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 External Resources

 26042https://www.addgene.org/26042  Addgene identifier (26042, reused)

 55218https://www.addgene.org/55218  Addgene identifier (55218, reused)

 EMD-12611https://www.ebi.ac.uk/pdbe/emdb/EMD-12611  EMBL-EBI EMDB identifier (EMD-12611)

 EMD-12630https://www.ebi.ac.uk/pdbe/emdb/EMD-12630  EMBL-EBI EMDB identifier (EMD-12630)

 gro-2/100173http://resolver.sub.uni-goettingen.de/purl?gro-2/100173  GRO.publications identifier

 0000-0003-2221-482Xhttps://orcid.org/0000-0003-2221-482X  ORCID identifier (Shintaro Aibara)

 0000-0001-9071-8515https://orcid.org/0000-0001-9071-8515  ORCID identifier (Sandra Schilbach)

 0000-0001-5454-7755https://orcid.org/0000-0001-5454-7755  ORCID identifier (Patrick Cramer)

 7NVShttps://www.rcsb.org/structure/7NVS  RCSB PDB Identifier (DOI:10.2210/pdb7NVS/pdb)

 7NVThttps://www.rcsb.org/structure/7NVT  RCSB PDB Identifier (DOI:10.2210/pdb7NVT/pdb)

 7NVUhttps://www.rcsb.org/structure/7NVU  RCSB PDB Identifier (DOI:10.2210/pdb7NVU/pdb)

 7NVVhttps://www.rcsb.org/structure/7NVV  RCSB PDB Identifier (DOI:10.2210/pdb7NVV/pdb)

 7NVWhttps://www.rcsb.org/structure/7NVW  RCSB PDB Identifier (DOI:10.2210/pdb7NVW/pdb)

 7NVXhttps://www.rcsb.org/structure/7NVX  RCSB PDB Identifier (DOI:10.2210/pdb7NVX/pdb)

 7NVYhttps://www.rcsb.org/structure/7NVY  RCSB PDB Identifier (DOI:10.2210/pdb7NVY/pdb)

 7NVZhttps://www.rcsb.org/structure/7NVZ  RCSB PDB Identifier (DOI:10.2210/pdb7NVZ/pdb)

 7NW0https://www.rcsb.org/structure/7NW0  RCSB PDB Identifier (DOI:10.2210/pdb7NW0/pdb)

 5FLMhttps://www.rcsb.org/structure/5FLM  RCSB PDB Identifier (DOI:10.2210/pdb5FLM/pdb, reused)

 5GPYhttps://www.rcsb.org/structure/5GPY  RCSB PDB Identifier (DOI:10.2210/pdb5GPY/pdb, reused)

 5IY7https://www.rcsb.org/structure/5IY7  RCSB PDB Identifier (DOI:10.2210/pdb5IY7/pdb, reused)

 6NMIhttps://www.rcsb.org/structure/6NMI  RCSB PDB Identifier (DOI:10.2210/pdb6NMI/pdb, reused)

 6RO4https://www.rcsb.org/structure/6RO4  RCSB PDB Identifier (DOI:10.2210/pdb6RO4/pdb, reused)

 1/395https://mbexc.uni-goettingen.de/archive/1/395  Research Data Archive (supplemental material)

 03e76ya46https://ror.org/03e76ya46  ROR identifier (03e76ya46, Max Planck Institute for Biophysical Chemistry)

 05xy1nn52https://ror.org/05xy1nn52  ROR identifier (05xy1nn52, Multiscale Bioimaging)

 SCR_014222https://scicrunch.org/resolver/SCR_014222  SciCrunch identifier (RRID:SCR_014222, Coot)

 SCR_016500https://scicrunch.org/resolver/SCR_016500  SciCrunch identifier (RRID:SCR_016500, GCTF)

 SCR_002798https://scicrunch.org/resolver/SCR_002798  SciCrunch identifier (RRID:SCR_002798, GraphPad Prism)

 SCR_014226https://scicrunch.org/resolver/SCR_014226  SciCrunch identifier (RRID:SCR_014226, MolProbity)

 SCR_014224https://scicrunch.org/resolver/SCR_014224  SciCrunch identifier (RRID:SCR_014224, Phenix)

 SCR_000305https://scicrunch.org/resolver/SCR_000305  SciCrunch identifier (RRID:SCR_000305, PyMOL)

 SCR_016274https://scicrunch.org/resolver/SCR_016274  SciCrunch identifier (RRID:SCR_016274, RELION)

 SCR_017293https://scicrunch.org/resolver/SCR_017293  SciCrunch identifier (RRID:SCR_017293, SerialEM)

 SCR_004097https://scicrunch.org/resolver/SCR_004097  SciCrunch identifier (RRID:SCR_004097, UCSF Chimera)

 SCR_015872https://scicrunch.org/resolver/SCR_015872  SciCrunch identifier (RRID:SCR_015872, UCSF ChimeraX)

 SCR_018071https://scicrunch.org/resolver/SCR_018071  SciCrunch identifier (RRID:SCR_018071, Warp)

 static-c...SM.pdfhttps://static-content.springer.com/esm/art%3A10.1038%2Fs41586-021-03554-8/MediaObjects/41586_2021_3554_MOESM1_ESM.pdf  Supplemental material

 static-c...SM.pdfhttps://static-content.springer.com/esm/art%3A10.1038%2Fs41586-021-03554-8/MediaObjects/41586_2021_3554_MOESM3_ESM.pdf  Supplemental material (peer review)

 static-c...SM.pdfhttps://static-content.springer.com/esm/art%3A10.1038%2Fs41586-021-03554-8/MediaObjects/41586_2021_3554_MOESM2_ESM.pdf  Supplemental material (reporting summary)

 static-c...SM.mp4https://static-content.springer.com/esm/art%3A10.1038%2Fs41586-021-03554-8/MediaObjects/41586_2021_3554_MOESM4_ESM.mp4  Supplemental material (video)

 static-c...SM.mp4https://static-content.springer.com/esm/art%3A10.1038%2Fs41586-021-03554-8/MediaObjects/41586_2021_3554_MOESM5_ESM.mp4  Supplemental material (video)

 static-c...SM.mp4https://static-content.springer.com/esm/art%3A10.1038%2Fs41586-021-03554-8/MediaObjects/41586_2021_3554_MOESM6_ESM.mp4  Supplemental material (video)

 mbexc.de...lexes/https://mbexc.de/structures-of-mammalian-rna-polymerase-ii-pre-initiation-complexes/  Website entry (mbexc.de)