The structure of Ebola virus nucleocapsid-like assemblies from recombinant virus-like particles (nucleoprotein, VP24,VP35,VP40)

2024-05-22 REL PDBe PDBe PDBe 2017-09-13 2017-11-08 2017-11-08 2024-05-22 European Research Council ERC-CoG-648432 MEMBRANEFUSION Germany European Molecular Biology Organization ALTF 748-2014 Germany German Research Foundation Sonderforschungsbereich 1021 Germany The structure of Ebola virus nucleocapsid-like assemblies from recombinant virus-like particles (nucleoprotein, VP24,VP35,VP40) Wan W Kolesnikova L nucleocapsid, virus-like particle, VIRUS LIKE PARTICLE Wan W Kolesnikova L Clarke M Koehler A Noda T Becker S Briggs JAG Structure and assembly of the Ebola virus nucleocapsid. Nature UK 551 394 397 2017 29144446 doi:10.1038/nature24490 1476-4687 0006 NATUAS 6ehm FULLOVERLAP Ebola virus - Mayinga, Zaire, 1976 Ebola virus - Mayinga, Zaire, 1976 0 1 2

Recombinantly expressed virus-like particles produced by expression of nucleoprotein, VP24, VP35, VP40.

Ebola virus - Mayinga, Zaire, 1976 Nucleocapsid 280.0 VIRUS-LIKE PARTICLE STRAIN true false Nucleoprotein Zaire ebolavirus (strain Mayinga-76) Mayinga-76 0.08338749999999999 2 Homo sapiens LEVO MDSRPQKIWMAPSLTESDMDYHKILTAGLSVQQGIVRQRVIPVYQVNNLEEICQLIIQAFEAGVDFQESADSFLLMLCLH HAYQGDYKLFLESGAVKYLEGHGFRFEVKKRDGVKRLEELLPAVSSGKNIKRTLAAMPEEETTEANAGQFLSFASLFLPK LVVGEKACLEKVQRQIQVHAEQGLIQYPTAWQSVGHMMVIFRLMRTNFLIKFLLIHQGMHMVAGHDANDAVISNSVAQAR FSGLLIVKTVLDHILQKTERGVRLHPLARTAKVKNEVNSFKAALSSLAKHGEYAPFARLLNLSGVNNLEHGLFPQLSAIA LGVATAHGSTLAGVNVGEQYQQLREAATEAEKQLQQYAESRELDHLGLDDQEKKILMNFHQKKNEISFQQTNAMVTLRKE RLAKLTEAITAASLPKTSGHYDDDDDIPFPGPINDDDNPGHQDDDPTDSQDTTIPDVVVDPDDGSYGEYQSYSENGMNAP DDLVLFDLDEDDEDTKPVPNRSTKGGQQKNSQKGQHIEGRQTQSRPIQNVPGPHRTIHHASAPLTDNDRRNEPSGSTSPR MLTPINEEADPLDDADDETSSLPPLESDDEEQDRDGTSNRTPTVAPPAPVYRDHSEKKELPQDEQQDQDHTQEARNQDSD NTQSEHSFEEMYRHILRSQGPFDAVLYYHMMKDEPVVFSTSDGKEYTYPDSLEEEYPPWLTEKEAMNEENRFVTLDGQQF YWPVMNHKNKFMAILQHHQ P18272 Membrane-associated protein VP24 Zaire ebolavirus (strain Mayinga-76) Mayinga-76 0.028250811 2 Homo sapiens LEVO MAKATGRYNLISPKKDLEKGVVLSDLCNFLVSQTIQGWKVYWAGIEFDVTHKGMALLHRLKTNDFAPAWSMTRNLFPHLF QNPNSTIESPLWALRVILAAGIQDQLIDQSLIEPLAGALGLISDWLLTTNTNHFNMRTQRVKEQLSLKMLSLIRSNILKF INKLDALHVVNYNGLLSSIEIGTQNHTIIITRTNMGFLVELQEPDKSAMNRMKPGPAKFSLLHESTLKAFTQGSSTRMQS LILEFNSSLAI Q05322 subtomogramAveraging helicalArray 7.4 100.0 NaCl sodium chloride 0.1 EDTA ethylenediaminetetraacetic acid 50.0 Tris-HCl trisaminomethane hydrochloride C-flat 2/1 3C COPPER 300 CARBON HOLEY 20.0 GLOW DISCHARGE 30 AIR 0.039 ETHANE 95 FEI VITROBOT MARK II FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 50.0 2.7 2.0 4.5 81000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN GIF Quantum LS -10 10 GATAN K2 QUANTUM (4k x 4k) SUPER-RESOLUTION 3708 3708 1-5 2.3 3.4 1

Frames were aligned using K2Align software, based off the MotionCorr algorithm. Tomograms were reconstructed with IMOD, using stripwise CTF-correction and weighted back projection. Subtomogram averaging was performed using scripts derived from TOM, AV3, and DYNAMO.

1 C1 BACK PROJECTION 7.3 FSC 0.143 CUT-OFF AV3

Local resolution was estimated using moving window FSC calculations. Resolution varies from 7.3 to 15.2 Angstroms.

1 63 379428 None Amira 4 placing spline points TOM Toolbox subtomogram extraction

Points along the helical axis were manually placed to define a spline. A cylindrical grid as defined at a given radius from the spline; grid spacing was chosen to provide ~4x oversampling.

OTHER AV3

Iterative angular search was performed via maximization of a modified constrained cross-correlation function.

emd_3871.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 192 192 192 0 0 0 192 192 192 341.76 341.76 341.76 90.0 90.0 90.0 X Y Z -5.856038 10.570264 -0.03055102 0.9822338 1.7800001 1.7800001 1.7800001 1.5 AUTHOR ::::EMDATABANK.org::::EMD-3871:::: Subtomogram averaging of nucleocapsid-like assembly formed from recombinantly expressed Ebola Nucleoprotein (NP), VP24, VP35, VP40. RIGID BODY FIT

Nucleoprotein model from Ebola virus nucleoprotein 1-450 was first rigid body fitted into the inner nucleoprotein densities. Densities were then subtracted, and VP24 pdb was then fit into remaining densities. All models were rigid-body fitted using UCSF Chimera.