Cryo-EM structure of the ZBTB9 BTB domain filament

2024-07-24 REL RCSB RCSB RCSB 2024-04-03 2024-07-24 2024-07-24 2024-07-24 Not funded Cryo-EM structure of the ZBTB9 BTB domain filament Park J Hunkeler M Fischer ES BTB domain, transcription factor, ZBTB protein, transcription Park PMC Park J Brown J Hunkeler M Roy Burman SS Donovan KA Yoon H Nowak RP Slabicki M Ebert BL Fischer ES Polymerization of ZBTB transcription factors regulates chromatin occupancy. Mol.Cell US 84 2511 2524.e8 2024 38996460 doi:10.1016/j.molcel.2024.06.010 1097-2765 2168 MOCEFL 9b9v FULLOVERLAP ZBTB9 BTB domain filament ZBTB9 BTB domain filament 0 1 Homo sapiens Zinc finger and BTB domain-containing protein 9 Homo sapiens 0.019387961 14 Trichoplusia ni LEVO MDWSHPQFEKSAVGLNDIFEAQKIEWHEGGGGSGENLYFQGGGRNPAPRTIQIEFPQHSSSLLESLNRHRLEGKFCDVSL LVQGRELRAHKAVLAAASPYFHDKLLLGDAPRLTLPSVIEADAFEGLLQLIYSGRLRLPLDALPAHLLVASGLQMWQVVD QCSEILRELETSGGGI Q96C00 helical filament 0.95 7.4 50.0 C8H18N2O4S/NaOH HEPES/NaOH pH 7.4 200.0 NaCl NaCl 0.25 C32H58N2O8S CHAPSO 1.0 C9H15O6P TCEP

50 mM HEPES/NaOH pH 7.4, 200 mM NaCl, 0.25 mM CHAPSO, 1 mM TCEP

Quantifoil R1.2/1.3 COPPER 300 CARBON HOLEY 12.0 GLOW DISCHARGE 60 AIR 0.039

Grids were glow-discharged for 60 s at 15-20 mA and 39 Pa

ETHANE 90 283 LEICA EM GP

Grids were vitrified using a Leica EM GP plunge freezer operated at 90% humidity and 10 C with 10 s pre-blot, 3 s blot, 3 s post-blot..

Elution fractions from Strep-tag affinity chromatography were dialyzed overnight against 50 mM HEPES/NaOH pH 7.4, 200 mM NaCl, 1 mM TCEP and concentrated by centrifugation.

FEI TALOS ARCTICA FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 200 50.0 2.7 0.8 2.0 36000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN GATAN K3 (6k x 4k) 1 1137 4.5 50.1

1 movie (45 frames) was acquired per hole and stage position.

1 36.1 101.9 C1 FOURIER SPACE 8.1 FSC 0.143 CUT-OFF

Asymmetric helical refinement followed by local refinement led to the final reconstruction. The helical symmetry values represent the angular rotation and axial rise for two dimers at the core of the map, where the local resolution was the highest. These values, however, were not applied during helical refinement as they did not improve the quality of the final reconstruction.

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Ab-initio reconstruction

MAXIMUM LIKELIHOOD emd_44391.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 270 270 270 0 0 0 270 270 270 634.5 634.5 634.5 90.0 90.0 90.0 X Y Z -0.3420041 1.0533093 -0.00026321408 0.025548274 2.35 2.35 2.35 0.4 AUTHOR ::::EMDATABANK.org::::EMD-44391:::: primary map AlphaFold in silico model OTHER

Real-space refinement without local grid search

REAL 762.0 emd_44391_msk_1.map emd_44391_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 270 270 270 0 0 0 270 270 270 634.5 634.5 634.5 90.0 90.0 90.0 X Y Z -1.749437 2.4363267 -0.00026321408 0.039370354 2.35 2.35 2.35 EMDB ::::EMDATABANK.org::::EMD-44391:::: sharpened emd_44391_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 270 270 270 0 0 0 270 270 270 634.5 634.5 634.5 90.0 90.0 90.0 X Y Z -0.45744708 1.1752628 0.000074262374 0.033714835 2.35 2.35 2.35 AUTHOR ::::EMDATABANK.org::::EMD-44391:::: emd_44391_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 270 270 270 0 0 0 270 270 270 634.5 634.5 634.5 90.0 90.0 90.0 X Y Z -0.35290644 1.1100404 0.00007918756 0.033751547 2.35 2.35 2.35 AUTHOR ::::EMDATABANK.org::::EMD-44391::::