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- EMDB-0968: Structure of human BAF Base module -

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Basic information

Entry
Database: EMDB / ID: EMD-0968
TitleStructure of human BAF Base module
Map data
Sample
  • Complex: Structure of nucleosome-bound human BAF Base module
Function / homology
Function and homology information


negative regulation of myeloid progenitor cell differentiation / single stranded viral RNA replication via double stranded DNA intermediate / positive regulation of pseudohyphal growth by positive regulation of transcription from RNA polymerase II promoter / positive regulation of glucose mediated signaling pathway / H3K9me3 modified histone binding / glucocorticoid receptor signaling pathway / blastocyst hatching / bBAF complex / npBAF complex / brahma complex ...negative regulation of myeloid progenitor cell differentiation / single stranded viral RNA replication via double stranded DNA intermediate / positive regulation of pseudohyphal growth by positive regulation of transcription from RNA polymerase II promoter / positive regulation of glucose mediated signaling pathway / H3K9me3 modified histone binding / glucocorticoid receptor signaling pathway / blastocyst hatching / bBAF complex / npBAF complex / brahma complex / nBAF complex / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / negative regulation of androgen receptor signaling pathway / neural retina development / GBAF complex / regulation of G0 to G1 transition / Tat protein binding / XY body / nucleosome disassembly / EGR2 and SOX10-mediated initiation of Schwann cell myelination / regulation of nucleotide-excision repair / RSC-type complex / hepatocyte differentiation / RNA polymerase I preinitiation complex assembly / N-acetyltransferase activity / positive regulation by host of viral transcription / SWI/SNF complex / ATP-dependent chromatin remodeler activity / regulation of mitotic metaphase/anaphase transition / positive regulation of double-strand break repair / germ cell nucleus / positive regulation of T cell differentiation / cellular response to fatty acid / nuclear androgen receptor binding / nuclear chromosome / positive regulation of stem cell population maintenance / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / androgen receptor signaling pathway / regulation of G1/S transition of mitotic cell cycle / negative regulation of cell differentiation / positive regulation of Wnt signaling pathway / positive regulation of myoblast differentiation / intracellular estrogen receptor signaling pathway / ATP-dependent activity, acting on DNA / Chromatin modifying enzymes / DNA polymerase binding / transcription initiation-coupled chromatin remodeling / Interleukin-7 signaling / neurogenesis / helicase activity / apoptotic signaling pathway / transcription coregulator binding / nuclear receptor binding / positive regulation of cell differentiation / transcription coregulator activity / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / Formation of the beta-catenin:TCF transactivating complex / lysine-acetylated histone binding / negative regulation of cell growth / kinetochore / fibrillar center / RMTs methylate histone arginines / nuclear matrix / positive regulation of miRNA transcription / DNA integration / transcription corepressor activity / positive regulation of DNA-binding transcription factor activity / p53 binding / nervous system development / positive regulation of cold-induced thermogenesis / histone binding / transcription coactivator activity / molecular adaptor activity / hydrolase activity / chromatin remodeling / cell cycle / negative regulation of cell population proliferation / signaling receptor binding / intracellular membrane-bounded organelle / centrosome / negative regulation of DNA-templated transcription / apoptotic process / chromatin binding / positive regulation of cell population proliferation / chromatin / nucleolus / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / extracellular space / RNA binding / nucleoplasm / ATP binding / membrane / identical protein binding / metal ion binding / nucleus
Similarity search - Function
SWI/SNF-like complex subunit BAF250a / SWI/SNF-like complex subunit BAF250/Osa / SWI/SNF-like complex subunit BAF250, C-terminal / SWI/SNF-like complex subunit BAF250/Osa / SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1 / SWIB domain / SWI complex, BAF60b domains / DPF1-3, N-terminal domain / SMARCC, SWIRM-associated domain / SMARCC, N-terminal ...SWI/SNF-like complex subunit BAF250a / SWI/SNF-like complex subunit BAF250/Osa / SWI/SNF-like complex subunit BAF250, C-terminal / SWI/SNF-like complex subunit BAF250/Osa / SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1 / SWIB domain / SWI complex, BAF60b domains / DPF1-3, N-terminal domain / SMARCC, SWIRM-associated domain / SMARCC, N-terminal / DPF1-3, N-terminal / SWIRM-associated domain at the N-terminal / SWIRM-associated domain at the C-terminal / MarR-like, BRCT and chromo domains module profile. / : / SWI/SNF Subunit INI1, DNA binding domain / SWI/SNF complex subunit BRG1 / Chromatin-remodeling complex component Sfh1/SNF5 / SMARCC, C-terminal / SWIRM-associated region 1 / SNF5/SMARCB1/INI1 / SNF5 / SMARCB1 / INI1 / BRK domain / BRK domain / BRK domain superfamily / domain in transcription and CHROMO domain helicases / domain in helicases and associated with SANT domains / Glutamine-Leucine-Glutamine, QLQ / QLQ / QLQ domain profile. / QLQ / Snf2, ATP coupling domain / Snf2-ATP coupling, chromatin remodelling complex / Snf2-ATP coupling, chromatin remodelling complex / HSA domain / Helicase/SANT-associated domain / HSA domain profile. / ARID/BRIGHT DNA binding domain / SWIRM domain / SWIRM domain / SWIRM domain profile. / ARID DNA-binding domain / ARID DNA-binding domain superfamily / ARID/BRIGHT DNA binding domain / ARID domain profile. / BRIGHT, ARID (A/T-rich interaction domain) domain / SWIB/MDM2 domain / SWIB/MDM2 domain / SWIB/MDM2 domain profile. / : / SANT domain profile. / SWIB/MDM2 domain superfamily / SANT domain / Chromo/chromo shadow domain / Chromatin organization modifier domain / HMG (high mobility group) box / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / HMG boxes A and B DNA-binding domains profile. / Myb-like DNA-binding domain / high mobility group / High mobility group box domain / High mobility group box domain superfamily / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SANT/Myb domain / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / BRCT domain superfamily / PHD-finger / Zinc finger C2H2 type domain signature. / Zinc finger PHD-type signature. / Zinc finger C2H2-type / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Helicase conserved C-terminal domain / Zinc finger, PHD-type / PHD zinc finger / Homeobox-like domain superfamily / Zinc finger, FYVE/PHD-type / Armadillo-like helical / Bromodomain, conserved site / Bromodomain signature. / helicase superfamily c-terminal domain / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / 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 / Armadillo-type fold / Zinc finger, RING/FYVE/PHD-type / Winged helix-like DNA-binding domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
AT-rich interactive domain-containing protein 1A / Transcription activator BRG1 / SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1 / SWI/SNF complex subunit SMARCC2 / Zinc finger protein ubi-d4 / SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1 / SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsShuang H / Zihan W / Yuan T / Zishuo Y / Jiali Y / Xinxin W / Jie L / Bijun L / Yanhui X
CitationJournal: Science / Year: 2020
Title: Structure of nucleosome-bound human BAF complex.
Authors: Shuang He / Zihan Wu / Yuan Tian / Zishuo Yu / Jiali Yu / Xinxin Wang / Jie Li / Bijun Liu / Yanhui Xu /
Abstract: Mammalian SWI/SNF family chromatin remodelers, BRG1/BRM-associated factor (BAF) and polybromo-associated BAF (PBAF), regulate chromatin structure and transcription, and their mutations are linked to ...Mammalian SWI/SNF family chromatin remodelers, BRG1/BRM-associated factor (BAF) and polybromo-associated BAF (PBAF), regulate chromatin structure and transcription, and their mutations are linked to cancers. The 3.7-angstrom-resolution cryo-electron microscopy structure of human BAF bound to the nucleosome reveals that the nucleosome is sandwiched by the base and the adenosine triphosphatase (ATPase) modules, which are bridged by the actin-related protein (ARP) module. The ATPase motor is positioned proximal to nucleosomal DNA and, upon ATP hydrolysis, engages with and pumps DNA along the nucleosome. The C-terminal α helix of SMARCB1, enriched in positively charged residues frequently mutated in cancers, mediates interactions with an acidic patch of the nucleosome. AT-rich interactive domain-containing protein 1A (ARID1A) and the SWI/SNF complex subunit SMARCC serve as a structural core and scaffold in the base module organization, respectively. Our study provides structural insights into subunit organization and nucleosome recognition of human BAF complex.
History
DepositionJan 21, 2020-
Header (metadata) releaseFeb 12, 2020-
Map releaseFeb 12, 2020-
UpdateAug 11, 2021-
Current statusAug 11, 2021Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1
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  • Surface view colored by radius
  • Surface level: 1
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  • Surface view with fitted model
  • Atomic models: PDB-6lth
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Structure viewerEM map:
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Supplemental images

emd_0968.png

Downloads & links

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Map

FileDownload / File: emd_0968.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.04 Å
Density
Contour LevelBy AUTHOR: 1.0 / Movie #1: 1
Minimum - Maximum-2.3567643 - 4.937579
Average (Standard dev.)0.0014853961 (±0.045854725)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 532.48 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.041.041.04
M x/y/z512512512
origin x/y/z0.0000.0000.000
length x/y/z532.480532.480532.480
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS512512512
D min/max/mean-2.3574.9380.001

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Supplemental data

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Sample components

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Entire : Structure of nucleosome-bound human BAF Base module

EntireName: Structure of nucleosome-bound human BAF Base module
Components
  • Complex: Structure of nucleosome-bound human BAF Base module

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Supramolecule #1: Structure of nucleosome-bound human BAF Base module

SupramoleculeName: Structure of nucleosome-bound human BAF Base module / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#20
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: HEK293T

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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 R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING
VitrificationCryogen name: ETHANE / Chamber humidity: 100 %

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: OTHER
Specialist opticsEnergy filter - Slit width: 20 eV
Sample stageCooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Frames/image: 1-32 / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: Gctf (ver. 1.06)
Initial angle assignmentType: OTHER / Software - Name: cryoSPARC (ver. 2.12.4)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0.8)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2.12.4) / Number images used: 197606

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-6lth:
Structure of human BAF Base module

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