7F60: Auxiliary protein

Crystal structure of auxiliary protein in complex with human nuclear protein. Determined by X-ray diffraction at 2.85 Å resolution. Released 14 Sept 2022.

Method: X-ray diffraction
Resolution: 2.85 Å
Organisms: Homo sapiens, Severe acute respiratory syndrome coronavirus 2
Chains: 6
Atoms: 6,151
Mol. weight: 492.15 kDa
Released: 14 Sept 2022

Explore 7F60 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7F60 contains 23 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: 9 helices, 30 β-strands

Element	Residues	Length	Sheet
β-strand	32-33	2	1
α-helix	34	1
β-strand	42-47	6	2
α-helix	48-49	2
β-strand	55-61	7	2
β-strand	65-71	7	2
α-helix	72	1
β-strand	77-84	8	2
β-strand	89-94	6	3
β-strand	100-105	6	3
β-strand	109-114	6	3
β-strand	119-125	7	3
β-strand	130-137	8	4
β-strand	142-148	7	4
β-strand	152-156	5	4
β-strand	165-168	4	4
β-strand	173-179	7	5
β-strand	182-187	6	5
α-helix	188-190	3
β-strand	191-196	6	5
β-strand	202-206	5	5
β-strand	215-222	8	6
β-strand	228-235	8	6
β-strand	239-244	6	6
α-helix	250-253	4
β-strand	255-258	4	6
β-strand	261-262	2	7
α-helix	270	1
β-strand	271-273	3	7
β-strand	276-281	6	8
β-strand	288-292	5	8
β-strand	297-301	5	8
β-strand	306-310	5	8
β-strand	318-323	6	1
β-strand	330-334	5	1
α-helix	342-344	3
α-helix	350-351	2
β-strand	352-356	5	1
α-helix	360-362	3

Chain B: 6 helices, 30 β-strands

Element	Residues	Length	Sheet
β-strand	32-33	2	9
β-strand	42-47	6	10
α-helix	48-49	2
β-strand	55-61	7	10
β-strand	65-71	7	10
β-strand	77-84	8	10
β-strand	89-94	6	11
β-strand	100-105	6	11
β-strand	109-114	6	11
β-strand	119-125	7	11
β-strand	130-137	8	12
β-strand	142-148	7	12
β-strand	152-156	5	12
β-strand	165-168	4	12
β-strand	173-179	7	13
β-strand	182-187	6	13
β-strand	193-196	4	13
β-strand	202-206	5	13
α-helix	207-209	3
β-strand	215-222	8	14
β-strand	228-235	8	14
β-strand	239-244	6	14
α-helix	250-253	4
β-strand	255-258	4	14
β-strand	261	1	15
α-helix	270	1
β-strand	271-273	3	15
β-strand	276-281	6	16
β-strand	288-292	5	16
β-strand	297-301	5	16
β-strand	306-310	5	16
α-helix	312-314	3
β-strand	318-323	6	9
β-strand	330-334	5	9
α-helix	350-351	2
β-strand	352-356	5	9

Chain C: 3 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	163-164	2
β-strand	168-171	4	15
β-strand	182-186	5	15
α-helix	189-191	3
α-helix	200-209	10

Chain D: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	163-164	2
α-helix	166-167	2
β-strand	168-173	6	7
β-strand	180-186	7	7
α-helix	189-191	3
α-helix	193-195	3
α-helix	200-209	10

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

Element	Residues	Length	Sheet
β-strand	56-57	2	8
β-strand	60	1	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
mRNA export factor	A, B	protein	368	Homo sapiens	P78406 (AlphaFold model)
Nuclear pore complex protein Nup98-Nup96	C, D	protein	1817	Homo sapiens	P52948 (AlphaFold model)
ORF6 protein	E, F	protein	61	Severe acute respiratory syndrome coronavirus 2	P0DTC6 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>7F60_1 mRNA export factor (chains A, B)
MSLFGTTSGFGTSGTSMFGSATTDNHNPMKDIEVTSSPDDSIGCLSFSPPTLPGNFLIAG
SWANDVRCWEVQDSGQTIPKAQQMHTGPVLDVCWSDDGSKVFTASCDKTAKMWDLSSNQA
IQIAQHDAPVKTIHWIKAPNYSCVMTGSWDKTLKFWDTRSSNPMMVLQLPERCYCADVIY
PMAVVATAERGLIVYQLENQPSEFRRIESPLKHQHRCVAIFKDKQNKPTGFALGSIEGRV
AIHYINPPNPAKDNFTFKCHRSNGTNTSAPQDIYAVNGIAFHPVHGTLATVGSDGRFSFW
DKDARTKLKTSEQLDQPISACCFNHNGNIFAYASSYDWSKGHEFYNPQKKNYIFLRNAAE
ELKPRNKK

Sequence of entity 2 (C, D), FASTA

>7F60_2 Nuclear pore complex protein Nup98-Nup96 (chains C, 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

Sequence of entity 3 (E, F), FASTA

>7F60_3 ORF6 protein (chains E, F)
MFHLVDFQVTIAEILLIIMRTFKVSIWNLDYIINLIIKNLSKSLTENKYSQLDEEQPMEI
D

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 P78406 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3MMY 1.65 Å, Structural and functional analysis of the interaction between the nucleoporin Nup98 and…
7F90 2.39 Å, Crystal structure of SARS auxiliary protein in complex with human nuclear protein
7VPG 2.49 Å, Crystal structure of the C-terminal tail of SARS-CoV-1 Orf6 complex with human…
7VPH 2.8 Å, Crystal structure of the C-terminal tail of SARS-CoV-2 Orf6 complex with human…
4OWR 3.15 Å, Vesiculoviral matrix (M) protein occupies nucleic acid binding site at nucleoporin pair…

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