7VLK: EIF2B-SFSV NSs C2-imposed
eIF2B-SFSV NSs C2-imposed. Determined by electron microscopy at 2.27 Å resolution. Released 1 Dec 2021.
- Method
- Electron microscopy
- Resolution
- 2.27 Å
- Organisms
- Homo sapiens, Sandfly fever sicilian virus
- Chains
- 12
- Atoms
- 28,774
- Mol. weight
- 582.11 kDa
- Released
- 1 Dec 2021
Explore 7VLK in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
7VLK contains 200 α-helices and 190 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: 16 helices, 11 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 3-16 | 14 | |
| α-helix | 22-35 | 14 | |
| α-helix | 46-59 | 14 | |
| α-helix | 63-82 | 20 | |
| α-helix | 86-115 | 30 | |
| α-helix | 116-118 | 3 | |
| α-helix | 119-120 | 2 | |
| β-strand | 123-126 | 4 | 1 |
| α-helix | 132-143 | 12 | |
| β-strand | 148-153 | 6 | 1 |
| α-helix | 160-170 | 11 | |
| β-strand | 175-178 | 4 | 1 |
| α-helix | 180-182 | 3 | |
| α-helix | 183-186 | 4 | |
| β-strand | 192-195 | 4 | 1 |
| β-strand | 199-200 | 2 | 2 |
| β-strand | 206-209 | 4 | 2 |
| α-helix | 212-221 | 10 | |
| β-strand | 226-229 | 4 | 1 |
| α-helix | 232-234 | 3 | |
| β-strand | 235 | 1 | 2 |
| α-helix | 248-251 | 4 | |
| β-strand | 273-276 | 4 | 2 |
| α-helix | 278-280 | 3 | |
| β-strand | 283-286 | 4 | 1 |
| β-strand | 289-291 | 3 | 1 |
| α-helix | 294-303 | 10 | |
Chain B: 17 helices, 11 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 3-16 | 14 | |
| α-helix | 22-35 | 14 | |
| α-helix | 46-59 | 14 | |
| α-helix | 63-82 | 20 | |
| α-helix | 86-105 | 20 | |
| α-helix | 107-115 | 9 | |
| α-helix | 116-118 | 3 | |
| α-helix | 119-120 | 2 | |
| β-strand | 123-127 | 5 | 3 |
| α-helix | 132-143 | 12 | |
| β-strand | 148-153 | 6 | 3 |
| α-helix | 160-170 | 11 | |
| β-strand | 175-178 | 4 | 3 |
| α-helix | 180-182 | 3 | |
| α-helix | 183-187 | 5 | |
| β-strand | 192-196 | 5 | 3 |
| β-strand | 199-200 | 2 | 4 |
| β-strand | 206-209 | 4 | 4 |
| α-helix | 212-221 | 10 | |
| β-strand | 226-229 | 4 | 3 |
| α-helix | 232-234 | 3 | |
| β-strand | 235 | 1 | 4 |
| α-helix | 248-251 | 4 | |
| β-strand | 273-276 | 4 | 4 |
| α-helix | 278-280 | 3 | |
| β-strand | 283-286 | 4 | 3 |
| β-strand | 289-291 | 3 | 3 |
| α-helix | 293-303 | 11 | |
Chain C: 22 helices, 14 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 9-24 | 16 | |
| α-helix | 31-48 | 18 | |
| α-helix | 54-71 | 18 | |
| α-helix | 76-97 | 22 | |
| α-helix | 109-114 | 6 | |
| α-helix | 129-145 | 17 | |
| α-helix | 147-152 | 6 | |
| β-strand | 164-168 | 5 | 5 |
| α-helix | 172-181 | 10 | |
| β-strand | 188-193 | 6 | 5 |
| α-helix | 200-209 | 10 | |
| β-strand | 213-218 | 6 | 5 |
| α-helix | 219-221 | 3 | |
| α-helix | 222-225 | 4 | |
| α-helix | 226-228 | 3 | |
| β-strand | 231-234 | 4 | 5 |
| β-strand | 238-239 | 2 | 6 |
| β-strand | 245-248 | 4 | 6 |
| α-helix | 251-260 | 10 | |
| β-strand | 265-268 | 4 | 5 |
| α-helix | 271-273 | 3 | |
| β-strand | 274 | 1 | 6 |
| α-helix | 287 | 1 | |
| β-strand | 288 | 1 | 7 |
| α-helix | 291-293 | 3 | |
| α-helix | 297-299 | 3 | |
| α-helix | 301-304 | 4 | |
| β-strand | 306-308 | 3 | 8 |
| β-strand | 311 | 1 | 7 |
| β-strand | 313-316 | 4 | 6 |
| α-helix | 318-320 | 3 | |
| β-strand | 323-326 | 4 | 5 |
| β-strand | 329-331 | 3 | 5 |
| α-helix | 333-335 | 3 | |
| α-helix | 336-343 | 8 | |
| α-helix | 346-348 | 3 | |
Chain D: 21 helices, 14 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 9-24 | 16 | |
| α-helix | 31-48 | 18 | |
| α-helix | 54-71 | 18 | |
| α-helix | 76-97 | 22 | |
| α-helix | 109-113 | 5 | |
| α-helix | 129-145 | 17 | |
| α-helix | 147-152 | 6 | |
| β-strand | 164-168 | 5 | 9 |
| α-helix | 172-181 | 10 | |
| β-strand | 188-193 | 6 | 9 |
| α-helix | 200-209 | 10 | |
| β-strand | 213-218 | 6 | 9 |
| α-helix | 219-221 | 3 | |
| α-helix | 222-226 | 5 | |
| β-strand | 231-234 | 4 | 9 |
| β-strand | 238-239 | 2 | 10 |
| β-strand | 245-248 | 4 | 10 |
| α-helix | 251-260 | 10 | |
| β-strand | 265-268 | 4 | 9 |
| α-helix | 271-273 | 3 | |
| β-strand | 274 | 1 | 10 |
| α-helix | 287 | 1 | |
| β-strand | 288 | 1 | 11 |
| α-helix | 291-293 | 3 | |
| α-helix | 297-299 | 3 | |
| α-helix | 301-304 | 4 | |
| β-strand | 306-308 | 3 | 12 |
| β-strand | 311 | 1 | 11 |
| β-strand | 313-316 | 4 | 10 |
| α-helix | 318-320 | 3 | |
| β-strand | 323-326 | 4 | 9 |
| β-strand | 329-331 | 3 | 9 |
| α-helix | 333-335 | 3 | |
| α-helix | 336-343 | 8 | |
| α-helix | 346-348 | 3 | |
Chain E: 13 helices, 12 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 4-8 | 5 | 13 |
| α-helix | 37-46 | 10 | |
| β-strand | 51-55 | 5 | 13 |
| α-helix | 63-67 | 5 | |
| β-strand | 75-79 | 5 | 13 |
| α-helix | 86-92 | 7 | |
| α-helix | 94-96 | 3 | |
| β-strand | 101-105 | 5 | 13 |
| α-helix | 115-123 | 9 | |
| β-strand | 128-134 | 7 | 13 |
| β-strand | 156-160 | 5 | 14 |
| β-strand | 166 | 1 | 13 |
| β-strand | 167-172 | 6 | 14 |
| α-helix | 173-175 | 3 | |
| β-strand | 180-183 | 4 | 15 |
| α-helix | 184-189 | 6 | |
| β-strand | 192-196 | 5 | 14 |
| β-strand | 199-207 | 9 | 13 |
| α-helix | 209-217 | 9 | |
| α-helix | 224-228 | 5 | |
| α-helix | 229-235 | 7 | |
| β-strand | 263-268 | 6 | 13 |
| α-helix | 273-275 | 3 | |
| α-helix | 278-280 | 3 | |
| α-helix | 281-292 | 12 | |
Chain F: 12 helices, 12 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 4-8 | 5 | 16 |
| α-helix | 37-46 | 10 | |
| β-strand | 51-55 | 5 | 16 |
| α-helix | 63-67 | 5 | |
| β-strand | 75-79 | 5 | 16 |
| α-helix | 86-92 | 7 | |
| α-helix | 94-96 | 3 | |
| β-strand | 101-105 | 5 | 16 |
| α-helix | 115-123 | 9 | |
| β-strand | 128-134 | 7 | 16 |
| β-strand | 156-160 | 5 | 17 |
| β-strand | 166 | 1 | 16 |
| β-strand | 167-172 | 6 | 17 |
| β-strand | 179-183 | 5 | 18 |
| α-helix | 184-189 | 6 | |
| β-strand | 192-196 | 5 | 17 |
| β-strand | 199-207 | 9 | 16 |
| α-helix | 209-217 | 9 | |
| α-helix | 224-228 | 5 | |
| α-helix | 229-235 | 7 | |
| β-strand | 263-268 | 6 | 16 |
| α-helix | 273-275 | 3 | |
| α-helix | 278-280 | 3 | |
| α-helix | 281-291 | 11 | |
Chain G: 25 helices, 17 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 167-172 | 6 | |
| α-helix | 175-177 | 3 | |
| α-helix | 178-180 | 3 | |
| β-strand | 185 | 1 | 19 |
| α-helix | 192-195 | 4 | |
| α-helix | 205-215 | 11 | |
| α-helix | 222-239 | 18 | |
| α-helix | 242-243 | 2 | |
| α-helix | 248-266 | 19 | |
| α-helix | 268-270 | 3 | |
| α-helix | 271-285 | 15 | |
| α-helix | 293-308 | 16 | |
| α-helix | 309-314 | 6 | |
| α-helix | 315-324 | 10 | |
| β-strand | 332-336 | 5 | 12 |
| α-helix | 340-351 | 12 | |
| β-strand | 357-362 | 6 | 12 |
| α-helix | 369-379 | 11 | |
| β-strand | 383-387 | 5 | 12 |
| α-helix | 388-390 | 3 | |
| α-helix | 391-394 | 4 | |
| α-helix | 395-397 | 3 | |
| β-strand | 400-404 | 5 | 12 |
| β-strand | 407-408 | 2 | 20 |
| β-strand | 414-417 | 4 | 20 |
| α-helix | 420-429 | 10 | |
| β-strand | 434-437 | 4 | 12 |
| α-helix | 440-442 | 3 | |
| β-strand | 443 | 1 | 20 |
| β-strand | 457 | 1 | 19 |
| α-helix | 460-463 | 4 | |
| β-strand | 466-467 | 2 | 21 |
| β-strand | 470-471 | 2 | 21 |
| α-helix | 476-478 | 3 | |
| β-strand | 482-484 | 3 | 9 |
| β-strand | 487 | 1 | 19 |
| β-strand | 489-492 | 4 | 20 |
| α-helix | 494-496 | 3 | |
| β-strand | 499-502 | 4 | 12 |
| β-strand | 505-507 | 3 | 12 |
| α-helix | 509-511 | 3 | |
| α-helix | 512-520 | 9 | |
Chain H: 25 helices, 17 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 167-172 | 6 | |
| α-helix | 175-177 | 3 | |
| α-helix | 178-180 | 3 | |
| β-strand | 185 | 1 | 22 |
| α-helix | 193-195 | 3 | |
| α-helix | 205-215 | 11 | |
| α-helix | 222-239 | 18 | |
| α-helix | 242-243 | 2 | |
| α-helix | 248-266 | 19 | |
| α-helix | 268-270 | 3 | |
| α-helix | 271-285 | 15 | |
| α-helix | 293-308 | 16 | |
| α-helix | 309-314 | 6 | |
| α-helix | 315-324 | 10 | |
| β-strand | 332-336 | 5 | 8 |
| α-helix | 340-352 | 13 | |
| β-strand | 357-362 | 6 | 8 |
| α-helix | 369-379 | 11 | |
| β-strand | 383-387 | 5 | 8 |
| α-helix | 388-390 | 3 | |
| α-helix | 391-394 | 4 | |
| α-helix | 395-397 | 3 | |
| β-strand | 400-404 | 5 | 8 |
| β-strand | 407-408 | 2 | 23 |
| β-strand | 414-417 | 4 | 23 |
| α-helix | 420-429 | 10 | |
| β-strand | 434-437 | 4 | 8 |
| α-helix | 440-442 | 3 | |
| β-strand | 443 | 1 | 23 |
| β-strand | 457 | 1 | 22 |
| α-helix | 460-463 | 4 | |
| β-strand | 467 | 1 | 24 |
| β-strand | 470 | 1 | 24 |
| α-helix | 476-478 | 3 | |
| β-strand | 482-484 | 3 | 5 |
| β-strand | 487 | 1 | 22 |
| β-strand | 489-492 | 4 | 23 |
| α-helix | 494-496 | 3 | |
| β-strand | 499-502 | 4 | 8 |
| β-strand | 505-507 | 3 | 8 |
| α-helix | 509-511 | 3 | |
| α-helix | 512-520 | 9 | |
4 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 alpha | A, B | protein | 307 | Homo sapiens | Q14232 (AlphaFold model) |
| Translation initiation factor eIF-2B subunit beta | C, D | protein | 351 | Homo sapiens | P49770 (AlphaFold model) |
| Translation initiation factor eIF-2B subunit gamma | E, F | protein | 452 | Homo sapiens | Q9NR50 (AlphaFold model) |
| Translation initiation factor eIF-2B subunit delta | G, H | protein | 523 | Homo sapiens | Q9UI10 (AlphaFold model) |
| Translation initiation factor eIF-2B subunit epsilon | I, J | protein | 721 | Homo sapiens | Q13144 |
| Non-structural protein NS-S | K, L | protein | 261 | Sandfly fever sicilian virus | P12792 |
Sequence of entity 1 (A, B), FASTA
>7VLK_1 Translation initiation factor eIF-2B subunit alpha (chains A, B)
GPMDDKELIEYFKSQMKEDPDMASAVAAIRTLLEFLKRDKGETIQGLRANLTSAIETLCG
VDSSVAVSSGGELFLRFISLASLEYSDYSKCKKIMIERGELFLRRISLSRNKIADLCHTF
IKDGATILTHAYSRVVLRVLEAAVAAKKRFSVYVTESQPDLSGKKMAKALCHLNVPVTVV
LDAAVGYIMEKADLVIVGAEGVVENGGIINKIGTNQMAVCAKAQNKPFYVVAESFKFVRL
FPLNQQDVPDKFKYKADTLKVAQTGQDLKEEHPWVDYTAPSLITLLFTDLGVLTPSAVSD
ELIKLYL
Sequence of entity 2 (C, D), FASTA
>7VLK_2 Translation initiation factor eIF-2B subunit beta (chains C, D)
MPGSAAKGSELSERIESFVETLKRGGGPRSSEEMARETLGLLRQIITDHRWSNAGELMEL
IRREGRRMTAAQPSETTVGNMVRRVLKIIREEYGRLHGRSDESDQQESLHKLLTSGGLNE
DFSFHYAQLQSNIIEAINELLVELEGTMENIAAQALEHIHSNEVIMTIGFSRTVEAFLKE
AARKRKFHVIVAECAPFCQGHEMAVNLSKAGIETTVMTDAAIFAVMSRVNKVIIGTKTIL
ANGALRAVTGTHTLALAAKHHSTPLIVCAPMFKLSPQFPNEEDSFHKFVAPEEVLPFTEG
DILEKVSVHCPVFDYVPPELITLFISNIGGNAPSYIYRLMSELYHPDDHVL
Sequence of entity 3 (E, F), FASTA
>7VLK_3 Translation initiation factor eIF-2B subunit gamma (chains E, F)
MEFQAVVMAVGGGSRMTDLTSSIPKPLLPVGNKPLIWYPLNLLERVGFEEVIVVTTRDVQ
KALCAEFKMKMKPDIVCIPDDADMGTADSLRYIYPKLKTDVLVLSCDLITDVALHEVVDL
FRAYDASLAMLMRKGQDSIEPVPGQKGKKKAVEQRDFIGVDSTGKRLLFMANEADLDEEL
VIKGSILQKHPRIRFHTGLVDAHLYCLKKYIVDFLMENGSITSIRSELIPYLVRKQFSSA
SSQQGQEEKEEDLKKKELKSLDIYSFIKEANTLNLAPYDACWNACRGDRWEDLSRSQVRC
YVHIMKEGLCSRVSTLGLYMEANRQVPKLLSALCPEEPPVHSSAQIVSKHLVGVDSLIGP
ETQIGEKSSIKRSVIGSSCLIKDRVTITNCLLMNSVTVEEGSNIQGSVICNNAVIEKGAD
IKDCLIGSGQRIEAKAKRVNEVIVGNDQLMEI
Sequence of entity 4 (G, H), FASTA
>7VLK_4 Translation initiation factor eIF-2B subunit delta (chains G, H)
MAAVAVAVREDSGSGMKAELPPGPGAVGREMTKEEKLQLRKEKKQQKKKRKEEKGAEPET
GSAVSAAQCQVGPTRELPESGIQLGTPREKVPAGRSKAELRAERRAKQEAERALKQARKG
EQGGPPPKASPSTAGETPSGVKRLPEYPQVDDLLLRRLVKKPERQQVPTRKDYGSKVSLF
SHLPQYSRQNSLTQFMSIPSSVIHPAMVRLGLQYSQGLVSGSNARCIALLRALQQVIQDY
TTPPNEELSRDLVNKLKPYMSFLTQCRPLSASMHNAIKFLNKEITSVGSSKREEEAKSEL
RAAIDRYVQEKIVLAAQAISRFAYQKISNGDVILVYGCSSLVSRILQEAWTEGRRFRVVV
VDSRPWLEGRHTLRSLVHAGVPASYLLIPAASYVLPEVSKVLLGAHALLANGSVMSRVGT
AQLALVARAHNVPVLVCCETYKFCERVQTDAFVSNELDDPDDLQCKRGEHVALANWQNHA
SLRLLNLVYDVTPPELVDLVITELGMIPCSSVPVVLRVKSSDQ
Sequence of entity 5 (I, J), FASTA
>7VLK_5 Translation initiation factor eIF-2B subunit epsilon (chains I, J)
MAAPVVAPPGVVVSRANKRSGAGPGGSGGGGARGAEEEPPPPLQAVLVADSFDRRFFPIS
KDQPRVLLPLANVALIDYTLEFLTATGVQETFVFCCWKAAQIKEHLLKSKWCRPTSLNVV
RIITSELYRSLGDVLRDVDAKALVRSDFLLVYGDVISNINITRALEEHRLRRKLEKNVSV
MTMIFKESSPSHPTRCHEDNVVVAVDSTTNRVLHFQKTQGLRRFAFPLSLFQGSSDGVEV
RYDLLDCHISICSPQVAQLFTDNFDYQTRDDFVRGLLVNEEILGNQIHMHVTAKEYGARV
SNLHMYSAVCADVIRRWVYPLTPEANFTDSTTQSCTHSRHNIYRGPEVSLGHGSILEENV
LLGSGTVIGSNCFITNSVIGPGCHIGDNVVLDQTYLWQGVRVAAGAQIHQSLLCDNAEVK
ERVTLKPRSVLTSQVVVGPNITLPEGSVISLHPPDAEEDEDDGEFSDDSGADQEKDKVKM
KGYNPAEVGAAGKGYLWKAAGMNMEEEEELQQNLWGLKINMEEESESESEQSMDSEEPDS
RGGSPQMDDIKVFQNEVLGTLQRGKEENISCDNLVLEINSLKYAYNISLKEVMQVLSHVV
LEFPLQQMDSPLDSSRYCALLLPLLKAWSPVFRNYIKRAADHLEALAAIEDFFLEHEALG
ISMAKVLMAFYQLEILAEETILSWFSQRDTTDKGQQLRKNQQLQRFIQWLKEAEEESSED
D
Sequence of entity 6 (K, L), FASTA
>7VLK_6 Non-structural protein NS-S (chains K, L)
MNSQYMFDYPAINIDVRCHRLLSSVSYVAYNKFHTHDVSTYEHCEIPLEKLRLGFGRRNS
LADFYSLGELPASWGPACYFSSVKPMMYTFQGMASDLSRFDLTSFSRKGLPNVLKALSWP
LGIPDCEIFSICSDRFVRGLQTRDQLMSYILRMGDSHSLDECIVQAHKKILQEARRLGLS
DEHYNGYDLFREIGSLVCLRLINAEPFDTASSGEALDVRTVIRSYRASDPSTGLTEYGNS
LWTPIHSHVDENDESSSDSDF
Primary citation
eIF2B-capturing viral protein NSs suppresses the integrated stress response. Kashiwagi, K., Shichino, Y., Osaki, T. et al. Nat Commun (2021) 12:7102-7102. DOI 10.1038/s41467-021-27337-x · PubMed
Other PDB entries of the same protein (UniProt Q14232 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 9Y4B 2.1 Å, Eukaryotic translation initiation factor 2-B (eIF2B) with a truncation in the beta…
- 9ZUZ 2.25 Å, Translation Initiation Factor eIF-2B complex with the Isohexide Diamine GSK735
- 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…
- 7RLO 2.6 Å, Structure of the human eukaryotic translation initiation factor 2B (eIF2B) in complex…
- 3ECS 2.65 Å, Crystal structure of human eIF2B alpha
- 7KMA 2.7 Å, Crystal structure of eif2Balpha with a ligand.
- 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)
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