2025-05-14 REL RCSB INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY EXPERIMENTAL_SUMMARY em_admin em_software _em_admin.last_update _em_software.name DATABASE_REFERENCES citation citation_author _citation.pdbx_database_id_PubMed _citation.title _citation_author.identifier_ORCID DATABASE_REFERENCES citation _citation.journal_volume _citation.page_first _citation.page_last DATA_COLLECTION chem_comp_atom chem_comp_bond STRUCTURE_SUMMARY em_admin em_software pdbx_entry_details _em_admin.last_update _em_software.name RCSB RCSB 2023-02-17 2023-03-22 2023-03-22 2025-05-14 National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) 1R01GM135599-01 United States National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) 1R01GM141694-01 United States Nucleosome with human nMatn1 sequence in complex with Human Oct4 Sinha KK Bilokapic S Du Y Malik D Halic M Oct4, Nucleosome, LIN28B DNA, DNA BINDING PROTEIN-DNA complex Sinha KK Bilokapic S Du Y Malik D Halic M Histone modifications regulate pioneer transcription factor cooperativity. Nature UK 619 378 384 2023 37225990 doi:10.1038/s41586-023-06112-6 1476-4687 0006 NATUAS EMD-29841 other EM volume
Human Oct4 bound to nucleosome with human nMatn1 sequence (focused refinement of Oct4 bound region)
 EMD-29837 other EM volume
Human Oct4 bound to nucleosome with human nMatn1 sequence (focused refinement of nucleosome)
 EMD-29843 other EM volume
Human Oct4 bound to nucleosome with human nMatn1 sequence
 EMD-29846 other EM volume
Human Oct4 bound to nucleosome with human LIN28B sequence
 EMD-29850 other EM volume
Human Oct4 bound to nucleosome with human LIN28B sequence
 8g8b FULLOVERLAP Human Oct4 bound to Nucleosome with human nMatn1 sequence Human Oct4 bound to Nucleosome with human nMatn1 sequence 0 1 2 3 4 5 6 7 Xenopus laevis Histone H3 Xenopus laevis 0.01530393
Histone H3.2|Xenopus laevis
2 Escherichia coli LEVO ARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKT DLRFQSSAVMALQEASEAYLVALFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA P84233 Histone H4 Xenopus laevis 0.011263230999999999
Histone H4|Xenopus laevis
2 Escherichia coli LEVO SGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKT VTAMDVVYALKRQGRTLYGFGG P62799 Histone H2A Xenopus laevis 0.013978240999999999
Histone H2A|Xenopus laevis
2 Escherichia coli LEVO SGRGKQGGKTRAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIP RHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLPKKTESSKSAKSK Q6AZJ8 Histone H2B Xenopus laevis 0.013524752
Histone H2B 1.1|Xenopus laevis
2 Escherichia coli LEVO AKSAPAPKKGSKKAVTKTQKKDGKKRRKTRKESYAIYVYKVLKQVHPDTGISSKAMSIMNSFVNDVFERIAGEASRLAHY NKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSAK P02281 nMatn1 DNA (top strand,168-MER) Homo sapiens 0.05693358999999999 1 (DA)(DC)(DA)(DT)(DG)(DC)(DA)(DC)(DA)(DC)(DA)(DT)(DG)(DC)(DT)(DA)(DA)(DT)(DA)(DT) (DA)(DT)(DG)(DC)(DA)(DC)(DA)(DC)(DA)(DA)(DT)(DG)(DC)(DA)(DC)(DA)(DC)(DA)(DG)(DG) (DT)(DT)(DA)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DC)(DA)(DC)(DA)(DT)(DA)(DC)(DA)(DC)(DA) (DC)(DA)(DC)(DA)(DT)(DG)(DC)(DA)(DC)(DA)(DC)(DA)(DC)(DA)(DC)(DG)(DT)(DG)(DC)(DA) (DC)(DA)(DC)(DA)(DT)(DA)(DT)(DA)(DT)(DG)(DC)(DA)(DC)(DA)(DT)(DG)(DC)(DA)(DT)(DG) (DC)(DA)(DC)(DA)(DC)(DA)(DC)(DG)(DT)(DA)(DT)(DA)(DT)(DG)(DC)(DA)(DC)(DA)(DC)(DA) (DC)(DA)(DT)(DG)(DC)(DA)(DC)(DA)(DT)(DG)(DC)(DA)(DT)(DG)(DC)(DG)(DC)(DA)(DC)(DA) (DT)(DA)(DG)(DT)(DC)(DA)(DC)(DA)(DC)(DA)(DC)(DA)(DT)(DG)(DC)(DA)(DC)(DA)(DC)(DA) (DT)(DT)(DA)(DG)(DC)(DA)(DT)(DA)(DT)(DG)(DC)(DA)(DT)(DA)(DC)(DA)(DC)(DA)(DT)(DA) (DC)(DA)(DT)(DG)(DC)(DA) DNA nMatn1 DNA (bottom strand, 168-MER) Homo sapiens 0.057889855000000004 1 (DT)(DG)(DC)(DA)(DT)(DG)(DT)(DA)(DT)(DG)(DT)(DG)(DT)(DA)(DT)(DG)(DC)(DA)(DT)(DA) (DT)(DG)(DC)(DT)(DA)(DA)(DT)(DG)(DT)(DG)(DT)(DG)(DC)(DA)(DT)(DG)(DT)(DG)(DT)(DG) (DT)(DG)(DA)(DC)(DT)(DA)(DT)(DG)(DT)(DG)(DC)(DG)(DC)(DA)(DT)(DG)(DC)(DA)(DT)(DG) (DT)(DG)(DC)(DA)(DT)(DG)(DT)(DG)(DT)(DG)(DT)(DG)(DC)(DA)(DT)(DA)(DT)(DA)(DC)(DG) (DT)(DG)(DT)(DG)(DT)(DG)(DC)(DA)(DT)(DG)(DC)(DA)(DT)(DG)(DT)(DG)(DC)(DA)(DT)(DA) (DT)(DA)(DT)(DG)(DT)(DG)(DT)(DG)(DC)(DA)(DC)(DG)(DT)(DG)(DT)(DG)(DT)(DG)(DT)(DG) (DC)(DA)(DT)(DG)(DT)(DG)(DT)(DG)(DT)(DG)(DT)(DA)(DT)(DG)(DT)(DG)(DT)(DA)(DT)(DA) (DT)(DA)(DT)(DT)(DA)(DA)(DC)(DC)(DT)(DG)(DT)(DG)(DT)(DG)(DC)(DA)(DT)(DT)(DG)(DT) (DG)(DT)(DG)(DC)(DA)(DT)(DA)(DT)(DA)(DT)(DT)(DA)(DG)(DC)(DA)(DT)(DG)(DT)(DG)(DT) (DG)(DC)(DA)(DT)(DG)(DT) DNA POU domain, class 5, transcription factor 1 Homo sapiens 0.042299453 1 Escherichia coli LEVO GSSHHHHHHSSGLVPRGSHMASMTGGQQMGRDPNSMAGHLASDFAFSPPPGGGGDGPGGPEPGWVDPRTWLSFQGPPGGP GIGPGVGPGSEVWGIPPCPPPYEFCGGMAYCGPQVGVGLVPQGGLETSQPEGEAGVGVESNSDGASPEPCTVTPGAVKLE KEKLEQNPEESQDIKALQKELEQFAKLLKQKRITLGYTQADVGLTLGVLFGKVFSQTTICRFEALQLSFKNMCKLRPLLQ KWVEEADNNENLQEICKAETLVQARKRKRTSIENRVRGNLENLFLQCPKPTLQQISHIAQQLGLEKDVVRVWFCNRRQKG KRSSSDYAQREDFEAAGSPFSGGPVSFPLAPGPHFGTPGYGSPHFTALYSSVPFPEGEAFPPVSVTTLGSPMHSN Q01860 singleParticle particle 0.2 7.5 50.0 C8H18N2O4S HEPES 1.0 C4H10O2S2 DTT
50 mM HEPES pH 7.5, 1 mM DTT
 Quantifoil R2/1 COPPER 300 CARBON HOLEY ETHANE 95 283 FEI VITROBOT MARK IV FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 0.7000000000000001 2.5 FEI FALCON IV (4k x 4k) 50.0 1 PHASE FLIPPING AND AMPLITUDE CORRECTION EMD-21970 4.3 FSC 0.143 CUT-OFF 4000 MAXIMUM LIKELIHOOD MAXIMUM LIKELIHOOD emd_29845.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 200 200 200 0 0 0 200 200 200 322.0 322.0 322.0 90.0 90.0 90.0 X Y Z -0.021186035 0.060868792 0.000045112614 0.0026694562 1.61 1.61 1.61 0.01 AUTHOR emd_29845_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 200 200 200 0 0 0 200 200 200 322.0 322.0 322.0 90.0 90.0 90.0 X Y Z -0.058191516 0.1013367 0.00004078895 0.006463177 1.61 1.61 1.61 AUTHOR emd_29845_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 200 200 200 0 0 0 200 200 200 322.0 322.0 322.0 90.0 90.0 90.0 X Y Z -0.053421613 0.10362762 0.000049478313 0.006443026 1.61 1.61 1.61 AUTHOR