7RLO: PDB entry 7RLO

Name: PDB 7RLO: Structure of the human eukaryotic translation initiation factor 2B (eIF2B) in complex with a viral protein NSs
Published: 2021-12-22
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: translation

Structure of the human eukaryotic translation initiation factor 2B (eIF2B) in complex with a viral protein NSs. Determined by electron microscopy at 2.6 Å resolution. Released 22 Dec 2021.

Method: Electron microscopy
Resolution: 2.6 Å
Organisms: Homo sapiens, Sandfly fever sicilian virus
Chains: 12
Atoms: 28,707
Mol. weight: 583.75 kDa
Released: 22 Dec 2021

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

Secondary structure: helices and β-sheets

7RLO contains 175 α-helices and 207 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: 13 helices, 35 β-strands

Element	Residues	Length	Sheet
β-strand	44-48	5	1
α-helix	57-60	4
α-helix	65-67	3
β-strand	69	1	2
β-strand	74	1	2
α-helix	75-86	12
β-strand	90-95	6	1
α-helix	99-107	9
β-strand	119-124	6	1
α-helix	131-141	11
β-strand	148-152	5	1
β-strand	155-157	3	3
α-helix	163-174	12
β-strand	181-187	7	1
α-helix	193-195	3
β-strand	201-205	5	4
β-strand	211	1	1
β-strand	212-217	6	4
β-strand	223-227	5	5
α-helix	228-232	5
β-strand	238-241	4	4
β-strand	244-252	9	1
α-helix	254-262	9
α-helix	269-277	9
β-strand	287-292	6	1
β-strand	297-299	3	3
α-helix	303-314	12
β-strand	336-338	3	6
β-strand	342-344	3	6
α-helix	350-351	2
β-strand	355-356	2	7
β-strand	360-362	3	6
β-strand	367	1	8
β-strand	373-375	3	7
β-strand	378-379	2	6
β-strand	384-385	2	8
β-strand	390-392	3	7
β-strand	395-396	2	6
β-strand	401-402	2	8
β-strand	407-409	3	7
β-strand	411-413	3	6
β-strand	418-419	2	8
β-strand	423-425	3	7
β-strand	429-431	3	6
β-strand	436-437	2	8
α-helix	438	1
β-strand	441-443	3	7
β-strand	448-449	2	6

Chain B: 12 helices, 37 β-strands

Element	Residues	Length	Sheet
β-strand	44-48	5	9
β-strand	69	1	10
β-strand	74	1	10
α-helix	75-86	12
β-strand	90-95	6	9
α-helix	99-106	8
β-strand	119-124	6	9
α-helix	132-141	10
β-strand	148-152	5	9
β-strand	155-157	3	11
α-helix	163-174	12
β-strand	181-187	7	9
β-strand	201-206	6	12
β-strand	211	1	9
β-strand	212-217	6	12
β-strand	223-226	4	13
α-helix	229-233	5
β-strand	238-241	4	12
β-strand	244-252	9	9
α-helix	254-262	9
α-helix	269-278	10
β-strand	287-292	6	9
β-strand	297-299	3	11
α-helix	303-314	12
α-helix	331-333	3
β-strand	336-337	2	14
α-helix	339-341	3
β-strand	342-344	3	14
β-strand	350	1	15
α-helix	351	1
β-strand	355-356	2	16
β-strand	360-362	3	14
β-strand	367-368	2	15
β-strand	373-375	3	16
β-strand	378-379	2	14
β-strand	384-385	2	15
β-strand	390-392	3	16
β-strand	395-396	2	14
β-strand	401-402	2	15
β-strand	407-409	3	16
β-strand	411-413	3	14
β-strand	418-419	2	15
β-strand	423-425	3	16
β-strand	429-431	3	14
β-strand	436-437	2	15
β-strand	441-443	3	16
α-helix	444	1
β-strand	448-449	2	14
β-strand	457	1	14

Chains C and D: 18 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	9-24	16
α-helix	31-47	17
β-strand	53	1	17
α-helix	54-71	18
α-helix	76-97	22
α-helix	109-113	5
β-strand	125	1	17
α-helix	129-152	24
β-strand	164-168	5	18
α-helix	172-181	10
β-strand	188-192	5	18
α-helix	200-208	9
β-strand	214-217	4	18
α-helix	226-228	3
β-strand	231-234	4	18
β-strand	238-239	2	19
β-strand	245-248	4	19
α-helix	251-260	10
β-strand	265-268	4	18
α-helix	271-273	3
β-strand	274	1	19
α-helix	287	1
β-strand	288	1	20
α-helix	297-299	3
α-helix	301-304	4
β-strand	306-308	3	21
β-strand	311	1	20
β-strand	313-316	4	19
α-helix	318-320	3
β-strand	323-326	4	18
β-strand	329-331	3	18
α-helix	333-335	3
α-helix	336-341	6
α-helix	346-348	3

Chain E: 21 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	168-172	5
α-helix	175-177	3
β-strand	185	1	27
α-helix	193-195	3
α-helix	205-216	12
α-helix	223-238	16
α-helix	242-243	2
α-helix	248-266	19
α-helix	271-285	15
α-helix	293-308	16
α-helix	309-313	5
α-helix	314-322	9
β-strand	332-336	5	26
α-helix	340-352	13
β-strand	357-362	6	26
α-helix	370-377	8
β-strand	383-387	5	26
α-helix	388-390	3
α-helix	391-394	4
α-helix	395-397	3
β-strand	400-404	5	26
β-strand	407-408	2	28
β-strand	414-417	4	28
α-helix	421-428	8
β-strand	434-437	4	26
α-helix	440-442	3
β-strand	443	1	28
β-strand	457	1	27
α-helix	460-463	4
β-strand	467	1	29
β-strand	470	1	29
β-strand	482-484	3	23
β-strand	487	1	27
β-strand	489-492	4	28
α-helix	494-496	3
β-strand	499-501	3	26
β-strand	506-507	2	26
α-helix	512-518	7

Chain F: 21 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	175-177	3
β-strand	185	1	30
α-helix	193-195	3
α-helix	205-216	12
α-helix	222-238	17
α-helix	242-243	2
α-helix	248-266	19
α-helix	271-285	15
α-helix	293-308	16
α-helix	309-313	5
α-helix	314-324	11
β-strand	332-336	5	21
α-helix	340-352	13
β-strand	357-362	6	21
α-helix	370-378	9
β-strand	383-387	5	21
α-helix	388-390	3
α-helix	391-394	4
α-helix	395-397	3
β-strand	400-404	5	21
β-strand	407-408	2	31
β-strand	414-417	4	31
α-helix	421-428	8
β-strand	434-437	4	21
α-helix	440-442	3
β-strand	443	1	31
β-strand	457	1	30
α-helix	460-463	4
β-strand	467	1	32
β-strand	470	1	32
α-helix	476-478	3
β-strand	483-484	2	18
β-strand	487	1	30
β-strand	489-492	4	31
α-helix	494-496	3
β-strand	499-502	4	21
β-strand	505-508	4	21
α-helix	512-518	7

Chain G: 16 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	8-14	7
α-helix	22-35	14
α-helix	42-59	18
α-helix	63-79	17
α-helix	88-104	17
α-helix	107-115	9
α-helix	116-118	3
β-strand	123-127	5	33
α-helix	132-142	11
β-strand	148-153	6	33
α-helix	161-170	10
β-strand	175-178	4	33
α-helix	180-182	3
α-helix	183-186	4
α-helix	187-189	3
β-strand	192-195	4	33
β-strand	199-200	2	34
β-strand	206-208	3	34
α-helix	213-221	9
β-strand	226-229	4	33
β-strand	235	1	34
α-helix	248-251	4
β-strand	274-276	3	34
α-helix	278-280	3
β-strand	283-286	4	33
β-strand	289-291	3	33
α-helix	296-303	8

Chain H: 14 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	7-14	8
α-helix	22-35	14
α-helix	42-59	18
α-helix	63-80	18
α-helix	88-104	17
α-helix	107-115	9
α-helix	116-118	3
β-strand	124-127	4	35
α-helix	132-142	11
β-strand	149-153	5	35
α-helix	160-169	10
β-strand	175-178	4	35
α-helix	180-182	3
β-strand	192-195	4	35
β-strand	199-200	2	36
β-strand	206-208	3	36
α-helix	213-220	8
β-strand	226-229	4	35
β-strand	235	1	36
α-helix	248-251	4
β-strand	274-276	3	36
α-helix	278-280	3
β-strand	283-286	4	35
β-strand	289-291	3	35
α-helix	295-303	9

Chain I: 10 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	37
α-helix	25-27	3
α-helix	37-43	7
β-strand	51-55	5	37
β-strand	73-77	5	37
α-helix	86-90	5
α-helix	94-96	3
β-strand	100-105	6	37
β-strand	109	1	38
α-helix	115-122	8
β-strand	128-134	7	37
β-strand	157-161	5	4
β-strand	166	1	37
β-strand	167-171	5	4
β-strand	179-183	5	5
α-helix	184-189	6
β-strand	192-196	5	4
β-strand	199-207	9	37
α-helix	209-217	9
α-helix	224-233	10
α-helix	263-266	4
β-strand	300-304	5	37
β-strand	311	1	38
α-helix	316-333	18

3 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
Translation initiation factor eIF-2B subunit epsilon	A, B	protein	721	Homo sapiens	Q13144 (AlphaFold model)
Translation initiation factor eIF-2B subunit beta	C, D	protein	351	Homo sapiens	P49770 (AlphaFold model)
Translation initiation factor eIF-2B subunit delta	E, F	protein	523	Homo sapiens	Q9UI10 (AlphaFold model)
Translation initiation factor eIF-2B subunit alpha	G, H	protein	305	Homo sapiens	Q14232 (AlphaFold model)
Translation initiation factor eIF-2B subunit gamma	I, J	protein	452	Homo sapiens	Q9NR50
Non-structural protein NS-S	K, L	protein	269	Sandfly fever sicilian virus	P12792

Sequence of entity 1 (A, B), FASTA

>7RLO_1 Translation initiation factor eIF-2B subunit epsilon (chains A, B)
MAAPVVAPPGVVVSRANKRSGAGPGGSGGGGARGAEEEPPPPLQAVLVADSFDRRFFPIS
KDQPRVLLPLANVALIDYTLEFLTATGVQETFVFCCWKAAQIKEHLLKSKWCRPTSLNVV
RIITSELYRSLGDVLRDVDAKALVRSDFLLVYGDVISNINITRALEEHRLRRKLEKNVSV
MTMIFKESSPSHPTRCHEDNVVVAVDSTTNRVLHFQKTQGLRRFAFPLSLFQGSSDGVEV
RYDLLDCHISICSPQVAQLFTDNFDYQTRDDFVRGLLVNEEILGNQIHMHVTAKEYGARV
SNLHMYSAVCADVIRRWVYPLTPEANFTDSTTQSCTHSRHNIYRGPEVSLGHGSILEENV
LLGSGTVIGSNCFITNSVIGPGCHIGDNVVLDQTYLWQGVRVAAGAQIHQSLLCDNAEVK
ERVTLKPRSVLTSQVVVGPNITLPEGSVISLHPPDAEEDEDDGEFSDDSGADQEKDKVKM
KGYNPAEVGAAGKGYLWKAAGMNMEEEEELQQNLWGLKINMEEESESESEQSMDSEEPDS
RGGSPQMDDIKVFQNEVLGTLQRGKEENISCDNLVLEINSLKYAYNISLKEVMQVLSHVV
LEFPLQQMDSPLDSSRYCALLLPLLKAWSPVFRNYIKRAADHLEALAAIEDFFLEHEALG
ISMAKVLMAFYQLEILAEETILSWFSQRDTTDKGQQLRKNQQLQRFIQWLKEAEEESSED
D

Sequence of entity 2 (C, D), FASTA

>7RLO_2 Translation initiation factor eIF-2B subunit beta (chains C, D)
MPGSAAKGSELSERIESFVETLKRGGGPRSSEEMARETLGLLRQIITDHRWSNAGELMEL
IRREGRRMTAAQPSETTVGNMVRRVLKIIREEYGRLHGRSDESDQQESLHKLLTSGGLNE
DFSFHYAQLQSNIIEAINELLVELEGTMENIAAQALEHIHSNEVIMTIGFSRTVEAFLKE
AARKRKFHVIVAECAPFCQGHEMAVNLSKAGIETTVMTDAAIFAVMSRVNKVIIGTKTIL
ANGALRAVTGTHTLALAAKHHSTPLIVCAPMFKLSPQFPNEEDSFHKFVAPEEVLPFTEG
DILEKVSVHCPVFDYVPPELITLFISNIGGNAPSYIYRLMSELYHPDDHVL

Sequence of entity 3 (E, F), FASTA

>7RLO_3 Translation initiation factor eIF-2B subunit delta (chains E, F)
MAAVAVAVREDSGSGMKAELPPGPGAVGREMTKEEKLQLRKEKKQQKKKRKEEKGAEPET
GSAVSAAQCQVGPTRELPESGIQLGTPREKVPAGRSKAELRAERRAKQEAERALKQARKG
EQGGPPPKASPSTAGETPSGVKRLPEYPQVDDLLLRRLVKKPERQQVPTRKDYGSKVSLF
SHLPQYSRQNSLTQFMSIPSSVIHPAMVRLGLQYSQGLVSGSNARCIALLRALQQVIQDY
TTPPNEELSRDLVNKLKPYMSFLTQCRPLSASMHNAIKFLNKEITSVGSSKREEEAKSEL
RAAIDRYVQEKIVLAAQAISRFAYQKISNGDVILVYGCSSLVSRILQEAWTEGRRFRVVV
VDSRPWLEGRHTLRSLVHAGVPASYLLIPAASYVLPEVSKVLLGAHALLANGSVMSRVGT
AQLALVARAHNVPVLVCCETYKFCERVQTDAFVSNELDDPDDLQCKRGEHVALANWQNHA
SLRLLNLVYDVTPPELVDLVITELGMIPCSSVPVVLRVKSSDQ

Sequence of entity 4 (G, H), FASTA

>7RLO_4 Translation initiation factor eIF-2B subunit alpha (chains G, H)
MDDKELIEYFKSQMKEDPDMASAVAAIRTLLEFLKRDKGETIQGLRANLTSAIETLCGVD
SSVAVSSGGELFLRFISLASLEYSDYSKCKKIMIERGELFLRRISLSRNKIADLCHTFIK
DGATILTHAYSRVVLRVLEAAVAAKKRFSVYVTESQPDLSGKKMAKALCHLNVPVTVVLD
AAVGYIMEKADLVIVGAEGVVENGGIINKIGTNQMAVCAKAQNKPFYVVAESFKFVRLFP
LNQQDVPDKFKYKADTLKVAQTGQDLKEEHPWVDYTAPSLITLLFTDLGVLTPSAVSDEL
IKLYL

Sequence of entity 5 (I, J), FASTA

>7RLO_5 Translation initiation factor eIF-2B subunit gamma (chains I, J)
MEFQAVVMAVGGGSRMTDLTSSIPKPLLPVGNKPLIWYPLNLLERVGFEEVIVVTTRDVQ
KALCAEFKMKMKPDIVCIPDDADMGTADSLRYIYPKLKTDVLVLSCDLITDVALHEVVDL
FRAYDASLAMLMRKGQDSIEPVPGQKGKKKAVEQRDFIGVDSTGKRLLFMANEADLDEEL
VIKGSILQKHPRIRFHTGLVDAHLYCLKKYIVDFLMENGSITSIRSELIPYLVRKQFSSA
SSQQGQEEKEEDLKKKELKSLDIYSFIKEANTLNLAPYDACWNACRGDRWEDLSRSQVRC
YVHIMKEGLCSRVSTLGLYMEANRQVPKLLSALCPEEPPVHSSAQIVSKHLVGVDSLIGP
ETQIGEKSSIKRSVIGSSCLIKDRVTITNCLLMNSVTVEEGSNIQGSVICNNAVIEKGAD
IKDCLIGSGQRIEAKAKRVNEVIVGNDQLMEI

Sequence of entity 6 (K, L), FASTA

>7RLO_6 Non-structural protein NS-S (chains K, L)
MNSQYMFDYPAINIDVRCHRLLSSVSYVAYNKFHTHDVSTYEHCEIPLEKLRLGFGRRNS
LADFYSLGELPASWGPACYFSSVKPMMYTFQGMASDLSRFDLTSFSRKGLPNVLKALSWP
LGIPDCEIFSICSDRFVRGLQTRDQLMSYILRMGDSHSLDECIVQAHKKILQEARRLGLS
DEHYNGYDLFREIGSLVCLRLINAEPFDTASSGEALDVRTVIRSYRASDPSTGLTEYGNS
LWTPIHSHVDENDESSSDSDFGSHHHHHH

Primary citation

Viral evasion of the integrated stress response through antagonism of eIF2-P binding to eIF2B. Schoof, M., Wang, L., Cogan, J.Z. et al. Nat Commun (2021) 12:7103-7103. DOI 10.1038/s41467-021-26164-4 · PubMed

Other PDB entries of the same protein (UniProt Q13144 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3JUI 2.0 Å, Crystal Structure of the C-terminal Domain of Human Translation Initiation Factor eIF2B…
9Y4B 2.1 Å, Eukaryotic translation initiation factor 2-B (eIF2B) with a truncation in the beta…
7VLK 2.27 Å, eIF2B-SFSV NSs C2-imposed
9Y3U 2.4 Å, Eukaryotic translation initiation factor 2-B (eIF2B) with a truncation in the beta…
9Y4W 2.4 Å, Eukaryotic translation initiation factor 2-B (eIF2B) with a truncation in the beta…
7F64 2.42 Å, eIF2B-SFSV NSs
9Y3T 2.5 Å, Eukaryotic translation initiation factor 2-B (eIF2B) with a truncation in the beta…
9HVE 2.7 Å, Native human eIF2-eIF2B complex
7F66 2.76 Å, eIF2B-SFSV NSs-1-eIF2
9Y5T 2.78 Å, eIF2B lacking the latch helix bound to ISRACT-02 (Active state)
6CAJ 2.8 Å, Electron cryo-microscopy of the eukaryotic translation initiation factor 2B from Homo…
7L70 2.8 Å, The eukaryotic translation initiation factor 2B from Homo sapiens in its apo form

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