7VPH: MRNA export factor

Crystal structure of the C-terminal tail of SARS-CoV-2 Orf6 complex with human nucleoporin pair Rae1-Nup98. Determined by X-ray diffraction at 2.8 Å resolution. Released 19 Jan 2022.

Method: X-ray diffraction
Resolution: 2.8 Å
Organisms: Homo sapiens, Severe acute respiratory syndrome coronavirus 2
Chains: 12
Atoms: 12,567
Mol. weight: 210.68 kDa
Released: 19 Jan 2022

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

Secondary structure: helices and β-sheets

7VPH contains 49 α-helices and 136 β-strands across 12 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: 10 helices, 30 β-strands

Element	Residues	Length	Sheet
α-helix	31	1
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
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	130-138	9	4
β-strand	141-148	8	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	1	7
α-helix	270	1
β-strand	271-273	3	7
α-helix	274-275	2
β-strand	276-281	6	8
β-strand	288-292	5	8
β-strand	297-301	5	8
β-strand	306-310	5	8
α-helix	311-314	4
β-strand	318-323	6	1
β-strand	330-334	5	1
α-helix	342-344	3
β-strand	352-356	5	1
α-helix	360-362	3

Chain B: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	163-164	2
α-helix	166-167	2
β-strand	168-172	5	7
β-strand	181-186	6	7
α-helix	189-191	3
α-helix	200-210	11

Chain C: 8 helices, 30 β-strands

Element	Residues	Length	Sheet
β-strand	32-33	2	9
α-helix	34	1
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	191-196	6	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	342-344	3
β-strand	352-356	5	9
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	15
β-strand	184-186	3	15
α-helix	189-191	3
α-helix	200-210	11

Chain E: 9 helices, 30 β-strands

Element	Residues	Length	Sheet
α-helix	31	1
β-strand	32-33	2	17
α-helix	34	1
β-strand	42-47	6	18
α-helix	48-49	2
β-strand	55-61	7	18
β-strand	65-71	7	18
β-strand	77-84	8	18
β-strand	89-94	6	19
β-strand	100-105	6	19
β-strand	109-114	6	19
β-strand	119-125	7	19
β-strand	130-137	8	20
β-strand	142-148	7	20
β-strand	152-156	5	20
β-strand	165-168	4	20
β-strand	173-179	7	21
β-strand	182-187	6	21
α-helix	188-190	3
β-strand	192-196	5	21
β-strand	202-206	5	21
β-strand	215-222	8	22
β-strand	228-235	8	22
β-strand	239-244	6	22
α-helix	250-253	4
β-strand	255-258	4	22
β-strand	261	1	23
α-helix	270	1
β-strand	271-273	3	23
α-helix	274-275	2
β-strand	276-281	6	24
β-strand	288-292	5	24
β-strand	297-301	5	24
β-strand	306-310	5	24
β-strand	318-323	6	17
β-strand	330-334	5	17
α-helix	342-344	3
β-strand	352-356	5	17
α-helix	360-362	3

Chain F: 3 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	163-164	2
β-strand	168-173	6	23
β-strand	180-186	7	23
α-helix	189-191	3
α-helix	200-209	10

Chain G: 7 helices, 30 β-strands

Element	Residues	Length	Sheet
β-strand	32-33	2	25
α-helix	34-35	2
β-strand	42-47	6	26
α-helix	48-49	2
β-strand	55-61	7	26
β-strand	65-71	7	26
β-strand	77-84	8	26
β-strand	89-94	6	27
β-strand	100-105	6	27
β-strand	109-114	6	27
β-strand	119-125	7	27
β-strand	130-137	8	28
β-strand	142-148	7	28
β-strand	152-156	5	28
β-strand	165-168	4	28
β-strand	173-179	7	29
β-strand	182-187	6	29
β-strand	191-196	6	29
β-strand	202-206	5	29
β-strand	215-222	8	30
β-strand	228-235	8	30
β-strand	240-244	5	30
α-helix	250-253	4
β-strand	255-258	4	30
β-strand	261	1	31
α-helix	270	1
β-strand	271-273	3	31
α-helix	274-275	2
β-strand	276-281	6	32
β-strand	288-292	5	32
β-strand	297-301	5	32
β-strand	306-310	5	32
α-helix	312-314	3
β-strand	318-323	6	25
β-strand	330-334	5	25
α-helix	342-344	3
β-strand	352-356	5	25

Chain H: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	163-164	2
α-helix	166-167	2
β-strand	168	1	31
β-strand	184-186	3	31
α-helix	189-191	3
α-helix	200-210	11

2 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
mRNA export factor	A, C, E, G	protein	378	Homo sapiens	P78406 (AlphaFold model)
Isoform 3 of Nuclear pore complex protein Nup98-Nup96	B, D, F, H	protein	67	Homo sapiens	P52948 (AlphaFold model)
ORF6 protein	I, J, K, X	protein	21	Severe acute respiratory syndrome coronavirus 2	P0DTC6 (AlphaFold model)

Sequence of entity 1 (A, C, E, G), FASTA

>7VPH_1 mRNA export factor (chains A, C, E, G)
MSLFGTTSGFGTSGTSMFGSATTDNHNPMKDIEVTSSPDDSIGCLSFSPPTLPGNFLIAG
SWANDVRCWEVQDSGQTIPKAQQMHTGPVLDVCWSDDGSKVFTASCDKTAKMWDLSSNQA
IQIAQHDAPVKTIHWIKAPNYSCVMTGSWDKTLKFWDTRSSNPMMVLQLPERCYCADVIY
PMAVVATAERGLIVYQLENQPSEFRRIESPLKHQHRCVAIFKDKQNKPTGFALGSIEGRV
AIHYINPPNPAKDNFTFKCHRSNGTNTSAPQDIYAVNGIAFHPVHGTLATVGSDGRFSFW
DKDARTKLKTSEQLDQPISACCFNHNGNIFAYASSYDWSKGHEFYNPQKKNYIFLRNAAE
ELKPRNKKHHHHHHHHHH

Sequence of entity 2 (B, D, F, H), FASTA

>7VPH_2 Isoform 3 of Nuclear pore complex protein Nup98-Nup96 (chains B, D, F, H)
MHHHHHHHHHHTGTTIKFNPPTGTDTMVKAGVSTNISTKHQCITAMKEYESKSLEELRLE
DYQANRK

Sequence of entity 3 (I, J, K, X), FASTA

>7VPH_3 ORF6 protein (chains I, J, K, X)
SKSLTENKYSQLDEEQPMEID

Primary citation

Molecular Mechanism of SARS-CoVs Orf6 Targeting the Rae1-Nup98 Complex to Compete With mRNA Nuclear Export. Li, T., Wen, Y., Guo, H. et al. Front Mol Biosci (2021) 8:813248-813248. DOI 10.3389/fmolb.2021.813248 · PubMed

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…
7F60 2.85 Å, Crystal structure of auxiliary protein in complex with human nuclear protein
4OWR 3.15 Å, Vesiculoviral matrix (M) protein occupies nucleic acid binding site at nucleoporin pair…

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