proliferation / platelet morphogenesis / histone H2A deubiquitinase activity / positive regulation of retinoic acid receptor signaling pathway / macrophage homeostasis / lung saccule development ...thrombocyte differentiation / nucleate erythrocyte differentiation / negative regulation of peroxisome proliferator activated receptor signaling pathway / PR-DUB complex / leukocyte proliferation / platelet morphogenesis / histone H2A deubiquitinase activity / positive regulation of retinoic acid receptor signaling pathway / macrophage homeostasis / lung saccule development / podocyte development / neutrophil differentiation / regulation of kidney size / myeloid cell apoptotic process / hematopoietic stem cell homeostasis / monoubiquitinated protein deubiquitination / common myeloid progenitor cell proliferation / protein K48-linked deubiquitination / tissue homeostasis / nuclear retinoic acid receptor binding / peroxisome proliferator activated receptor binding / bone marrow development / positive regulation of protein targeting to mitochondrion / negative regulation of fat cell differentiation / protein deubiquitination / erythrocyte maturation / regulation of cytokine production involved in inflammatory response / hemopoiesis / homeostasis of number of cells / response to inorganic substance / heart morphogenesis / response to retinoic acid / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Membrane binding and targetting of GAG proteins / Constitutive Signaling by NOTCH1 HD Domain Mutants / Endosomal Sorting Complex Required For Transport (ESCRT) / NOTCH2 Activation and Transmission of Signal to the Nucleus / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FLT3 / Regulation of FZD by ubiquitination / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / Downregulation of ERBB4 signaling / p75NTR recruits signalling complexes / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / APC-Cdc20 mediated degradation of Nek2A / PINK1-PRKN Mediated Mitophagy / TRAF6-mediated induction of TAK1 complex within TLR4 complex / InlA-mediated entry of Listeria monocytogenes into host cells / Pexophagy / Regulation of innate immune responses to cytosolic DNA / VLDLR internalisation and degradation / Downregulation of ERBB2:ERBB3 signaling / NRIF signals cell death from the nucleus / Activated NOTCH1 Transmits Signal to the Nucleus / Translesion synthesis by REV1 / NF-kB is activated and signals survival / Regulation of PTEN localization / Translesion synthesis by POLK / Regulation of BACH1 activity / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Downregulation of TGF-beta receptor signaling / Josephin domain DUBs / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Regulation of activated PAK-2p34 by proteasome mediated degradation / InlB-mediated entry of Listeria monocytogenes into host cell / IKK complex recruitment mediated by RIP1 / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / thymus development / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Autodegradation of Cdh1 by Cdh1:APC/C / TNFR1-induced NF-kappa-B signaling pathway / APC/C:Cdc20 mediated degradation of Securin / Asymmetric localization of PCP proteins / TCF dependent signaling in response to WNT / SCF-beta-TrCP mediated degradation of Emi1 / Regulation of NF-kappa B signaling / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / AUF1 (hnRNP D0) binds and destabilizes mRNA / Negative regulators of DDX58/IFIH1 signaling / TNFR2 non-canonical NF-kB pathway / NOTCH3 Activation and Transmission of Signal to the Nucleus
Similarity search - Function
Polycomb protein ASX/ASX-like / Protein ASX-like, PHD domain / ASX, DEUBAD domain / Asx homology domain / PHD domain of transcriptional enhancer, Asx / ASXL, HARE-HTH domain / HB1, ASXL, restriction endonuclease HTH domain / HARE-type HTH domain profile. / Peptidase C12, C-terminal domain / Ubiquitin carboxyl-terminal hydrolases ...Polycomb protein ASX/ASX-like / Protein ASX-like, PHD domain / ASX, DEUBAD domain / Asx homology domain / PHD domain of transcriptional enhancer, Asx / ASXL, HARE-HTH domain / HB1, ASXL, restriction endonuclease HTH domain / HARE-type HTH domain profile. / Peptidase C12, C-terminal domain / Ubiquitin carboxyl-terminal hydrolases / DEUBAD domain / DEUBAD (DEUBiquitinase ADaptor) domain profile. / Peptidase C12, ubiquitin carboxyl-terminal hydrolase superfamily / Ubiquitin carboxyl-terminal hydrolase, family 1 / Peptidase C12, ubiquitin carboxyl-terminal hydrolase / 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 / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Papain-like cysteine peptidase superfamily / Histone H3 signature 1. / Ubiquitin conserved site / Ubiquitin domain / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Ubiquitin domain signature. / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / Ubiquitin family / Ubiquitin homologues / Ubiquitin-like domain / Ubiquitin domain profile. / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Histone H2B 1.1 / Histone H2A type 1 / Polyubiquitin-C / Histone H4 / Histone H3.2 / Polycomb group protein ASXL1 / Ubiquitin carboxyl-terminal hydrolase BAP1
Similarity search - Component
Biological speciesHomo sapiens (human) / Xenopus laevis (African clawed frog) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsThomas JF / Valencia-Sanchez MI / Armache K-J
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM115882 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)R01CA266978 United States
The Mark Foundation United States
CitationJournal: Sci Adv / Year: 2023
Title: Structural basis of histone H2A lysine 119 deubiquitination by Polycomb repressive deubiquitinase BAP1/ASXL1.
Authors: Jonathan F Thomas / Marco Igor Valencia-Sánchez / Simone Tamburri / Susan L Gloor / Samantha Rustichelli / Victoria Godínez-López / Pablo De Ioannes / Rachel Lee / Stephen Abini-Agbomson ...Authors: Jonathan F Thomas / Marco Igor Valencia-Sánchez / Simone Tamburri / Susan L Gloor / Samantha Rustichelli / Victoria Godínez-López / Pablo De Ioannes / Rachel Lee / Stephen Abini-Agbomson / Kristjan Gretarsson / Jonathan M Burg / Allison R Hickman / Lu Sun / Saarang Gopinath / Hailey F Taylor / Zu-Wen Sun / Ryan J Ezell / Anup Vaidya / Matthew J Meiners / Marcus A Cheek / William J Rice / Vladimir Svetlov / Evgeny Nudler / Chao Lu / Michael-Christopher Keogh / Diego Pasini / Karim-Jean Armache /
Abstract: Histone H2A lysine 119 (H2AK119Ub) is monoubiquitinated by Polycomb repressive complex 1 and deubiquitinated by Polycomb repressive deubiquitinase complex (PR-DUB). PR-DUB cleaves H2AK119Ub to ...Histone H2A lysine 119 (H2AK119Ub) is monoubiquitinated by Polycomb repressive complex 1 and deubiquitinated by Polycomb repressive deubiquitinase complex (PR-DUB). PR-DUB cleaves H2AK119Ub to restrict focal H2AK119Ub at Polycomb target sites and to protect active genes from aberrant silencing. The PR-DUB subunits (BAP1 and ASXL1) are among the most frequently mutated epigenetic factors in human cancers. How PR-DUB establishes specificity for H2AK119Ub over other nucleosomal ubiquitination sites and how disease-associated mutations of the enzyme affect activity are unclear. Here, we determine a cryo-EM structure of human BAP1 and the ASXL1 DEUBAD in complex with a H2AK119Ub nucleosome. Our structural, biochemical, and cellular data reveal the molecular interactions of BAP1 and ASXL1 with histones and DNA that are critical for restructuring the nucleosome and thus establishing specificity for H2AK119Ub. These results further provide a molecular explanation for how >50 mutations in BAP1 and ASXL1 found in cancer can dysregulate H2AK119Ub deubiquitination, providing insight into understanding cancer etiology.
History
DepositionMay 16, 2023-
Header (metadata) releaseAug 30, 2023-
Map releaseAug 30, 2023-
UpdateFeb 14, 2024-
Current statusFeb 14, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_40789.png

Downloads & links

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Map

FileDownload / File: emd_40789.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map DNA clamp BAP1/ASXL1-H2AK119Ub nucleosome complex
Voxel sizeX=Y=Z: 1.05375 Å
Density
Contour LevelBy AUTHOR: 0.12
Minimum - Maximum-0.33851472 - 0.96552455
Average (Standard dev.)0.0015060223 (±0.02780574)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 316.125 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_40789_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram

Histogram (log scale)

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Additional map: Unsharpened map DNA clamp BAP1/ASXL1-H2AK119Ub nucleosome complex

Fileemd_40789_additional_1.map
AnnotationUnsharpened map DNA clamp BAP1/ASXL1-H2AK119Ub nucleosome complex
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram

Histogram (log scale)

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Additional map: Sharpened map Bfactor -63 DNA clamp BAP1/ASXL1-H2AK119Ub nucleosome...

Fileemd_40789_additional_2.map
AnnotationSharpened map Bfactor -63 DNA clamp BAP1/ASXL1-H2AK119Ub nucleosome complex
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram

Histogram (log scale)

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Half map: Half-map B DNA clamp BAP1/ASXL1-H2AK119Ub nucleosome complex

Fileemd_40789_half_map_1.map
AnnotationHalf-map B DNA clamp BAP1/ASXL1-H2AK119Ub nucleosome complex
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map A DNA clamp BAP1/ASXL1-H2AK119Ub nucleosome complex

Fileemd_40789_half_map_2.map
AnnotationHalf-map A DNA clamp BAP1/ASXL1-H2AK119Ub nucleosome complex
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : BAP1/ASXL1 bound to the H2AK119Ub Nucleosome

EntireName: BAP1/ASXL1 bound to the H2AK119Ub Nucleosome
Components
  • Complex: BAP1/ASXL1 bound to the H2AK119Ub Nucleosome
    • Protein or peptide: Histone H3.2
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2A type 1
    • Protein or peptide: Histone H2B 1.1
    • Other: DNA/RNA (187-MER)
    • Other: DNA/RNA (327-MER)
    • Protein or peptide: Ubiquitin carboxyl-terminal hydrolase BAP1
    • Protein or peptide: Polycomb group protein ASXL1Polycomb-group proteins
    • Protein or peptide: Ubiquitin

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Supramolecule #1: BAP1/ASXL1 bound to the H2AK119Ub Nucleosome

SupramoleculeName: BAP1/ASXL1 bound to the H2AK119Ub Nucleosome / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#9
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Histone H3.2

MacromoleculeName: Histone H3.2 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 15.435126 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MARTKQTARK STGGKAPRKQ LATKAARKSA PATGGVKKPH RYRPGTVALR EIRRYQKSTE LLIRKLPFQR LVREIAQDFK TDLRFQSSA VMALQEASEA YLVALFEDTN LCAIHAKRVT IMPKDIQLAR RIRGERA

UniProtKB: Histone H3.2

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Macromolecule #2: Histone H4

MacromoleculeName: Histone H4 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 11.394426 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSGRGKGGKG LGKGGAKRHR KVLRDNIQGI TKPAIRRLAR RGGVKRISGL IYEETRGVLK VFLENVIRDA VTYTEHAKRK TVTAMDVVY ALKRQGRTLY GFGG

UniProtKB: Histone H4

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Macromolecule #3: Histone H2A type 1

MacromoleculeName: Histone H2A type 1 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 14.093436 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSGRGKQGGK TRAKAKTRSS RAGLQFPVGR VHRLLRKGNY AERVGAGAPV YLAAVLEYLT AEILELAGNA ARDNKKTRII PRHLQLAVR NDEELNKLLG RVTIAQGGVL PNIQSVLLPK KTESAKSAKS K

UniProtKB: Histone H2A type 1

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Macromolecule #4: Histone H2B 1.1

MacromoleculeName: Histone H2B 1.1 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 13.979291 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MPEPAKSAPA PKKGSKKAVT KTQKKDGKKR RKTRKESYAI YVYKVLKQVH PDTGISSKAM SIMNSFVNDV FERIAGEASR LAHYNKRST ITSREIQTAV RLLLPGELAK HAVSEGTKAV TKYTSAK

UniProtKB: Histone H2B 1.1

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Macromolecule #7: Ubiquitin carboxyl-terminal hydrolase BAP1

MacromoleculeName: Ubiquitin carboxyl-terminal hydrolase BAP1 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO / EC number: ubiquitinyl hydrolase 1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 80.472617 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MNKGWLELES DPGLFTLLVE DFGVKGVQVE EIYDLQSKCQ GPVYGFIFLF KWIEERRSRR KVSTLVDDTS VIDDDIVNNM FFAHQLIPN SCATHALLSV LLNCSSVDLG PTLSRMKDFT KGFSPESKGY AIGNAPELAK AHNSHARPEP RHLPEKQNGL S AVRTMEAF ...String:
MNKGWLELES DPGLFTLLVE DFGVKGVQVE EIYDLQSKCQ GPVYGFIFLF KWIEERRSRR KVSTLVDDTS VIDDDIVNNM FFAHQLIPN SCATHALLSV LLNCSSVDLG PTLSRMKDFT KGFSPESKGY AIGNAPELAK AHNSHARPEP RHLPEKQNGL S AVRTMEAF HFVSYVPITG RLFELDGLKV YPIDHGPWGE DEEWTDKARR VIMERIGLAT AGEPYHDIRF NLMAVVPDRR IK YEARLHV LKVNRQTVLE ALQQLIRVTQ PELIQTHKSQ ESQLPEESKS ASNKSPLVLE ANRAPAASEG NHTDGAEEAA GSC AQAPSH SPPNKPKLVV KPPGSSLNGV HPNPTPIVQR LPAFLDNHNY AKSPMQEEED LAAGVGRSRV PVRPPQQYSD DEDD YEDDE EDDVQNTNSA LRYKGKGTGK PGALSGSADG QLSVLQPNTI NVLAEKLKES QKDLSIPLSI KTSSGAGSPA VAVPT HSQP SPTPSNESTD TASEIGSAFN SPLRSPIRSA NPTRPSSPVT SHISKVLFGE DDSLLRVDCI RYNRAVRDLG PVISTG LLH LAEDGVLSPL ALTEGGKGSS PSIRPIQGSQ GSSSPVEKEV VEATDSREKT GMVRPGEPLS GEKYSPKELL ALLKCVE AE IANYEACLKE EVEKRKKFKI DDQRRTHNYD EFICTFISML AQEGMLANLV EQNISVRRRQ GVSIGRLHKQ RKPDRRKR S RPYKAKRQ

UniProtKB: Ubiquitin carboxyl-terminal hydrolase BAP1

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Macromolecule #8: Polycomb group protein ASXL1

MacromoleculeName: Polycomb group protein ASXL1 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 165.635203 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKDKQKKKKE RTWAEAARLV LENYSDAPMT PKQILQVIEA EGLKEMRSGT SPLACLNAML HSNSRGGEGL FYKLPGRISL FTLKKDALQ WSRHPATVEG EEPEDTADVE SCGSNEASTV SGENDVSLDE TSSNASCSTE SQSRPLSNPR DSYRASSQAN K QKKKTGVM ...String:
MKDKQKKKKE RTWAEAARLV LENYSDAPMT PKQILQVIEA EGLKEMRSGT SPLACLNAML HSNSRGGEGL FYKLPGRISL FTLKKDALQ WSRHPATVEG EEPEDTADVE SCGSNEASTV SGENDVSLDE TSSNASCSTE SQSRPLSNPR DSYRASSQAN K QKKKTGVM LPRVVLTPLK VNGAHVESAS GFSGCHADGE SGSPSSSSSG SLALGSAAIR GQAEVTQDPA PLLRGFRKPA TG QMKRNRG EEIDFETPGS ILVNTNLRAL INSRTFHALP SHFQQQLLFL LPEVDRQVGT DGLLRLSSSA LNNEFFTHAA QSW RERLAD GEFTHEMQVR IRQEMEKEKK VEQWKEKFFE DYYGQKLGLT KEESLQQNVG QEEAEIKSGL CVPGESVRIQ RGPA TRQRD GHFKKRSRPD LRTRARRNLY KKQESEQAGV AKDAKSVASD VPLYKDGEAK TDPAGLSSPH LPGTSSAAPD LEGPE FPVE SVASRIQAEP DNLARASASP DRIPSLPQET VDQEPKDQKR KSFEQAASAS FPEKKPRLED RQSFRNTIES VHTEKP QPT KEEPKVPPIR IQLSRIKPPW VVKGQPTYQI CPRIIPTTES SCRGWTGART LADIKARALQ VRGARGHHCH REAATTA IG GGGGPGGGGG GATDEGGGRG SSSGDGGEAC GHPEPRGGPS TPGKCTSDLQ RTQLLPPYPL NGEHTQAGTA MSRARRED L PSLRKEESCL LQRATVGLTD GLGDASQLPV APTGDQPCQA LPLLSSQTSV AERLVEQPQL HPDVRTECES GTTSWESDD EEQGPTVPAD NGPIPSLVGD DTLEKGTGQA LDSHPTMKDP VNVTPSSTPE SSPTDCLQNR AFDDELGLGG SCPPMRESDT RQENLKTKA LVSNSSLHWI PIPSNDEVVK QPKPESREHI PSVEPQVGEE WEKAAPTPPA LPGDLTAEEG LDPLDSLTSL W TVPSRGGS DSNGSYCQQV DIEKLKINGD SEALSPHGES TDTASDFEGH LTEDSSEADT REAAVTKGSS VDKDEKPNWN QS APLSKVN GDMRLVTRTD GMVAPQSWVS RVCAVRQKIP DSLLLASTEY QPRAVCLSMP GSSVEATNPL VMQLLQGSLP LEK VLPPAH DDSMSESPQV PLTKDQSHGS LRMGSLHGLG KNSGMVDGSS PSSLRALKEP LLPDSCETGT GLARIEATQA PGAP QKNCK AVPSFDSLHP VTNPITSSRK LEEMDSKEQF SSFSCEDQKE VRAMSQDSNS NAAPGKSPGD LTTSRTPRFS SPNVI SFGP EQTGRALGDQ SNVTGQGKKL FGSGNVAATL QRPRPADPMP LPAEIPPVFP SGKLGPSTNS MSGGVQTPRE DWAPKP HAF VGSVKNEKTF VGGPLKANAE NRKATGHSPL ELVGHLEGMP FVMDLPFWKL PREPGKGLSE PLEPSSLPSQ LSIKQAF YG KLSKLQLSST SFNYSSSSPT FPKGLAGSVV QLSHKANFGA SHSASLSLQM FTDSSTVESI SLQCACSLKA MIMCQGCG A FCHDDCIGPS KLCVLCLVVR

UniProtKB: Polycomb group protein ASXL1

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Macromolecule #9: Ubiquitin

MacromoleculeName: Ubiquitin / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 8.576831 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MQIFVKTLTG KTITLEVEPS DTIENVKAKI QDKEGIPPDQ QRLIFAGKQL EDGRTLSDYN IQKESTLHLV LRLRGG

UniProtKB: Polyubiquitin-C

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Macromolecule #5: DNA/RNA (187-MER)

MacromoleculeName: DNA/RNA (187-MER) / type: other / ID: 5 / Number of copies: 1
Classification: polydeoxyribonucleotide/polyribonucleotide hybrid
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 58.56877 KDa
SequenceString: AUCUGAUAUC GCGACACCGG C(DA)(DC)(DT)G(DG)A(DA)(DC)(DA) (DG)(DG)(DA)(DT)(DG)(DT)(DA) (DT)(DA) (DT)(DA)(DT)(DC)(DT)(DG)(DA)(DC)(DA)(DC) (DG)(DT)(DG)(DC)(DC)(DT)(DG)(DG) (DA) (DG)(DA)(DC)(DT)(DA) ...String:
AUCUGAUAUC GCGACACCGG C(DA)(DC)(DT)G(DG)A(DA)(DC)(DA) (DG)(DG)(DA)(DT)(DG)(DT)(DA) (DT)(DA) (DT)(DA)(DT)(DC)(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)CCA GGGGAUCGGG CAUC

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Macromolecule #6: DNA/RNA (327-MER)

MacromoleculeName: DNA/RNA (327-MER) / type: other / ID: 6 / Number of copies: 1
Classification: polydeoxyribonucleotide/polyribonucleotide hybrid
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 102.866516 KDa
SequenceString: GAUGCCCGAU CCCCUGGAGA AU(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) ...String:
GAUGCCCGAU CCCCUGGAGA AU(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) (DG)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DC)(DA) (DT)(DC) (DC)(DT)(DG)(DT)(DT)(DC)C A(DG)GGUGCCGA GGCCGCUCAA UUGGUCGUAG ACAGCUCUAG CACCGCUUAA AC GCACGUA CGCGCUGUCC CCCGCGUUUU AACCGCCAAG GGGAUUACUC CCUAGUCUCC AGGCACGUGU CAGAUAUAUA CAU CCUGUU CCAGUGCCGG UGUCGCGAUA UCAGAU

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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

Concentration0.1 mg/mL
BufferpH: 7.5
GridModel: Quantifoil / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1.9000000000000001 µm / Nominal defocus min: 0.9 µm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 57.12 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER / Details: Ab initio
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.1.1) / Number images used: 39056
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
ChainDetailsPDB ID
source_name: AlphaFold, initial_model_type: in silico modelMultimer prediction
source_name: PDB, initial_model_type: experimental model

3tu4

source_name: Other, initial_model_type: integrative modelSwissModel template

4uel

source_name: Other, initial_model_type: integrative modelSwissModel template

6hgc

source_name: PDB, initial_model_type: experimental model

7k5y

RefinementSpace: REAL
Output model

PDB-8svf:
BAP1/ASXL1 bound to the H2AK119Ub Nucleosome

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