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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 CDH1 Gene Transcription / positive regulation of glucose mediated signaling pathway / bBAF complex / nBAF complex / npBAF complex / brahma complex / perichromatin fibrils / negative regulation of androgen receptor signaling pathway ...negative regulation of myeloid progenitor cell differentiation / single stranded viral RNA replication via double stranded DNA intermediate / Positive Regulation of CDH1 Gene Transcription / positive regulation of glucose mediated signaling pathway / bBAF complex / nBAF complex / npBAF complex / brahma complex / perichromatin fibrils / negative regulation of androgen receptor signaling pathway / GBAF complex / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / neural retina development / N-acetyltransferase activity / Formation of the embryonic stem cell BAF (esBAF) complex / EGR2 and SOX10-mediated initiation of Schwann cell myelination / Formation of the canonical BAF (cBAF) complex / RSC-type complex / XY body / Formation of the polybromo-BAF (pBAF) complex / Formation of neuronal progenitor and neuronal BAF (npBAF and nBAF) / Formation of the non-canonical BAF (ncBAF) complex / histone H3K14ac reader activity / regulation of G0 to G1 transition / RNA polymerase I preinitiation complex assembly / Tat protein binding / cellular response to fatty acid / host-mediated activation of viral transcription / SWI/SNF complex / nucleosome disassembly / ATP-dependent chromatin remodeler activity / positive regulation of T cell differentiation / regulation of mitotic metaphase/anaphase transition / nuclear androgen receptor binding / regulation of nucleotide-excision repair / nuclear chromosome / positive regulation of stem cell population maintenance / lncRNA binding / positive regulation of double-strand break repair / Regulation of MITF-M-dependent genes involved in pigmentation / negative regulation of cell differentiation / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / Differentiation of naive CD4+ T cells to T helper 2 cells (Th2 cells) / histone H4K16ac reader activity / positive regulation of myoblast differentiation / ATP-dependent activity, acting on DNA / positive regulation of Wnt signaling pathway / positive regulation of signal transduction by p53 class mediator / regulation of G1/S transition of mitotic cell cycle / Chromatin modifying enzymes / DNA polymerase binding / helicase activity / apoptotic signaling pathway / Interleukin-7 signaling / nuclear receptor binding / transcription initiation-coupled chromatin remodeling / transcription coregulator binding / positive regulation of cell differentiation / DNA integration / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / euchromatin / negative regulation of cell growth / positive regulation of miRNA transcription / Negative Regulation of CDH1 Gene Transcription / fibrillar center / Formation of the beta-catenin:TCF transactivating complex / kinetochore / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / transcription coregulator activity / nuclear matrix / RMTs methylate histone arginines / p53 binding / transcription corepressor activity / nervous system development / positive regulation of cold-induced thermogenesis / histone binding / molecular adaptor activity / transcription coactivator activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin remodeling / apoptotic process / signaling receptor binding / negative regulation of DNA-templated transcription / chromatin binding / positive regulation of cell population proliferation / regulation of transcription by RNA polymerase II / nucleolus / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / chromatin / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / ATP hydrolysis activity / protein-containing complex / DNA binding / RNA binding / nucleoplasm / extracellular region / ATP binding / membrane
Similarity search - Function
SWI/SNF-like complex subunit BAF250a / SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1 / SWI/SNF-like complex subunit BAF250/Osa / SWI/SNF-like complex subunit BAF250, C-terminal / SWI/SNF-like complex subunit BAF250/Osa / DPF1-3, N-terminal domain / DPF1-3, N-terminal / SMARCC, SWIRM-associated domain / SMARCC, N-terminal / : ...SWI/SNF-like complex subunit BAF250a / SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1 / SWI/SNF-like complex subunit BAF250/Osa / SWI/SNF-like complex subunit BAF250, C-terminal / SWI/SNF-like complex subunit BAF250/Osa / DPF1-3, N-terminal domain / DPF1-3, N-terminal / SMARCC, SWIRM-associated domain / SMARCC, 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 / SWIB domain / SWI complex, BAF60b domains / Chromatin-remodeling complex component Sfh1/SNF5 / : / SWIFT domain / SWI/SNF complex subunit BRG1 / 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 / QLQ / Glutamine-Leucine-Glutamine, QLQ / QLQ domain profile. / QLQ / Snf2-ATP coupling, chromatin remodelling complex / Snf2, ATP coupling domain / Snf2-ATP coupling, chromatin remodelling complex / domain in helicases and associated with SANT domains / 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 / ARID/BRIGHT DNA binding domain / SWIRM domain / SWIRM domain / SWIRM domain profile. / HSA domain / SWIB/MDM2 domain / SWIB/MDM2 domain / SWIB/MDM2 domain profile. / Helicase/SANT-associated domain / HSA domain profile. / SWIB/MDM2 domain superfamily / HMG (high mobility group) box / SANT domain profile. / Chromo/chromo shadow domain / SANT domain / Chromatin organization modifier domain / HMG boxes A and B DNA-binding domains profile. / high mobility group / High mobility group box domain / High mobility group box domain superfamily / Myb-like DNA-binding domain / : / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SANT/Myb domain / zinc finger / BRCT domain superfamily / PHD-finger / Zinc finger C2H2 type domain profile. / Zinc finger PHD-type signature. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / Zinc finger PHD-type profile. / Zinc finger C2H2-type / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / Homeobox-like domain superfamily / Helicase conserved C-terminal domain / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily / Armadillo-like helical / 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 / Zinc finger, RING/FYVE/PHD-type / Armadillo-type fold
Similarity search - Domain/homology
AT-rich interactive domain-containing protein 1A / SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 4 / 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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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
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)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 512 pix.
= 532.48 Å		1.04 Å/pix.
x 512 pix.
= 532.48 Å		1.04 Å/pix.
x 512 pix.
= 532.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.04 Å
Density

Histogram

Histogram (log scale)
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
Specialist opticsEnergy filter - Slit width: 20 eV
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
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: OTHER
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: Gctf (ver. 1.06)
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
Initial angle assignmentType: OTHER / Software - Name: cryoSPARC (ver. 2.12.4)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0.8)

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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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