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- PDB-9rl4: Structure of BAF in complex with OCT4-SOX2-bound nucleosome - SHL-6 -

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Basic information

Entry
Database: PDB / ID: 9rl4
TitleStructure of BAF in complex with OCT4-SOX2-bound nucleosome - SHL-6
Components
  • (DNA (148-MER)) x 2
  • (SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily ...) x 3
  • (Transcription ...) x 2
  • AT-rich interactive domain-containing protein 1A
  • Actin, cytoplasmic 1, N-terminally processed
  • Actin-like protein 6A
  • Green fluorescent protein,POU domain, class 5, transcription factor 1
  • Histone H2A type 1-B/E
  • Histone H2B type 1-J
  • Histone H3.1
  • Histone H4
  • SWI/SNF complex subunit SMARCC2
  • Zinc finger protein ubi-d4
KeywordsGENE REGULATION / remodelling / chromatin / transcription
Function / homology
Function and homology information


negative regulation of myeloid progenitor cell differentiation / glial cell fate commitment / single stranded viral RNA replication via double stranded DNA intermediate / Formation of the posterior neural plate / cell fate commitment involved in formation of primary germ layer / cardiac cell fate determination / POU5F1 (OCT4), SOX2, NANOG repress genes related to differentiation / Formation of the anterior neural plate / Positive Regulation of CDH1 Gene Transcription / endodermal-mesodermal cell signaling ...negative regulation of myeloid progenitor cell differentiation / glial cell fate commitment / single stranded viral RNA replication via double stranded DNA intermediate / Formation of the posterior neural plate / cell fate commitment involved in formation of primary germ layer / cardiac cell fate determination / POU5F1 (OCT4), SOX2, NANOG repress genes related to differentiation / Formation of the anterior neural plate / Positive Regulation of CDH1 Gene Transcription / endodermal-mesodermal cell signaling / regulation of asymmetric cell division / endodermal cell fate specification / positive regulation of glucose mediated signaling pathway / pituitary gland development / blastocyst development / heart induction / bBAF complex / negative regulation of cell cycle G1/S phase transition / POU5F1 (OCT4), SOX2, NANOG activate genes related to proliferation / Specification of the neural plate border / neuronal stem cell population maintenance / Specification of primordial germ cells / nBAF complex / Regulation of MITF-M-dependent genes involved in extracellular matrix, focal adhesion and epithelial-to-mesenchymal transition / npBAF complex / brahma complex / positive regulation of norepinephrine uptake / positive regulation of telomere maintenance in response to DNA damage / Transcriptional regulation of pluripotent stem cells / regulation of DNA strand elongation / perichromatin fibrils / negative regulation of androgen receptor signaling pathway / GBAF complex / Transcriptional Regulation by MECP2 / Germ layer formation at gastrulation / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / eye development / N-acetyltransferase activity / cellular response to cytochalasin B / neural retina development / Formation of the embryonic stem cell BAF (esBAF) complex / EGR2 and SOX10-mediated initiation of Schwann cell myelination / response to growth factor / regulation of transepithelial transport / Formation of the canonical BAF (cBAF) complex / morphogenesis of a polarized epithelium / RSC-type complex / Formation of annular gap junctions / XY body / Formation of the dystrophin-glycoprotein complex (DGC) / Formation of the polybromo-BAF (pBAF) complex / somatic stem cell population maintenance / structural constituent of postsynaptic actin cytoskeleton / Gap junction degradation / GBP-mediated host defense / Formation of neuronal progenitor and neuronal BAF (npBAF and nBAF) / protein localization to adherens junction / Formation of the non-canonical BAF (ncBAF) complex / Cell-extracellular matrix interactions / regulation of G0 to G1 transition / histone H3K14ac reader activity / dense body / Tat protein binding / RNA polymerase I preinitiation complex assembly / Folding of actin by CCT/TriC / cellular response to fatty acid / Regulation of CDH1 Function / Ino80 complex / postsynaptic actin cytoskeleton / host-mediated activation of viral transcription / forebrain development / apical protein localization / Adherens junctions interactions / Prefoldin mediated transfer of substrate to CCT/TriC / microtubule nucleation / RHOF GTPase cycle / adherens junction assembly / regulation of double-strand break repair / SWI/SNF complex / Sensory processing of sound by outer hair cells of the cochlea / nucleosome disassembly / negative regulation of neuron differentiation / ATP-dependent chromatin remodeler activity / miRNA binding / spinal cord development / tight junction / positive regulation of T cell differentiation / regulation of mitotic metaphase/anaphase transition / Sensory processing of sound by inner hair cells of the cochlea / nuclear androgen receptor binding / maintenance of blood-brain barrier / Interaction between L1 and Ankyrins / apical junction complex / inner ear development / regulation of nucleotide-excision repair / nuclear chromosome / positive regulation of stem cell population maintenance / NuA4 histone acetyltransferase complex / regulation of chromosome organization / regulation of norepinephrine uptake
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 / Transcription factor SOX / 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 / Transcription factor SOX / SMARCC, SWIRM-associated domain / SMARCC, N-terminal / : / SOX transcription factor / 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 / : / POU-specific domain / POU domain / Pou domain - N-terminal to homeobox domain / POU-specific (POUs) domain signature 1. / POU-specific (POUs) domain signature 2. / POU-specific (POUs) domain profile. / Found in Pit-Oct-Unc transcription factors / : / 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 / Homeobox, conserved site / SWIB/MDM2 domain / SWIB/MDM2 domain / SWIB/MDM2 domain profile. / 'Homeobox' domain signature. / Helicase/SANT-associated domain / HSA domain profile. / SWIB/MDM2 domain superfamily / Homeodomain / 'Homeobox' domain profile. / Homeodomain / Homeobox domain / HMG (high mobility group) box / SANT domain profile. / Chromo/chromo shadow domain / Chromatin organization modifier domain / SANT 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 / Lambda repressor-like, DNA-binding domain superfamily / SNF2, N-terminal / SNF2-related domain / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SANT/Myb domain / zinc finger / PHD-finger / BRCT domain superfamily / Zinc finger C2H2 type domain profile. / Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Zinc finger PHD-type signature. / Zinc finger C2H2 superfamily / Green fluorescent protein, GFP / Zinc finger C2H2 type domain signature.
Similarity search - Domain/homology
PENTANEDIAL / DNA / DNA (> 10) / DNA (> 100) / AT-rich interactive domain-containing protein 1A / Actin-like protein 6A / Histone H2A type 1-B/E / Histone H2B type 1-J / Green fluorescent protein / Transcription factor SOX-2 ...PENTANEDIAL / DNA / DNA (> 10) / DNA (> 100) / AT-rich interactive domain-containing protein 1A / Actin-like protein 6A / Histone H2A type 1-B/E / Histone H2B type 1-J / Green fluorescent protein / Transcription factor SOX-2 / SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 4 / Actin, cytoplasmic 1 / Histone H4 / Histone H3.1 / POU domain, class 5, transcription factor 1 / 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)
Aequorea victoria (jellyfish)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsVecchia, L. / Weiss, J. / Cavadini, S. / Kempf, G. / Kater, L. / Pathare, G. / Thoma, N.H.
Funding supportEuropean Union, Switzerland, 5items
OrganizationGrant numberCountry
European Research Council (ERC)European Union
Swiss National Science Foundation Switzerland
European Molecular Biology Organization (EMBO)European Union
Other private
Other private
CitationJournal: Mol Cell / Year: 2026
Title: The human BAF chromatin remodeler processes nucleosomes bound by pioneer transcription factors OCT4-SOX2.
Authors: Joscha Weiss / Luca Vecchia / David Domjan / Simone Cavadini / Anton Sabantsev / Georg Kempf / Ganesh R Pathare / Klaus Brackmann / Alicia K Michael / Lukas Kater / Eric Hietter-Pfeiffer / ...Authors: Joscha Weiss / Luca Vecchia / David Domjan / Simone Cavadini / Anton Sabantsev / Georg Kempf / Ganesh R Pathare / Klaus Brackmann / Alicia K Michael / Lukas Kater / Eric Hietter-Pfeiffer / Mina Haddawi / Urja P Kuber / Sandra Mühlhäusser / Ralph S Grand / Michael B Stadler / Sebastian Deindl / Nicolas H Thomä /
Abstract: Chromatin remodeling complexes mobilize nucleosomes and promote transcription factor (TF) binding. Using ensemble and single-molecule assays combined with cryo-electron microscopy (cryo-EM), we ...Chromatin remodeling complexes mobilize nucleosomes and promote transcription factor (TF) binding. Using ensemble and single-molecule assays combined with cryo-electron microscopy (cryo-EM), we studied the interaction between pioneer TFs OCT4-SOX2 and the human BRG1/BRM-associated factor (BAF) complex on nucleosomes. BAF engages TF-bound substrates in two orientations, placing OCT4-SOX2 at either the remodeler ENTRY or EXIT site. At the ENTRY site, OCT4-SOX2 initially coexists with BAF without structural interference. However, continued DNA translocation is expected to cause collisions with bound TFs, which can trigger remodeling direction reversals or may induce TF dissociation. To accommodate TFs at the EXIT site, BAF undergoes structural rearrangements, and ensemble assays reveal a nucleosome subpopulation translocating away from TF-binding sites. Moreover, single-molecule experiments show that nucleosome-bound BAF frequently changes remodeling direction, and we identify an ADP-bound remodeler conformation as a potential intermediate. Together, these findings reveal key aspects of the conformational dynamics and remodeling outcomes underlying BAF processing of TF-bound nucleosomes.
History
DepositionJun 16, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 11, 2026Provider: repository / Type: Initial release
Revision 1.0Feb 11, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Feb 11, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histone H3.1
B: Histone H4
C: Histone H2A type 1-B/E
D: Histone H2B type 1-J
E: Histone H3.1
F: Histone H4
G: Histone H2A type 1-B/E
H: Histone H2B type 1-J
I: Transcription activator BRG1
J: Actin-like protein 6A
K: Actin, cytoplasmic 1, N-terminally processed
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
V: Green fluorescent protein,POU domain, class 5, transcription factor 1
W: Transcription factor SOX-2
X: DNA (148-MER)
Y: DNA (148-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,317,50339
Polymers1,315,83622
Non-polymers1,66717
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein , 10 types, 15 molecules AEBFCGDHJKLNORV

#1: Protein Histone H3.1 / Histone H3/a / Histone H3/b / Histone H3/c / Histone H3/d / Histone H3/f / Histone H3/h / Histone ...Histone H3/a / Histone H3/b / Histone H3/c / Histone H3/d / Histone H3/f / Histone H3/h / Histone H3/i / Histone H3/j / Histone H3/k / Histone H3/l


Mass: 15719.445 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: HIST1H3A, H3FA, HIST1H3B, H3FL, HIST1H3C, H3FC, HIST1H3D, H3FB, HIST1H3E, H3FD, HIST1H3F, H3FI, HIST1H3G, H3FH, HIST1H3H, H3FK, HIST1H3I, H3FF, HIST1H3J, H3FJ
Production host: Escherichia coli (E. coli) / References: UniProt: P68431
#2: Protein Histone H4


Mass: 11676.703 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: HIST1H4A, H4/A, H4FA, HIST1H4B, H4/I, H4FI, HIST1H4C, H4/G, H4FG, HIST1H4D, H4/B, H4FB, HIST1H4E, H4/J, H4FJ, HIST1H4F, H4/C, H4FC, HIST1H4H, H4/H, H4FH, HIST1H4I, H4/M, H4FM, HIST1H4J, H4/E, ...Gene: HIST1H4A, H4/A, H4FA, HIST1H4B, H4/I, H4FI, HIST1H4C, H4/G, H4FG, HIST1H4D, H4/B, H4FB, HIST1H4E, H4/J, H4FJ, HIST1H4F, H4/C, H4FC, HIST1H4H, H4/H, H4FH, HIST1H4I, H4/M, H4FM, HIST1H4J, H4/E, H4FE, HIST1H4K, H4/D, H4FD, HIST1H4L, H4/K, H4FK, HIST2H4A, H4/N, H4F2, H4FN, HIST2H4, HIST2H4B, H4/O, H4FO, HIST4H4
Production host: Escherichia coli (E. coli) / References: UniProt: P62805
#3: Protein Histone H2A type 1-B/E / Histone H2A.2 / Histone H2A/a / Histone H2A/m


Mass: 14447.825 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HIST1H2AB, H2AFM, HIST1H2AE, H2AFA / Production host: Escherichia coli (E. coli) / References: UniProt: P04908
#4: Protein Histone H2B type 1-J / Histone H2B.1 / Histone H2B.r / H2B/r


Mass: 14088.336 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HIST1H2BJ, H2BFR / Production host: Escherichia coli (E. coli) / References: UniProt: P06899
#6: Protein Actin-like protein 6A / 53 kDa BRG1-associated factor A / Actin-related protein Baf53a / ArpNbeta / BRG1-associated factor ...53 kDa BRG1-associated factor A / Actin-related protein Baf53a / ArpNbeta / BRG1-associated factor 53A / BAF53A / INO80 complex subunit K


Mass: 47509.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 / References: UniProt: O96019
#7: Protein Actin, cytoplasmic 1, N-terminally processed


Mass: 41782.660 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 / References: UniProt: P60709
#8: Protein AT-rich interactive domain-containing protein 1A / ARID domain-containing protein 1A / B120 / BRG1-associated factor 250 / BAF250 / BRG1-associated ...ARID domain-containing protein 1A / B120 / BRG1-associated factor 250 / BAF250 / BRG1-associated factor 250a / BAF250A / Osa homolog 1 / hOSA1 / SWI-like protein / SWI/SNF complex protein p270 / SWI/SNF-related / matrix-associated / actin-dependent regulator of chromatin subfamily F member 1 / hELD


Mass: 242250.312 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 / References: UniProt: O14497
#10: 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 natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 / References: UniProt: Q8TAQ2
#13: Protein Zinc finger protein ubi-d4 / Apoptosis response zinc finger protein / BRG1-associated factor 45D / BAF45D / D4 / zinc and double ...Apoptosis response zinc finger protein / BRG1-associated factor 45D / BAF45D / D4 / zinc and double PHD fingers family 2 / Protein requiem


Mass: 48554.125 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DPF2, BAF45D, REQ, UBID4 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q92785
#14: Protein Green fluorescent protein,POU domain, class 5, transcription factor 1 / Octamer-binding protein 3 / Oct-3 / Octamer-binding protein 4 / Oct-4 / Octamer-binding ...Octamer-binding protein 3 / Oct-3 / Octamer-binding protein 4 / Oct-4 / Octamer-binding transcription factor 3 / OTF-3


Mass: 70735.531 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aequorea victoria (jellyfish), (gene. exp.) Homo sapiens (human)
Gene: GFP, POU5F1, OCT3, OCT4, OTF3 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P42212, UniProt: Q01860

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Transcription ... , 2 types, 2 molecules IW

#5: 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 natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293
References: UniProt: P51532, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
#15: Protein Transcription factor SOX-2


Mass: 12718.679 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SOX2 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P48431

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

#9: Protein SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1 / BRG1-associated factor 47 / BAF47 / Integrase interactor 1 protein / SNF5 homolog / hSNF5


Mass: 44199.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 / References: UniProt: Q12824
#11: Protein SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1 / 60 kDa BRG-1/Brm-associated factor subunit A / BRG1-associated factor 60A / BAF60A / SWI/SNF ...60 kDa BRG-1/Brm-associated factor subunit A / BRG1-associated factor 60A / BAF60A / SWI/SNF complex 60 kDa subunit


Mass: 58311.391 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 / References: UniProt: Q96GM5
#12: Protein SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1 / BRG1-associated factor 57 / BAF57


Mass: 46710.371 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 / References: UniProt: Q969G3

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DNA chain , 2 types, 2 molecules XY

#16: DNA chain DNA (148-MER)


Mass: 69816.469 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#17: DNA chain DNA (148-MER)


Mass: 70362.789 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 2 types, 17 molecules

#18: Chemical
ChemComp-PTD / PENTANEDIAL


Mass: 100.116 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C5H8O2
#19: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

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Details

Has ligand of interestN
Has protein modificationY

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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

Component
IDNameTypeEntity IDParent-IDSource
1BAF in complex with a OCT4/SOX2-bound nucleosomeCOMPLEX#1-#170MULTIPLE SOURCES
2Nucleosome core particleCOMPLEX#1-#4, #16-#171NATURAL
3BAF complexCOMPLEX#5-#131NATURAL
4OCT4/SOX2 heterodimerCOMPLEX#14-#151RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-IDStrain
21Homo sapiens (human)9606
22Homo sapiens (human)9606
33Homo sapiens (human)9606HEK293
44Homo sapiens (human)9606
Source (recombinant)Organism: Trichoplusia ni (cabbage looper)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameCategory
1RELIONparticle selection
2EPUimage acquisition
7ISOLDEmodel fitting
8PHENIXmodel refinement
12cryoSPARCclassification
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 179373 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL

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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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