Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
Author
Journal
IF	>30 >20 >10 >5 all

Title	Structure of the mature Rous sarcoma virus lattice reveals a role for IP6 in the formation of the capsid hexamer.
Journal, issue, pages	Nat Commun, Vol. 12, Issue 1, Page 3226, Year 2021
Publish date	May 28, 2021
Authors	Martin Obr / Clifton L Ricana / Nadia Nikulin / Jon-Philip R Feathers / Marco Klanschnig / Andreas Thader / Marc C Johnson / Volker M Vogt / Florian K M Schur / Robert A Dick /
PubMed Abstract	Inositol hexakisphosphate (IP6) is an assembly cofactor for HIV-1. We report here that IP6 is also used for assembly of Rous sarcoma virus (RSV), a retrovirus from a different genus. IP6 is ~100-fold ...Inositol hexakisphosphate (IP6) is an assembly cofactor for HIV-1. We report here that IP6 is also used for assembly of Rous sarcoma virus (RSV), a retrovirus from a different genus. IP6 is ~100-fold more potent at promoting RSV mature capsid protein (CA) assembly than observed for HIV-1 and removal of IP6 in cells reduces infectivity by 100-fold. Here, visualized by cryo-electron tomography and subtomogram averaging, mature capsid-like particles show an IP6-like density in the CA hexamer, coordinated by rings of six lysines and six arginines. Phosphate and IP6 have opposing effects on CA in vitro assembly, inducing formation of T = 1 icosahedrons and tubes, respectively, implying that phosphate promotes pentamer and IP6 hexamer formation. Subtomogram averaging and classification optimized for analysis of pleomorphic retrovirus particles reveal that the heterogeneity of mature RSV CA polyhedrons results from an unexpected, intrinsic CA hexamer flexibility. In contrast, the CA pentamer forms rigid units organizing the local architecture. These different features of hexamers and pentamers determine the structural mechanism to form CA polyhedrons of variable shape in mature RSV particles.
External links	Nat Commun / PubMed:34050170 / PubMed Central
Methods	EM (single particle) / EM (subtomogram averaging) / EM (tomography)
Resolution	3.1 - 9.1 Å
Structure data	12485 7no0 EMDB-12485, PDB-7no0: Structure of the mature RSV CA lattice: T=1 CA icosahedron Method: EM (single particle) / Resolution: 3.1 Å 12486 7no1 EMDB-12486, PDB-7no1: Structure of the mature RSV CA lattice: T=3 CA icosahedron Method: EM (single particle) / Resolution: 7.6 Å 12487 7no2 EMDB-12487, PDB-7no2: Structure of the mature RSV CA lattice: hexamer derived from tubes (C2-symmetric) Method: EM (subtomogram averaging) / Resolution: 4.3 Å 12488 7no3 EMDB-12488, PDB-7no3: Structure of the mature RSV CA lattice: pentamer derived from polyhedral VLPs Method: EM (subtomogram averaging) / Resolution: 5.8 Å 12489 7no4 EMDB-12489, PDB-7no4: Structure of the mature RSV CA lattice: hexamer with 3 adjacent pentamers (C3 symmetric) Method: EM (subtomogram averaging) / Resolution: 7.5 Å 12490 7no5 EMDB-12490, PDB-7no5: Structure of the mature RSV CA lattice: hexamer with 2 adjacent pentamers (C2 symmetric) Method: EM (subtomogram averaging) / Resolution: 7.4 Å 12491 7no6 EMDB-12491, PDB-7no6: Structure of the mature RSV CA lattice: Group I, pentamer-hexamer interface, class 1 Method: EM (subtomogram averaging) / Resolution: 6.0 Å 12492 7no7 EMDB-12492, PDB-7no7: Structure of the mature RSV CA lattice: Group I, pentamer-hexamer interface, class 1"2 Method: EM (subtomogram averaging) / Resolution: 7.5 Å 12493 7no8 EMDB-12493, PDB-7no8: Structure of the mature RSV CA lattice: Group I, pentamer-hexamer interface, class 1"6 Method: EM (subtomogram averaging) / Resolution: 7.9 Å 12494 7no9 EMDB-12494, PDB-7no9: Structure of the mature RSV CA lattice: Group I, pentamer-pentamer interface, class 1'1 Method: EM (subtomogram averaging) / Resolution: 7.6 Å 12495 7noa EMDB-12495, PDB-7noa: Structure of the mature RSV CA lattice: Group II, hexamer-hexamer interface, class 6 Method: EM (subtomogram averaging) / Resolution: 6.4 Å 12496 7nob EMDB-12496, PDB-7nob: Structure of the mature RSV CA lattice: Group II, hexamer-hexamer interface, class 2'6 Method: EM (subtomogram averaging) / Resolution: 6.7 Å 12497 7noc EMDB-12497, PDB-7noc: Structure of the mature RSV CA lattice: Group III, hexamer-hexamer interface, class 3'3 Method: EM (subtomogram averaging) / Resolution: 7.8 Å 12498 7nod EMDB-12498, PDB-7nod: Structure of the mature RSV CA lattice: Group III, hexamer-hexamer interface, class 3'4 Method: EM (subtomogram averaging) / Resolution: 7.8 Å 12499 7noe EMDB-12499, PDB-7noe: Structure of the mature RSV CA lattice: Group III, hexamer-hexamer interface, class 3'5 Method: EM (subtomogram averaging) / Resolution: 7.5 Å 12500 7nof EMDB-12500, PDB-7nof: Structure of the mature RSV CA lattice: Group III, hexamer-hexamer interface, class 4'4 Method: EM (subtomogram averaging) / Resolution: 7.6 Å 12501 7nog EMDB-12501, PDB-7nog: Structure of the mature RSV CA lattice: Group III, hexamer-hexamer interface, class 4'5 Method: EM (subtomogram averaging) / Resolution: 7.8 Å 12502 7noh EMDB-12502, PDB-7noh: Structure of the mature RSV CA lattice: Group III, hexamer-hexamer interface, class 5'5 Method: EM (subtomogram averaging) / Resolution: 7.1 Å 12503 7noi EMDB-12503, PDB-7noi: Structure of the mature RSV CA lattice: Group IV, hexamer-hexamer interface, class 3'Alpha Method: EM (subtomogram averaging) / Resolution: 7.2 Å 12504 7noj EMDB-12504, PDB-7noj: Structure of the mature RSV CA lattice: Group IV, hexamer-hexamer interface, class 3'Beta Method: EM (subtomogram averaging) / Resolution: 6.7 Å 12505 7nok EMDB-12505, PDB-7nok: Structure of the mature RSV CA lattice: Group IV, hexamer-hexamer interface, class 3'Gamma Method: EM (subtomogram averaging) / Resolution: 9.1 Å 12506 7nol EMDB-12506, PDB-7nol: Structure of the mature RSV CA lattice: Group IV, hexamer-hexamer interface, class 4'Alpha Method: EM (subtomogram averaging) / Resolution: 8.2 Å 12507 7nom EMDB-12507, PDB-7nom: Structure of the mature RSV CA lattice: Group IV, hexamer-hexamer interface, class 4'Beta Method: EM (subtomogram averaging) / Resolution: 6.7 Å 12508 7non EMDB-12508, PDB-7non: Structure of the mature RSV CA lattice: Group IV, hexamer-hexamer interface, class 4'Gamma Method: EM (subtomogram averaging) / Resolution: 6.8 Å 12509 7noo EMDB-12509, PDB-7noo: Structure of the mature RSV CA lattice: Group IV, hexamer-hexamer interface, class 5'Alpha Method: EM (subtomogram averaging) / Resolution: 7.9 Å 12510 7nop EMDB-12510, PDB-7nop: Structure of the mature RSV CA lattice: Group IV, hexamer-hexamer interface, class 5'Beta Method: EM (subtomogram averaging) / Resolution: 7.8 Å 12511 7noq EMDB-12511, PDB-7noq: Structure of the mature RSV CA lattice: Group IV, hexamer-hexamer interface, class 5'Gamma Method: EM (subtomogram averaging) / Resolution: 6.5 Å EMDB-12774: Cryo-electron tomogram of mature RSV CANC CLPs Method: EM (tomography)
Source	rous sarcoma virus (strain prague c) Rous sarcoma virus - Prague C
Keywords	VIRAL PROTEIN / Retrovirus / Rous sarcoma virus / capsid protein / IP6