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- PDB-6lth: Structure of human BAF Base module -

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Entry
Database: PDB / ID: 6lth
TitleStructure of human BAF Base module
Components
  • (SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily ...) x 3
  • AT-rich interactive domain-containing protein 1A
  • SWI/SNF complex subunit SMARCC2
  • Transcription activator BRG1
  • Zinc finger protein ubi-d4
KeywordsGENE REGULATION / Chromatin remodeler / Complex
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 glucose mediated signaling pathway / H3K9me3 modified histone binding / nuclear receptor-mediated glucocorticoid signaling pathway / blastocyst hatching / bBAF complex / negative regulation of androgen receptor signaling pathway / npBAF complex / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I ...negative regulation of myeloid progenitor cell differentiation / single stranded viral RNA replication via double stranded DNA intermediate / positive regulation of glucose mediated signaling pathway / H3K9me3 modified histone binding / nuclear receptor-mediated glucocorticoid signaling pathway / blastocyst hatching / bBAF complex / negative regulation of androgen receptor signaling pathway / npBAF complex / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / nBAF complex / brahma complex / Tat protein binding / GBAF complex / regulation of G0 to G1 transition / neural retina development / EGR2 and SOX10-mediated initiation of Schwann cell myelination / hepatocyte differentiation / regulation of nucleotide-excision repair / XY body / RSC-type complex / RNA polymerase I preinitiation complex assembly / Regulation of MITF-M-dependent genes involved in pigmentation / N-acetyltransferase activity / positive regulation by host of viral transcription / regulation of mitotic metaphase/anaphase transition / SWI/SNF complex / nucleosome disassembly / ATP-dependent chromatin remodeler activity / germ cell nucleus / positive regulation of double-strand break repair / 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 / estrogen receptor signaling pathway / positive regulation of myoblast differentiation / ATP-dependent activity, acting on DNA / neurogenesis / Chromatin modifying enzymes / DNA polymerase binding / transcription coregulator activity / lysine-acetylated histone binding / transcription coregulator binding / Interleukin-7 signaling / transcription initiation-coupled chromatin remodeling / positive regulation of miRNA transcription / helicase activity / nuclear receptor binding / positive regulation of cell differentiation / apoptotic signaling pathway / Formation of the beta-catenin:TCF transactivating complex / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / positive regulation of DNA-binding transcription factor activity / negative regulation of cell growth / p53 binding / RMTs methylate histone arginines / kinetochore / fibrillar center / nuclear matrix / DNA integration / transcription corepressor activity / nervous system development / positive regulation of cold-induced thermogenesis / histone binding / transcription coactivator activity / molecular adaptor activity / chromatin remodeling / hydrolase activity / negative regulation of cell population proliferation / intracellular membrane-bounded organelle / signaling receptor binding / negative regulation of DNA-templated transcription / chromatin binding / centrosome / positive regulation of cell population proliferation / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / chromatin / nucleolus / apoptotic process / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / RNA binding / extracellular space / nucleoplasm / ATP binding / identical protein binding / membrane / nucleus / metal ion binding / cytosol
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 / Glutamine-Leucine-Glutamine, QLQ / QLQ / QLQ domain profile. / QLQ / domain in helicases and associated with SANT domains / 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 / 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 / SWIRM domain / SWIRM domain / SWIRM domain profile. / SWIB/MDM2 domain / SWIB/MDM2 domain / SWIB/MDM2 domain profile. / SWIB/MDM2 domain superfamily / SANT domain profile. / SANT domain / HMG (high mobility group) box / Chromo/chromo shadow domain / : / Chromatin organization modifier domain / HMG boxes A and B DNA-binding domains profile. / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / high mobility group / High mobility group box domain / High mobility group box domain superfamily / Myb-like DNA-binding domain / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SANT/Myb domain / zinc finger / Zinc finger C2H2 type domain profile. / BRCT domain superfamily / Zinc finger C2H2 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 / Zinc finger, PHD-type / PHD zinc finger / Helicase conserved C-terminal domain / Bromodomain, conserved site / Bromodomain signature. / Homeobox-like domain superfamily / Zinc finger, FYVE/PHD-type / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Bromodomain / 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 / Armadillo-type fold / Zinc finger, RING/FYVE/PHD-type / Winged helix-like DNA-binding domain superfamily
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å
AuthorsHe, S. / Wu, Z. / Tian, Y. / Yu, Z. / Yu, J. / Wang, X. / Li, J. / Liu, B. / Xu, Y.
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 22, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 12, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 25, 2021Group: Database references / Structure summary
Category: audit_author / citation ...audit_author / citation / citation_author / database_2
Item: _audit_author.name / _citation.journal_volume ..._audit_author.name / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 13, 2021Group: Database references / Category: citation_author / Item: _citation_author.identifier_ORCID
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

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Assembly

Deposited unit
I: Transcription activator BRG1
L: AT-rich interactive domain-containing protein 1A
M: SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1
N: SWI/SNF complex subunit SMARCC2
O: SWI/SNF complex subunit SMARCC2
P: SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1
Q: SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1
R: Zinc finger protein ubi-d4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)886,7799
Polymers886,7148
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: cross-linking
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area55610 Å2
ΔGint-360 kcal/mol
Surface area83310 Å2

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Components

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Protein , 4 types, 5 molecules ILNOR

#1: Protein Transcription activator BRG1 / ATP-dependent helicase SMARCA4 / BRG1-associated factor 190A / BAF190A / Mitotic growth and ...ATP-dependent helicase SMARCA4 / BRG1-associated factor 190A / BAF190A / Mitotic growth and transcription activator / Protein BRG-1 / Protein brahma homolog 1 / SNF2-beta / SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 4


Mass: 184923.828 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SMARCA4 / Cell line (production host): HEK293T / Production host: Homo sapiens (human)
References: UniProt: P51532, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
#2: Protein AT-rich interactive domain-containing protein 1A / ARID domain-containing protein 1A


Mass: 242250.312 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ARID1A / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: O14497
#4: Protein SWI/SNF complex subunit SMARCC2 / BRG1-associated factor 170 / BAF170 / SWI/SNF complex 170 kDa subunit / SWI/SNF-related matrix- ...BRG1-associated factor 170 / BAF170 / SWI/SNF complex 170 kDa subunit / SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily C member 2


Mass: 133048.109 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SMARCC2 / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: Q8TAQ2
#7: Protein Zinc finger protein ubi-d4


Mass: 44222.547 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DPF2 / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: Q92785

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SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily ... , 3 types, 3 molecules MPQ

#3: Protein SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1


Mass: 44199.188 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SMARCB1 / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: Q12824
#5: Protein SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1


Mass: 58311.391 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SMARCD1 / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: Q96GM5
#6: Protein SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1


Mass: 46710.371 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SMARCE1 / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: Q969G3

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Non-polymers , 1 types, 1 molecules

#8: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Structure of human BAF Base module / Type: COMPLEX / Entity ID: #1-#7 / Source: RECOMBINANT
Molecular weightUnits: KILODALTONS/NANOMETER / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human) / Cell: HEK293T
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: OTHER
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 50 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
EM imaging opticsEnergyfilter slit width: 20 eV
Image scansMovie frames/image: 32 / Used frames/image: 1-32

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Processing

SoftwareName: PHENIX / Version: 1.16_3549: / Classification: refinement
EM software
IDNameVersionCategory
2SerialEMimage acquisition
4Gctf1.06CTF correction
7UCSF Chimera1.13model fitting
9cryoSPARC2.12.4initial Euler assignment
10RELION3.0.8final Euler assignment
11RELION3.0.8classification
12cryoSPARC2.12.43D reconstruction
13PHENIX1.16model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 197606 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00515266
ELECTRON MICROSCOPYf_angle_d0.66420605
ELECTRON MICROSCOPYf_dihedral_angle_d9.2239418
ELECTRON MICROSCOPYf_chiral_restr0.0432302
ELECTRON MICROSCOPYf_plane_restr0.0052653

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