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- EMDB-34431: Cryo-EM structure of BAP1-ASXL1 bound to chromatosome -

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Entry
Database: EMDB / ID: EMD-34431
TitleCryo-EM structure of BAP1-ASXL1 bound to chromatosome
Map data
Sample
  • Complex: Cryo-EM structure of BAP1-ASXL1 bound to chromatosome
    • Protein or peptide: Histone H3.1
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2A type 1-D
    • Protein or peptide: Histone H2B type 2-E
    • DNA: DNA (187-MER)
    • DNA: DNA (187-MER)
    • Protein or peptide: Histone H1.4
    • Protein or peptide: Ubiquitin carboxyl-terminal hydrolase BAP1
    • Protein or peptide: Ubiquitin
    • Protein or peptide: Polycomb group protein ASXL1
Keywordsnucleosome / histone deubiquitination / chromatin / GENE REGULATION
Function / homology
Function and homology information


thrombocyte differentiation / nucleate erythrocyte differentiation / PR-DUB complex / platelet morphogenesis / histone H2A deubiquitinase activity / positive regulation of retinoic acid receptor signaling pathway / lung saccule development / macrophage homeostasis / leukocyte proliferation / podocyte development ...thrombocyte differentiation / nucleate erythrocyte differentiation / PR-DUB complex / platelet morphogenesis / histone H2A deubiquitinase activity / positive regulation of retinoic acid receptor signaling pathway / lung saccule development / macrophage homeostasis / leukocyte proliferation / podocyte development / negative regulation of peroxisome proliferator activated receptor signaling pathway / myeloid cell apoptotic process / regulation of kidney size / neutrophil differentiation / hematopoietic stem cell homeostasis / common myeloid progenitor cell proliferation / monoubiquitinated protein deubiquitination / protein K48-linked deubiquitination / negative regulation of DNA recombination / tissue homeostasis / nuclear retinoic acid receptor binding / Apoptosis induced DNA fragmentation / peroxisome proliferator activated receptor binding / chromosome condensation / bone marrow development / symbiont entry into host cell via disruption of host cell glycocalyx / positive regulation of protein targeting to mitochondrion / nucleosomal DNA binding / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / symbiont entry into host cell via disruption of host cell envelope / erythrocyte maturation / negative regulation of fat cell differentiation / virus tail / regulation of cytokine production involved in inflammatory response / hemopoiesis / homeostasis of number of cells / protein deubiquitination / response to retinoic acid / heart morphogenesis / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / heterochromatin / Chromatin modifying enzymes / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Deposition of new CENPA-containing nucleosomes at the centromere / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / telomere organization / Interleukin-7 signaling / Inhibition of DNA recombination at telomere / RNA Polymerase I Promoter Opening / Meiotic synapsis / Assembly of the ORC complex at the origin of replication / SUMOylation of chromatin organization proteins / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / DNA methylation / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / epigenetic regulation of gene expression / HCMV Late Events / SIRT1 negatively regulates rRNA expression / thymus development / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / animal organ morphogenesis / PRC2 methylates histones and DNA / innate immune response in mucosa / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / HDMs demethylate histones / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / Nonhomologous End-Joining (NHEJ) / regulation of cell growth / Transcriptional regulation by small RNAs / chromatin DNA binding / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / euchromatin / G2/M DNA damage checkpoint / Metalloprotease DUBs / NoRC negatively regulates rRNA expression / protein modification process / cell morphogenesis / DNA Damage/Telomere Stress Induced Senescence / B-WICH complex positively regulates rRNA expression / PKMTs methylate histone lysines / Meiotic recombination / Pre-NOTCH Transcription and Translation / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / histone deacetylase binding / Transcriptional regulation of granulopoiesis / neuron cellular homeostasis / UCH proteinases
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 / UCH37-like (ULD) domain profile. / Peptidase C12, C-terminal domain / Ubiquitin carboxyl-terminal hydrolases / ASXL, HARE-HTH domain / HB1, ASXL, restriction endonuclease HTH domain ...Polycomb protein ASX/ASX-like / Protein ASX-like, PHD domain / ASX, DEUBAD domain / Asx homology domain / PHD domain of transcriptional enhancer, Asx / UCH37-like (ULD) domain profile. / Peptidase C12, C-terminal domain / Ubiquitin carboxyl-terminal hydrolases / ASXL, HARE-HTH domain / HB1, ASXL, restriction endonuclease HTH domain / HARE-type HTH domain profile. / DEUBAD domain / DEUBAD (DEUBiquitinase ADaptor) domain profile. / Peptidase C12, ubiquitin carboxyl-terminal hydrolase superfamily / Ubiquitin carboxyl-terminal hydrolase, family 1 / Ubiquitin carboxyl-terminal hydrolase (UCH) catalytic domain profile. / Peptidase C12, ubiquitin carboxyl-terminal hydrolase / Linker histone H1/H5 / linker histone H1 and H5 family / Linker histone H1/H5, domain H15 / Linker histone H1/H5 globular (H15) domain profile. / Domain in histone families 1 and 5 / Pectate lyase superfamily protein / Rhamnogalacturonase A/epimerase, pectate lyase-like / Pectin lyase fold / Pectin lyase fold/virulence factor / : / Histone H2B signature. / Histone H2A conserved site / Histone H2A signature. / Histone H2B / Histone H2B / Histone H2A, C-terminal domain / C-terminus of histone H2A / Papain-like cysteine peptidase superfamily / 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 / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Tail fiber / Histone H1.4 / Histone H2A type 1-D / Histone H4 / Histone H3.1 / Histone H2B type 2-E / Polycomb group protein ASXL1 / Ubiquitin carboxyl-terminal hydrolase BAP1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsGe W / Yu C / Xu RM
Funding support China, 4 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2019YFA0508900 China
National Natural Science Foundation of China (NSFC)31991162 China
National Natural Science Foundation of China (NSFC)918532204 China
National Natural Science Foundation of China (NSFC)92153302 China
CitationJournal: Nature / Year: 2023
Title: Basis of the H2AK119 specificity of the Polycomb repressive deubiquitinase.
Authors: Weiran Ge / Cong Yu / Jingjing Li / Zhenyu Yu / Xiaorong Li / Yan Zhang / Chao-Pei Liu / Yingfeng Li / Changlin Tian / Xinzheng Zhang / Guohong Li / Bing Zhu / Rui-Ming Xu /
Abstract: Repression of gene expression by protein complexes of the Polycomb group is a fundamental mechanism that governs embryonic development and cell-type specification. The Polycomb repressive ...Repression of gene expression by protein complexes of the Polycomb group is a fundamental mechanism that governs embryonic development and cell-type specification. The Polycomb repressive deubiquitinase (PR-DUB) complex removes the ubiquitin moiety from monoubiquitinated histone H2A K119 (H2AK119ub1) on the nucleosome, counteracting the ubiquitin E3 ligase activity of Polycomb repressive complex 1 (PRC1) to facilitate the correct silencing of genes by Polycomb proteins and safeguard active genes from inadvertent silencing by PRC1 (refs. ). The intricate biological function of PR-DUB requires accurate targeting of H2AK119ub1, but PR-DUB can deubiquitinate monoubiquitinated free histones and peptide substrates indiscriminately; the basis for its exquisite nucleosome-dependent substrate specificity therefore remains unclear. Here we report the cryo-electron microscopy structure of human PR-DUB, composed of BAP1 and ASXL1, in complex with the chromatosome. We find that ASXL1 directs the binding of the positively charged C-terminal extension of BAP1 to nucleosomal DNA and histones H3-H4 near the dyad, an addition to its role in forming the ubiquitin-binding cleft. Furthermore, a conserved loop segment of the catalytic domain of BAP1 is situated near the H2A-H2B acidic patch. This distinct nucleosome-binding mode displaces the C-terminal tail of H2A from the nucleosome surface, and endows PR-DUB with the specificity for H2AK119ub1.
History
DepositionOct 4, 2022-
Header (metadata) releaseFeb 1, 2023-
Map releaseFeb 1, 2023-
UpdateJul 3, 2024-
Current statusJul 3, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_34431.png

Downloads & links

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Map

FileDownload / File: emd_34431.map.gz / Format: CCP4 / Size: 166.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesX (Sec.)Y (Row.)Z (Col.)
1 Å/pix.
x 352 pix.
= 352. Å		1 Å/pix.
x 352 pix.
= 352. Å		1 Å/pix.
x 352 pix.
= 352. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 4.94
Minimum - Maximum-36.615960000000001 - 74.144189999999995
Average (Standard dev.)-0.0126599595 (±1.0796034)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions352352352
Spacing352352352
CellA=B=C: 352.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_34431_msk_1.map
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Half map: #2

Fileemd_34431_half_map_1.map
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Half map: #1

Fileemd_34431_half_map_2.map
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Sample components

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Entire : Cryo-EM structure of BAP1-ASXL1 bound to chromatosome

EntireName: Cryo-EM structure of BAP1-ASXL1 bound to chromatosome
Components
  • Complex: Cryo-EM structure of BAP1-ASXL1 bound to chromatosome
    • Protein or peptide: Histone H3.1
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2A type 1-D
    • Protein or peptide: Histone H2B type 2-E
    • DNA: DNA (187-MER)
    • DNA: DNA (187-MER)
    • Protein or peptide: Histone H1.4
    • Protein or peptide: Ubiquitin carboxyl-terminal hydrolase BAP1
    • Protein or peptide: Ubiquitin
    • Protein or peptide: Polycomb group protein ASXL1

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Supramolecule #1: Cryo-EM structure of BAP1-ASXL1 bound to chromatosome

SupramoleculeName: Cryo-EM structure of BAP1-ASXL1 bound to chromatosome / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#10
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Histone H3.1

MacromoleculeName: Histone H3.1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 15.437167 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MARTKQTARK STGGKAPRKQ LATKAARKSA PATGGVKKPH RYRPGTVALR EIRRYQKSTE LLIRKLPFQR LVREIAQDFK TDLRFQSSA VMALQEACEA YLVGLFEDTN LCAIHAKRVT IMPKDIQLAR RIRGERA

UniProtKB: Histone H3.1

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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: Homo sapiens (human)
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-D

MacromoleculeName: Histone H2A type 1-D / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 14.137537 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSGRGKQGGK ARAKAKTRSS RAGLQFPVGR VHRLLRKGNY SERVGAGAPV YLAAVLEYLT AEILELAGNA ARDNKKTRII PRHLQLAIR NDEELNKLLG KVTIAQGGVL PNIQAVLLPK KTESHHKAKG K

UniProtKB: Histone H2A type 1-D

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Macromolecule #4: Histone H2B type 2-E

MacromoleculeName: Histone H2B type 2-E / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.951239 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MPEPAKSAPA PKKGSKKAVT KAQKKDGKKR KRSRKESYSI YVYKVLKQVH PDTGISSKAM GIMNSFVNDI FERIAGEASR LAHYNKRST ITSREIQTAV RLLLPGELAK HAVSEGTKAV TKYTSSK

UniProtKB: Histone H2B type 2-E

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Macromolecule #7: Histone H1.4

MacromoleculeName: Histone H1.4 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.190926 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGMSETAPAA PAAPAPAEKT PVKKKARKSA GAAKRKASGP PVSELITKAV AASKERSGVS LAALKKALAA AGYDVEKNNS RIKLGLKSL VSKGTLVQTK GTGASGSFKL NKKAASGEAK PKAKKAGAAK AKKPAGAAKK PKKATGAATP KKSAKKTPKK A KKPAAAAG ...String:
MGMSETAPAA PAAPAPAEKT PVKKKARKSA GAAKRKASGP PVSELITKAV AASKERSGVS LAALKKALAA AGYDVEKNNS RIKLGLKSL VSKGTLVQTK GTGASGSFKL NKKAASGEAK PKAKKAGAAK AKKPAGAAKK PKKATGAATP KKSAKKTPKK A KKPAAAAG AKKAKSPKKA KAAKPKKAPK SPAKAKAVKP KAAKPKTAKP KAAKPKKAAA KKKLEHHHHH H

UniProtKB: Histone H1.4

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Macromolecule #8: Ubiquitin carboxyl-terminal hydrolase BAP1

MacromoleculeName: Ubiquitin carboxyl-terminal hydrolase BAP1 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO / EC number: ubiquitinyl hydrolase 1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 80.456555 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MNKGWLELES DPGLFTLLVE DFGVKGVQVE EIYDLQSKCQ GPVYGFIFLF KWIEERRSRR KVSTLVDDTS VIDDDIVNNM FFAHQLIPN SSATHALLSV LLNCSSVDLG PTLSRMKDFT KGFSPESKGY AIGNAPELAK AHNSHARPEP RHLPEKQNGL S AVRTMEAF ...String:
MNKGWLELES DPGLFTLLVE DFGVKGVQVE EIYDLQSKCQ GPVYGFIFLF KWIEERRSRR KVSTLVDDTS VIDDDIVNNM FFAHQLIPN SSATHALLSV 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 #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: Tail fiber

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Macromolecule #10: Polycomb group protein ASXL1

MacromoleculeName: Polycomb group protein ASXL1 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 41.788602 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 QE

UniProtKB: Polycomb group protein ASXL1

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Macromolecule #5: DNA (187-MER)

MacromoleculeName: DNA (187-MER) / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 57.438527 KDa
SequenceString: (DA)(DT)(DC)(DT)(DG)(DA)(DT)(DG)(DC)(DC) (DG)(DG)(DA)(DT)(DC)(DC)(DC)(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) ...String:
(DA)(DT)(DC)(DT)(DG)(DA)(DT)(DG)(DC)(DC) (DG)(DG)(DA)(DT)(DC)(DC)(DC)(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)(DT)(DC)(DC)(DA)(DG)(DT)(DG)(DC) (DC)(DG)(DG)(DT)(DG)(DT)(DC)(DG) (DC) (DT)(DT)(DG)(DG)(DA)(DT)

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Macromolecule #6: DNA (187-MER)

MacromoleculeName: DNA (187-MER) / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 58.030969 KDa
SequenceString: (DA)(DT)(DC)(DC)(DA)(DA)(DG)(DC)(DG)(DA) (DC)(DA)(DC)(DC)(DG)(DG)(DC)(DA)(DC)(DT) (DG)(DG)(DA)(DA)(DC)(DA)(DG)(DG)(DA) (DT)(DG)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DG) (DT) (DG)(DA)(DC)(DA)(DC)(DG) ...String:
(DA)(DT)(DC)(DC)(DA)(DA)(DG)(DC)(DG)(DA) (DC)(DA)(DC)(DC)(DG)(DG)(DC)(DA)(DC)(DT) (DG)(DG)(DA)(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)(DG)(DG) (DG)(DA)(DT)(DC)(DC)(DG)(DG)(DC) (DA) (DT)(DC)(DA)(DG)(DA)(DT)

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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: 8
GridModel: Quantifoil R2/1 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 284 K

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.5 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software: (Name: cryoSPARC (ver. 3.2), RELION (ver. 3.0.8)) / Number images used: 95225
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL
Output model

PDB-8h1t:
Cryo-EM structure of BAP1-ASXL1 bound to chromatosome

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Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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