7BYF: Mouse ORF10-Rae1-Nup98 complex

The crystal structure of mouse ORF10-Rae1-Nup98 complex. Determined by X-ray diffraction at 2.5 Å resolution. Released 24 Mar 2021.

Method: X-ray diffraction
Resolution: 2.5 Å
Organisms: Mus musculus, Murid herpesvirus 4
Chains: 6
Atoms: 12,838
Mol. weight: 188.29 kDa
Ligands: HG
Released: 24 Mar 2021

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

Secondary structure: helices and β-sheets

7BYF contains 41 α-helices and 145 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: 4 helices, 30 β-strands

Element	Residues	Length	Sheet
β-strand	32-33	2	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	130-137	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
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
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	329-334	6	1
α-helix	342-344	3
α-helix	350-351	2
β-strand	352-357	6	1

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	200-209	10

Chain C: 9 helices, 40 β-strands

Element	Residues	Length	Sheet
β-strand	16-17	2	19
β-strand	22-25	4	19
β-strand	30-31	2	20
β-strand	36	1	21
β-strand	39-47	9	21
α-helix	48-49	2
α-helix	50-54	5
β-strand	56-57	2	22
α-helix	64-66	3
β-strand	74-80	7	19
β-strand	86-88	3	21
β-strand	91-92	2	19
β-strand	99-106	8	21
β-strand	110-111	2	20
β-strand	117-123	7	19
α-helix	128-130	3
β-strand	131-134	4	23
β-strand	136-138	3	23
α-helix	141-143	3
β-strand	149-155	7	23
β-strand	159-170	12	23
α-helix	171	1
β-strand	177-182	6	23
β-strand	189-198	10	23
β-strand	203	1	23
β-strand	208-216	9	23
β-strand	222-229	8	23
β-strand	236-246	11	23
β-strand	252-254	3	23
β-strand	257	1	23
α-helix	259-261	3
β-strand	270-273	4	19
β-strand	279-280	2	24
β-strand	285-290	6	25
β-strand	295-296	2	23
β-strand	304-311	8	19
β-strand	320	1	25
β-strand	323-325	3	19
β-strand	331-336	6	25
β-strand	343-344	2	24
β-strand	350-360	11	19
β-strand	375-377	3	19
β-strand	382-385	4	19
β-strand	388-390	3	19
β-strand	403-404	2	22
α-helix	411	1
β-strand	412	1	8
α-helix	413	1
β-strand	415-416	2	6

Chain D: 7 helices, 30 β-strands

Element	Residues	Length	Sheet
β-strand	32-33	2	26
β-strand	42-47	6	27
α-helix	48-49	2
β-strand	56-61	6	27
β-strand	65-71	7	27
β-strand	77-84	8	27
β-strand	89-94	6	28
β-strand	100-105	6	28
β-strand	109-114	6	28
β-strand	119-125	7	28
β-strand	130-135	6	29
β-strand	144-148	5	29
β-strand	152-156	5	29
β-strand	165-168	4	29
β-strand	173-179	7	30
β-strand	182-187	6	30
α-helix	188-190	3
β-strand	191-196	6	30
β-strand	202-206	5	30
α-helix	207-209	3
β-strand	215-222	8	18
β-strand	228-235	8	18
β-strand	239-244	6	18
α-helix	250-253	4
β-strand	255-258	4	18
β-strand	261	1	31
α-helix	270	1
β-strand	271-273	3	31
β-strand	276-281	6	17
β-strand	288-292	5	17
β-strand	297-301	5	17
β-strand	306-310	5	17
β-strand	318-323	6	26
β-strand	329-334	6	26
α-helix	342-344	3
α-helix	350-351	2
β-strand	352-357	6	26

Chain E: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	163-164	2
α-helix	166-167	2
β-strand	168-174	7	31
β-strand	179-186	8	31
α-helix	189-191	3
α-helix	200-209	10

Chain F: 13 helices, 41 β-strands

Element	Residues	Length	Sheet
β-strand	7-9	3	9
β-strand	13-17	5	9
β-strand	22-26	5	9
α-helix	29	1
β-strand	30-31	2	10
β-strand	40-43	4	11
α-helix	48-49	2
α-helix	50-54	5
β-strand	56-58	3	12
α-helix	64-66	3
α-helix	70-72	3
β-strand	74-80	7	9
β-strand	86-88	3	11
β-strand	91-92	2	9
α-helix	99-100	2
β-strand	101-106	6	11
β-strand	110-111	2	10
β-strand	117-123	7	9
α-helix	125-127	3
α-helix	128-130	3
β-strand	131-135	5	13
β-strand	138	1	14
α-helix	141-143	3
β-strand	149-155	7	13
β-strand	159-170	12	13
β-strand	177-182	6	13
β-strand	189-198	10	13
β-strand	208-214	7	13
β-strand	216	1	14
β-strand	222-229	8	13
β-strand	236-246	11	13
β-strand	252-254	3	13
β-strand	257	1	13
α-helix	259-261	3
β-strand	270-273	4	9
β-strand	278-280	3	15
α-helix	281	1
β-strand	285-290	6	16
β-strand	295-296	2	13
β-strand	304-309	6	9
β-strand	311	1	9
β-strand	320	1	16
β-strand	323-325	3	9
β-strand	331-336	6	16
β-strand	343-345	3	15
β-strand	350-359	10	9
β-strand	374-377	4	9
β-strand	382-385	4	9
β-strand	388-390	3	9
α-helix	392-394	3
β-strand	402-404	3	12
β-strand	411-412	2	17
α-helix	413	1
β-strand	415-417	3	18

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
mRNA export factor	A, D	protein	347	Mus musculus	Q8C570 (AlphaFold model)
Peptidase S59 domain-containing protein	B, E	protein	57	Mus musculus	Q6PFD9 (AlphaFold model)
10 protein	C, F	protein	418	Murid herpesvirus 4	O41931 (AlphaFold model)

Sequence of entity 1 (A, D), FASTA

>7BYF_1 mRNA export factor (chains A, D)
LEDNHNPMKDIEVTSSPDDSIGCLSFSPPTLPGNFLIAGSWANDVRCWEVQDSGQTIPKA
QQMHTGPVLDVCWSDDGSKVFTASCDKTAKMWDLNSNQAIQIAQHDAPVKTIHWIKAPNY
SCVMTGSWDKTLKFWDTRSSNPMMVLQLPERCYCADVIYPMAVVATAERGLIVYQLENQP
SEFRRIESPLKHQHRCVAIFKDKQNKPTGFALGSIEGRVAIHYINPPNPAKDNFTFKCHR
SNGTNTSAPQDIYAVNGIAFHPVHGTLATVGSDGRFSFWDKDARTKLKTSEQLDQPIAAC
CFNHNGNIFAYASSYDWSKGHEFYNPQKKNYIFLRNAAEELKPRNKK

Sequence of entity 2 (B, E), FASTA

>7BYF_2 Peptidase S59 domain-containing protein (chains B, E)
PTGTTIKFNPPTGTDTMVKAGVSTNISTKHQCITAMKEYESKSLEELRLEDYQANRK

Sequence of entity 3 (C, F), FASTA

>7BYF_3 10 protein (chains C, F)
MEKSAPSIILNHWCVTWQGHHFLCRNLSNIKILNRRNGYTTLDLPLTLGDLTQYRLAHGL
SENLMALSPYSWTIPFLVSSSETPGIELLPKVINDFGTPLSLAIKTNLPSIPAHQLLFYI
IFLRPSPLTSMSCYARPLSLASTPSTNGLCQSVSVLDNKPGLLITTPLHRDPASGKYTSN
VQSPTTFNLFRVLYIKLSGEEGMVSQKVKHLTIDKDSLQEGFLQLCLNMCGVSYETLQCE
ILLELVQGPTNFIFPAAFPPPVSLPHRNCIELTCDTERCLKPGDVMKLKHRLLYELGQRG
DTPQNAFLIVGAHSPETVWISPSLWLPGQPLYINIINLSHKPLLLSRHSILALAIPISYT
RAPASAHEATDTTICYSGNSRVLTCGAAHVLEAHFKHPPITSRAITDGGESPMEWQTL

Ligands and cofactors

ID	Name	Formula	Copies
HG	Mercury (II) ion	Hg	24

Water and common crystallization additives (NA) are not listed.

Primary citation

Molecular mechanism underlying selective inhibition of mRNA nuclear export by herpesvirus protein ORF10. Feng, H., Tian, H., Wang, Y. et al. Proc Natl Acad Sci U S A (2020) 117:26719-26727. DOI 10.1073/pnas.2007774117 · PubMed

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