MVV cleaved synaptic complex (CSC) intasome at 3.4 A resolution

2025-05-28 REL RCSB INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY EXPERIMENTAL_SUMMARY em_admin em_software _em_admin.last_update STRUCTURE_SUMMARY em_admin em_software pdbx_entry_details _em_admin.last_update _pdbx_entry_details.has_protein_modification RCSB RCSB 2022-02-25 2022-05-11 2022-05-11 2025-05-28 National Science Foundation (NSF, United States) MCB-2048095 United States National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) U54 AI150472 United States National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) R01 AI136680 United States The Francis Crick Institute FC10061 United Kingdom National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) P50AI150481 United States MVV cleaved synaptic complex (CSC) intasome at 3.4 A resolution Shan Z Pye VE Cherepanov P Lyumkis D Integrase-DNA complex, hydrolase, VIRAL PROTEIN, VIRAL PROTEIN-DNA complex Ballandras-Colas A Chivukula V Gruszka DT Shan Z Singh PK Pye VE McLean RK Bedwell GJ Li W Nans A Cook NJ Fadel HJ Poeschla EM Griffiths DJ Vargas J Taylor IA Lyumkis D Yardimci H Engelman AN Cherepanov P Multivalent interactions essential for lentiviral integrase function. Nat Commun UK 13 2416 2416 2022 35504909 doi:10.1038/s41467-022-29928-8 2041-1723 EMD-14453 other EM volume 7u32 FULLOVERLAP MVV cleaved synaptic complex intasome MVV cleaved synaptic complex intasome 0 1 2 3 Streptomyces griseus 0.48 Integrase Visna/maedi virus EV1 KV1772 KV1772 0.032368825999999996 16 Escherichia coli LEVO WIENIPLAEEEHNKWHQDAVSLHLEFGIPRTAAEDIVQQCDVCQENKMPSTLRGSNKRGIDHWQVDYTHYEDKIILVWVE TNSGLIYAERVKGETGQEFRVQTMKWYAMFAPKSLQSDNGPAFVAESTQLLMKYLGIEHTTGIPWNPQSQALVERTHQTL KNTLEKLIPMFNAFESALAGTLITLNIKRKGGLGTSPMDIFIFNKEQQRIQQQSKSKQEKIRFCYYRTRKRGHPGEWQGP TQVLWGGDGAIVVKDRGTDRYLVIANKDVKFIPPPKEIQKE P35956 2.7.7.- DNA EV273 synthetic construct 0.008943719 2 (DG)(DC)(DT)(DG)(DC)(DG)(DA)(DG)(DA)(DT)(DC)(DC)(DG)(DC)(DT)(DC)(DC)(DG)(DG)(DT) (DG)(DT)(DT)(DG)(DC)(DA)(DC)(DG)(DG) DNA DNA EV272 synthetic construct 0.008272325999999998 2 (DC)(DC)(DG)(DT)(DG)(DC)(DA)(DA)(DC)(DA)(DC)(DC)(DG)(DG)(DA)(DG)(DC)(DG)(DG)(DA) (DT)(DC)(DT)(DC)(DG)(DC)(DA) DNA ZINC ION 6.5409e-05 12 ZN CALCIUM ION 4.0078e-05 2 CA singleParticle particle 6.5 25.0 Tris-HCl 350.0 NaCl sodium chloride 1.0 TCEP 3.0 CaCl2 Calcium chloride Quantifoil R1.2/1.3 GOLD 300 GOLD HOLEY PLASMA CLEANING 7 ETHANE HOMEMADE PLUNGER

Cryo-EM grids were prepared by freezing using a manual plunger in cold room at 4C.

MVV CSC intasomes, assembled and purified as previously described, were applied onto R1.2/1.3 gold UltrAufoil grids, Au 300 mesh (Quantifoil). Cryo-EM grids were prepared by manually freezing using a manual plunger in cold room at 4C and stored in liquid nitrogen for future data acquisition.

FEI TALOS ARCTICA FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 200 70.0 2.7 1.0 3.0 45000.0 54347.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN

The stage was tilted to 40 degrees during data collection to account for the preferential orientation of the sample within the vitreous ice.

GATAN K2 SUMMIT (4k x 4k) COUNTING 3838 3710 1-100 1 2295 10.0 43.6 1 926176 cryoSPARC 3.0 PHASE FLIPPING AND AMPLITUDE CORRECTION EMD-4138 C2 FOURIER SPACE 3.46 FSC 0.143 CUT-OFF cryoSPARC 3.0 147860 PROJECTION MATCHING cryoSPARC 3.0 PROJECTION MATCHING cryoSPARC 3.0 emd_26322.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 353.28 353.28 353.28 90.0 90.0 90.0 X Y Z -3.0471601 6.298784 0.020010429 0.09795843 0.92 0.92 0.92 0.4 AUTHOR ::::EMDATABANK.org::::EMD-26322:::: sharpened cryo-EM reconstruction of MVV CSC FLEXIBLE FIT

The STC model refined in study, with the tDNA removed, was docked into the CSC cryoEM map using UCSF Chimera. It was observed that there were some slight differences in some domain positions, to address this, individual domains that were not well fitted to the map were docked as individual domains to achieve a best-fit starting model. Two (C2 related) NTDs (aa 1-35) were removed from the model due to lack of supporting map. Adjustments were made to the model interactively using Coot and the coordinates were subjected to real-space refinement in Phenix dev-4213-000 employing C2 NCS constraints.

CC REAL 262.0 emd_26322_msk_1.map emd_26322_additional_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 353.28 353.28 353.28 90.0 90.0 90.0 X Y Z -0.0017747718 1.8198965 0.0012667003 0.023785912 0.92 0.92 0.92 AUTHOR ::::EMDATABANK.org::::EMD-26322:::: Reconstructed map after DeepEMhancer emd_26322_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 353.28 353.28 353.28 90.0 90.0 90.0 X Y Z -0.20789123 1.3484924 0.020010429 0.059353333 0.92 0.92 0.92 AUTHOR ::::EMDATABANK.org::::EMD-26322:::: unsharpened map emd_26322_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 353.28 353.28 353.28 90.0 90.0 90.0 X Y Z -0.31002492 1.416025 0.029701974 0.06740816 0.92 0.92 0.92 AUTHOR ::::EMDATABANK.org::::EMD-26322:::: half map #1 emd_26322_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 353.28 353.28 353.28 90.0 90.0 90.0 X Y Z -0.2934779 1.4254326 0.029816134 0.067531385 0.92 0.92 0.92 AUTHOR ::::EMDATABANK.org::::EMD-26322:::: half map #2