11HK

SARS-CoV-2 spike S2 trimer stabilized in the early fusion intermediate conformation (E-FICs-v3) bound to the VN01H1 Fab (Fab local refinement)

Entity

Entity ID	Chain ID	Description	Type	Chain length	Formula weight	Number of molecules	DB Name (Accession)	Biological source	Descriptive keywords
1	A, D, G (A, D, G)	E-FICS-v3	polymer	605	67787.2	3	UniProt (Q12306) UniProt (P0DTC2)	Saccharomyces cerevisiae S288C
2	B, E, H (B, E, H)	Heavy chain of VN01H1 Fab	polymer	226	24131.1	3		Homo sapiens (human)
3	C, F, I (C, F, I)	Light chain of VN01H1 Fab	polymer	215	23413.9	3		Homo sapiens (human)
4	J, K, L, M, N... (A, D, G)	2-acetamido-2-deoxy-beta-D-glucopyranose	non-polymer		221.2	6	Chemie (NAG)
5	P, Q, R, S, T... (A, B, C, D, E...)	water	water		18.0	84	Chemie (HOH)

Sequence modifications

A, D, G: 1 - 94 (UniProt: Q12306)

PDB	External Database	Details
Met -19	-	initiating methionine
Thr -18	-	expression tag
Arg -17	-	expression tag
Leu -16	-	expression tag
Thr -15	-	expression tag
Val -14	-	expression tag
Leu -13	-	expression tag
Ala -12	-	expression tag
Leu -11	-	expression tag
Leu -10	-	expression tag
Ala -9	-	expression tag
Gly -8	-	expression tag
Leu -7	-	expression tag
Leu -6	-	expression tag
Ala -5	-	expression tag
Ser -4	-	expression tag
Ser -3	-	expression tag
Arg -2	-	expression tag
Ala -1	-	expression tag
Ser 0	-	expression tag
Asn 95	-	linker
Asp 96	-	linker
Asp 97	-	linker
Asp 98	-	linker
Asp 99	-	linker
Lys 100	-	linker
Thr 101	-	linker
Gly 102	-	linker
Thr 103	-	linker
Gly 104	-	linker
Ser 105	-	linker
Gln 106	-	linker
Ser 107	-	linker
Asn 108	-	linker
Ala 109	-	linker
Glu 110	-	linker
Ser 111	-	linker
Val 112	-	linker
Gln 113	-	linker
Asn 114	-	linker
His 115	-	linker
Thr 116	-	linker
Phe 117	-	linker
Glu 118	-	linker
Val 119	-	linker
Leu 120	-	linker
Asn 121	-	linker
Asn 122	-	linker
Thr 123	-	linker
Ile 124	-	linker
Arg 125	-	linker
Ala 126	-	linker
Leu 127	-	linker
Glu 128	-	linker
Leu 129	-	linker
Ile 130	-	linker
Leu 131	-	linker
Arg 132	-	linker
Lys 133	-	linker
Leu 134	-	linker
Glu 135	-	linker
Ile 136	-	linker
Leu 137	-	linker
Tyr 138	-	linker
Glu 139	-	linker
Met 140	-	linker
Ile 141	-	linker
Leu 142	-	linker
Gln 143	-	linker
Leu 144	-	linker
His 145	-	linker
Glu 146	-	linker
Glu 147	-	linker
Val 148	-	linker
Glu 149	-	linker
Ala 150	-	linker
Ile 151	-	linker
Gln 152	-	linker
Lys 153	-	linker
Ala 154	-	linker
Ile 155	-	linker

A, D, G: 914 - 1131 (UniProt: P0DTC2)

PDB	External Database	Details
Ala 985	Asp 985	conflict

A, D, G: 1703 - 1833 (UniProt: P0DTC2)

PDB	External Database	Details
Thr 1132	-	linker
Thr 1834	-	expression tag
Ile 1835	-	expression tag
Asp 1836	-	expression tag
Lys 1837	-	expression tag
Glu 1838	-	expression tag
Lys 1839	-	expression tag
Trp 1840	-	expression tag
Lys 1841	-	expression tag
Glu 1842	-	expression tag
Trp 1843	-	expression tag
Arg 1844	-	expression tag
Lys 1845	-	expression tag
Glu 1846	-	expression tag
Met 1847	-	expression tag
Glu 1848	-	expression tag
Asn 1849	-	expression tag
Leu 1850	-	expression tag
Thr 1851	-	expression tag
Lys 1852	-	expression tag
Glu 1853	-	expression tag
Ile 1854	-	expression tag
Lys 1855	-	expression tag
Glu 1856	-	expression tag
Thr 1857	-	expression tag
Leu 1858	-	expression tag
Glu 1859	-	expression tag
Glu 1860	-	expression tag
Ala 1861	-	expression tag
Arg 1862	-	expression tag
Lys 1863	-	expression tag
Thr 1864	-	expression tag
Leu 1865	-	expression tag
Lys 1866	-	expression tag
Gln 1867	-	expression tag
Ala 1868	-	expression tag
Glu 1869	-	expression tag
Glu 1870	-	expression tag
Thr 1871	-	expression tag
Phe 1872	-	expression tag
Lys 1873	-	expression tag
Thr 1874	-	expression tag
Pro 1875	-	expression tag
Ser 1876	-	expression tag
Ser 1877	-	expression tag
Gly 1878	-	expression tag
Gly 1879	-	expression tag
Thr 1880	-	expression tag
Asp 1881	-	expression tag
Asp 1882	-	expression tag
Asp 1883	-	expression tag
Asp 1884	-	expression tag
Lys 1885	-	expression tag
Thr 1886	-	expression tag
Gly 1887	-	expression tag
Ser 1888	-	expression tag
Leu 1889	-	expression tag
Asn 1890	-	expression tag
Asp 1891	-	expression tag
Ile 1892	-	expression tag
Phe 1893	-	expression tag
Glu 1894	-	expression tag
Ala 1895	-	expression tag
Gln 1896	-	expression tag
Lys 1897	-	expression tag
Ile 1898	-	expression tag
Glu 1899	-	expression tag
Trp 1900	-	expression tag
His 1901	-	expression tag
Glu 1902	-	expression tag
Gln 1903	-	expression tag
Gly 1904	-	expression tag
Ser 1905	-	expression tag
His 1906	-	expression tag
His 1907	-	expression tag
His 1908	-	expression tag
His 1909	-	expression tag
His 1910	-	expression tag
His 1911	-	expression tag
His 1912	-	expression tag
His 1913	-	expression tag

Contents of the asymmetric unit

Polymers	Number of chains	9
	Total formula weight	345996.6
Non-Polymers*	Number of molecules	6
	Total formula weight	1327.2
All*	Total formula weight	347323.8

*Water molecules are not included.