7F90: SARS auxiliary protein

Crystal structure of SARS auxiliary protein in complex with human nuclear protein. Determined by X-ray diffraction at 2.39 Å resolution. Released 14 Sept 2022.

Method: X-ray diffraction
Resolution: 2.39 Å
Organisms: Severe acute respiratory syndrome coronavirus, Homo sapiens
Chains: 6
Atoms: 6,292
Mol. weight: 492.66 kDa
Released: 14 Sept 2022

Explore 7F90 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7F90 contains 21 α-helices and 68 β-strands across 6 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 6 helices, 30 β-strands

Element	Residues	Length	Sheet
β-strand	32-33	2	5
α-helix	34	1
β-strand	42-47	6	6
α-helix	48-49	2
β-strand	55-61	7	6
β-strand	65-71	7	6
β-strand	77-84	8	6
β-strand	89-94	6	7
β-strand	100-105	6	7
β-strand	109-114	6	7
β-strand	119-125	7	7
β-strand	130-137	8	8
β-strand	142-148	7	8
β-strand	152-156	5	8
β-strand	165-168	4	8
β-strand	173-179	7	9
β-strand	182-187	6	9
β-strand	192-196	5	9
β-strand	202-206	5	9
β-strand	215-222	8	2
β-strand	228-235	8	2
β-strand	239-244	6	2
α-helix	250-253	4
β-strand	255-258	4	2
β-strand	261	1	10
β-strand	271-273	3	10
β-strand	276-281	6	1
β-strand	288-292	5	1
β-strand	296-301	6	1
β-strand	306-310	5	1
β-strand	318-323	6	5
β-strand	330-334	5	5
α-helix	342-344	3
α-helix	350-351	2
β-strand	352-356	5	5
α-helix	360-362	3

Chain B: 3 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	163-164	2
β-strand	168-169	2	10
β-strand	184-186	3	10
α-helix	189-191	3
α-helix	200-209	10

Chain C: 8 helices, 30 β-strands

Element	Residues	Length	Sheet
β-strand	32-33	2	11
α-helix	34	1
β-strand	42-47	6	12
α-helix	48-49	2
β-strand	55-61	7	12
β-strand	65-71	7	12
α-helix	72	1
β-strand	77-84	8	12
β-strand	89-94	6	13
β-strand	100-105	6	13
β-strand	109-114	6	13
β-strand	119-125	7	13
β-strand	130-137	8	14
β-strand	142-148	7	14
β-strand	152-156	5	14
β-strand	165-168	4	14
β-strand	173-179	7	15
β-strand	182-187	6	15
β-strand	192-196	5	15
β-strand	202-206	5	15
β-strand	215-222	8	4
β-strand	228-235	8	4
β-strand	239-244	6	4
α-helix	250-253	4
β-strand	255-258	4	4
β-strand	261	1	16
β-strand	271-273	3	16
β-strand	276-281	6	3
β-strand	288-292	5	3
β-strand	296-301	6	3
β-strand	306-310	5	3
α-helix	312-314	3
β-strand	318-323	6	11
β-strand	330-334	5	11
α-helix	342-344	3
α-helix	350-351	2
β-strand	352-356	5	11
α-helix	359-362	4

Chain D: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	163-164	2
α-helix	166-167	2
β-strand	168-169	2	16
β-strand	184-186	3	16
α-helix	189-191	3
α-helix	200-209	10

Chains E and F: 0 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	56-57	2	1
β-strand	60	1	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
ORF6 protein	E, F	protein	63	Severe acute respiratory syndrome coronavirus	P59634 (AlphaFold model)
mRNA export factor	A, C	protein	368	Homo sapiens	P78406 (AlphaFold model)
Nuclear pore complex protein Nup98-Nup96	B, D	protein	1817	Homo sapiens	P52948 (AlphaFold model)

Sequence of entity 1 (E, F), FASTA

>7F90_1 ORF6 protein (chains E, F)
MFHLVDFQVTIAEILIIIMRTFRIAIWNLDVIISSIVRQLFKPLTKKNYSELDDEEPMEL
DYP

Sequence of entity 2 (A, C), FASTA

>7F90_2 mRNA export factor (chains A, C)
MSLFGTTSGFGTSGTSMFGSATTDNHNPMKDIEVTSSPDDSIGCLSFSPPTLPGNFLIAG
SWANDVRCWEVQDSGQTIPKAQQMHTGPVLDVCWSDDGSKVFTASCDKTAKMWDLSSNQA
IQIAQHDAPVKTIHWIKAPNYSCVMTGSWDKTLKFWDTRSSNPMMVLQLPERCYCADVIY
PMAVVATAERGLIVYQLENQPSEFRRIESPLKHQHRCVAIFKDKQNKPTGFALGSIEGRV
AIHYINPPNPAKDNFTFKCHRSNGTNTSAPQDIYAVNGIAFHPVHGTLATVGSDGRFSFW
DKDARTKLKTSEQLDQPISACCFNHNGNIFAYASSYDWSKGHEFYNPQKKNYIFLRNAAE
ELKPRNKK

Sequence of entity 3 (B, D), FASTA

>7F90_3 Nuclear pore complex protein Nup98-Nup96 (chains B, D)
MFNKSFGTPFGGGTGGFGTTSTFGQNTGFGTTSGGAFGTSAFGSSNNTGGLFGNSQTKPG
GLFGTSSFSQPATSTSTGFGFGTSTGTANTLFGTASTGTSLFSSQNNAFAQNKPTGFGNF
GTSTSSGGLFGTTNTTSNPFGSTSGSLFGPSSFTAAPTGTTIKFNPPTGTDTMVKAGVST
NISTKHQCITAMKEYESKSLEELRLEDYQANRKGPQNQVGAGTTTGLFGSSPATSSATGL
FSSSTTNSGFAYGQNKTAFGTSTTGFGTNPGGLFGQQNQQTTSLFSKPFGQATTTQNTGF
SFGNTSTIGQPSTNTMGLFGVTQASQPGGLFGTATNTSTGTAFGTGTGLFGQTNTGFGAV
GSTLFGNNKLTTFGSSTTSAPSFGTTSGGLFGNKPTLTLGTNTNTSNFGFGTNTSGNSIF
GSKPAPGTLGTGLGAGFGTALGAGQASLFGNNQPKIGGPLGTGAFGAPGFNTTTATLGFG
APQAPVALTDPNASAAQQAVLQQHINSLTYSPFGDSPLFRNPMSDPKKKEERLKPTNPAA
QKALTTPTHYKLTPRPATRVRPKALQTTGTAKSHLFDGLDDDEPSLANGAFMPKKSIKKL
VLKNLNNSNLFSPVNRDSENLASPSEYPENGERFSFLSKPVDENHQQDGDEDSLVSHFYT
NPIAKPIPQTPESAGNKHSNSNSVDDTIVALNMRAALRNGLEGSSEETSFHDESLQDDRE
EIENNSYHMHPAGIILTKVGYYTIPSMDDLAKITNEKGECIVSDFTIGRKGYGSIYFEGD
VNLTNLNLDDIVHIRRKEVVVYLDDNQKPPVGEGLNRKAEVTLDGVWPTDKTSRCLIKSP
DRLADINYEGRLEAVSRKQGAQFKEYRPETGSWVFKVSHFSKYGLQDSDEEEEEHPSKTS
TKKLKTAPLPPASQTTPLQMALNGKPAPPPQSQSPEVEQLGRVVELDSDMVDITQEPVLD
TMLEESMPEDQEPVSASTHIASSLGINPHVLQIMKASLLTDEEDVDMALDQRFSRLPSKA
DTSQEICSPRLPISASHSSKTRSLVGGLLQSKFTSGAFLSPSVSVQECRTPRAASLMNIP
STSSWSVPPPLTSVFTMPSPAPEVPLKTVGTRRQLGLVPREKSVTYGKGKLLMDMALFMG
RSFRVGWGPNWTLANSGEQLNGSHELENHQIADSMEFGFLPNPVAVKPLTESPFKVHLEK
LSLRQRKPDEDMKLYQTPLELKLKHSTVHVDELCPLIVPNLGVAVIHDYADWVKEASGDL
PEAQIVKHWSLTWTLCEALWGHLKELDSQLNEPREYIQILERRRAFSRWLSCTATPQIEE
EVSLTQKNSPVEAVFSYLTGKRISEACSLAQQSGDHRLALLLSQFVGSQSVRELLTMQLV
DWHQLQADSFIQDERLRIFALLAGKPVWQLSEKKQINVCSQLDWKRSLAIHLWYLLPPTA
SISRALSMYEEAFQNTSDSDRYACSPLPSYLEGSGCVIAEEQNSQTPLRDVCFHLLKLYS
DRHYDLNQLLEPRSITADPLDYRLSWHLWEVLRALNYTHLSAQCEGVLQASYAGQLESEG
LWEWAIFVLLHIDNSGIREKAVRELLTRHCQLLETPESWAKETFLTQKLRVPAKWIHEAK
AVRAHMESDKHLEALCLFKAEHWNRCHKLIIRHLASDAIINENYDYLKGFLEDLAPPERS
SLIQDWETSGLVYLDYIRVIEMLRHIQQVDCSGNDLEQLHIKVTSLCSRIEQIQCYSAKD
RLAQSDMAKRVANLLRVVLSLHHPPDRTSDSTPDPQRVPLRLLAPHIGRLPMPEDYAMDE
LRSLTQSYLRELAVGSL

Primary citation

Structural basis for Sarbecovirus ORF6 mediated blockage of nucleocytoplasmic transport. Gao, X., Tian, H., Zhu, K. et al. Nat Commun (2022) 13:4782. DOI 10.1038/s41467-022-32489-5

Other PDB entries of the same protein (UniProt P59634 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7VPG 2.49 Å, Crystal structure of the C-terminal tail of SARS-CoV-1 Orf6 complex with human…

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