6O9Z: PDB entry 6O9Z

Name: PDB 6O9Z: Electron cryo-microscopy of the eukaryotic translation initiation factor 2B bound to eukaryotic translation initiation factor 2 from Homo sapiens
Published: 2019-05-15
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: translation

Electron cryo-microscopy of the eukaryotic translation initiation factor 2B bound to eukaryotic translation initiation factor 2 from Homo sapiens. Determined by electron microscopy at 3.03 Å resolution. Released 15 May 2019.

Method: Electron microscopy
Resolution: 3.03 Å
Organism: Homo sapiens
Chains: 12
Atoms: 25,788
Mol. weight: 600.8 kDa
Released: 15 May 2019

Explore 6O9Z in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6O9Z contains 158 α-helices and 188 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.

Chains A and B: 14 helices, 36 β-strands

Element	Residues	Length	Sheet
α-helix	42-43	2
β-strand	44-48	5	1
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	1	1
β-strand	122-124	3	1
α-helix	131-141	11
β-strand	149-152	4	1
β-strand	155-157	3	3
α-helix	162-174	13
β-strand	182-187	6	1
β-strand	201-206	6	1
β-strand	211-217	7	1
β-strand	224-225	2	4
α-helix	229-233	5
β-strand	238-241	4	1
β-strand	244-246	3	1
β-strand	251	1	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	336-337	2	5
α-helix	339-341	3
β-strand	343-344	2	5
α-helix	350-351	2
β-strand	355-356	2	6
β-strand	361-362	2	5
β-strand	367-368	2	7
β-strand	373-375	3	6
β-strand	378-379	2	5
β-strand	384-385	2	7
β-strand	390-392	3	6
β-strand	395-396	2	5
β-strand	401-402	2	7
β-strand	407-409	3	6
β-strand	411-413	3	5
β-strand	418-419	2	7
β-strand	424-425	2	6
α-helix	426	1
β-strand	429-431	3	5
β-strand	436-437	2	7
α-helix	438	1
β-strand	447-450	4	5
β-strand	458-459	2	5

Chain C: 17 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	9-24	16
α-helix	31-46	16
α-helix	54-71	18
α-helix	77-97	21
α-helix	129-145	17
α-helix	147-153	7
α-helix	154-157	4
β-strand	164-168	5	15
α-helix	172-181	10
β-strand	188-192	5	15
α-helix	200-207	8
β-strand	214-217	4	15
α-helix	222-225	4
β-strand	231-234	4	15
β-strand	238-239	2	16
β-strand	245-248	4	16
α-helix	251-260	10
β-strand	265-268	4	15
β-strand	274	1	16
β-strand	288	1	17
α-helix	297-299	3
α-helix	301-303	3
β-strand	306-308	3	18
β-strand	311	1	17
β-strand	313-316	4	16
α-helix	318-320	3
β-strand	323-326	4	15
β-strand	329-331	3	15
α-helix	333-335	3
α-helix	336-343	8
α-helix	346-348	3

Chain D: 15 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	9-24	16
α-helix	31-47	17
α-helix	54-71	18
α-helix	77-97	21
α-helix	127-144	18
α-helix	147-153	7
α-helix	154-157	4
β-strand	164-168	5	19
α-helix	172-181	10
β-strand	188-192	5	19
α-helix	200-207	8
β-strand	214-217	4	19
α-helix	222-225	4
β-strand	231-234	4	19
β-strand	238-239	2	20
β-strand	245-248	4	20
α-helix	251-260	10
β-strand	265-268	4	19
β-strand	274	1	20
β-strand	288	1	21
α-helix	297-299	3
α-helix	301-303	3
β-strand	306-308	3	22
β-strand	311	1	21
β-strand	313-316	4	20
α-helix	318-320	3
β-strand	323-326	4	19
β-strand	329-331	3	19
α-helix	336-343	8

Chains E and F: 18 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	169-172	4
β-strand	185	1	23
α-helix	192-195	4
α-helix	205-215	11
α-helix	222-238	17
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	22
α-helix	340-352	13
β-strand	357-362	6	22
α-helix	369-378	10
β-strand	383-387	5	22
α-helix	391-394	4
β-strand	400-404	5	22
β-strand	407-408	2	24
β-strand	414-417	4	24
α-helix	419-429	11
α-helix	432-433	2
β-strand	434-437	4	22
α-helix	440-442	3
β-strand	443	1	24
β-strand	457	1	23
α-helix	460-462	3
β-strand	482-484	3	19
β-strand	487	1	23
β-strand	489-492	4	24
β-strand	499-502	4	22
β-strand	505-508	4	22
α-helix	512-517	6

Chains G and H: 14 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	4-15	12
α-helix	22-35	14
α-helix	46-59	14
α-helix	63-76	14
α-helix	87-115	29
α-helix	116-118	3
α-helix	119-120	2
β-strand	123-127	5	27
α-helix	132-143	12
β-strand	148-153	6	27
α-helix	161-169	9
β-strand	175-178	4	27
α-helix	180-182	3
β-strand	192-195	4	27
β-strand	199-200	2	28
β-strand	206-208	3	28
α-helix	212-221	10
β-strand	226-229	4	27
β-strand	235	1	28
α-helix	248-251	4
β-strand	269	1	29
β-strand	274-276	3	28
α-helix	278-280	3
β-strand	283-286	4	27
β-strand	289-291	3	27
α-helix	293-304	12

Chains I and J: 9 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	3-8	6	31
α-helix	37-45	9
β-strand	51-54	4	31
α-helix	63-67	5
β-strand	75-78	4	31
α-helix	86-92	7
α-helix	94-96	3
β-strand	100-105	6	31
α-helix	115-123	9
β-strand	128-133	6	31
β-strand	157-161	5	1
β-strand	167-171	5	1
β-strand	181-182	2	4
α-helix	184-189	6
β-strand	192-196	5	1
β-strand	200-201	2	31
β-strand	207	1	31
α-helix	209-217	9
α-helix	228-235	8
β-strand	263-268	6	31
α-helix	283-291	9

Chains L and M: 8 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	13-14	2
β-strand	18-26	9	33
β-strand	30-35	6	33
α-helix	36-38	3
β-strand	41-46	6	33
α-helix	49-51	3
β-strand	67-76	10	33
β-strand	81-85	5	33
α-helix	91-117	27
α-helix	123-141	19
α-helix	146-157	12
α-helix	159-162	4
α-helix	169-179	11

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	368	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
Eukaryotic translation initiation factor 2 subunit 1	L, M	protein	323	Homo sapiens	P05198

Sequence of entity 1 (A, B), FASTA

>6O9Z_1 Translation initiation factor eIF-2B subunit epsilon (chains A, B)
MAAPVVAPPGVVVSRANKRSGAGPGGSGGGGARGAEEEPPPPLQAVLVADSFDRRFFPIS
KDQPRVLLPLANVALIDYTLEFLTATGVQETFVFCCWKAAQIKEHLLKSKWCRPTSLNVV
RIITSELYRSLGDVLRDVDAKALVRSDFLLVYGDVISNINITRALEEHRLRRKLEKNVSV
MTMIFKESSPSHPTRCHEDNVVVAVDSTTNRVLHFQKTQGLRRFAFPLSLFQGSSDGVEV
RYDLLDCHISICSPQVAQLFTDNFDYQTRDDFVRGLLVNEEILGNQIHMHVTAKEYGARV
SNLHMYSAVCADVIRRWVYPLTPEANFTDSTTQSCTHSRHNIYRGPEVSLGHGSILEENV
LLGSGTVIGSNCFITNSVIGPGCHIGDNVVLDQTYLWQGVRVAAGAQIHQSLLCDNAEVK
ERVTLKPRSVLTSQVVVGPNITLPEGSVISLHPPDAEEDEDDGEFSDDSGADQEKDKVKM
KGYNPAEVGAAGKGYLWKAAGMNMEEEEELQQNLWGLKINMEEESESESEQSMDSEEPDS
RGGSPQMDDIKVFQNEVLGTLQRGKEENISCDNLVLEINSLKYAYNVSLKEVMQVLSHVV
LEFPLQQMDSPLDSSRYCALLLPLLKAWSPVFRNYIKRAADHLEALAAIEDFFLEHEALG
ISMAKVLMAFYQLEILAEETILSWFSQRDTTDKGQQLRKNQQLQRFIQWLKEAEEESSED
D

Sequence of entity 2 (C, D), FASTA

>6O9Z_2 Translation initiation factor eIF-2B subunit beta (chains C, D)
MHHHHHHGGGSENLYFQSPGSAAKGSELSERIESFVETLKRGGGPRSSEEMARETLGLLR
QIITDHRWSNAGELMELIRREGRRMTAAQPSETTVGNMVRRVLKIIREEYGRLHGRSDES
DQQESLHKLLTSGGLNEDFSFHYAQLQSNIIEAINELLVELEGTMENIAAQALEHIHSNE
VIMTIGFSRTVEAFLKEAARKRKFHVIVAECAPFCQGHEMAVNLSKAGIETTVMTDAAIF
AVMSRVNKVIIGTKTILANGALRAVTGTHTLALAAKHHSTPLIVCAPMFKLSPQFPNEED
SFHKFVAPEEVLPFTEGDILEKVSVHCPVFDYVPPELITLFISNIGGNAPSYIYRLMSEL
YHPDDHVL

Sequence of entity 3 (E, F), FASTA

>6O9Z_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

>6O9Z_4 Translation initiation factor eIF-2B subunit alpha (chains G, H)
MDDKELIEYFKSQMKEDPDMASAVAAIRTLLEFLKRDKGETIQGLRANLTSAIETLCGVD
SSVAVSSGGELFLRFISLASLEYSDYSKCKKIMIERGELFLRRISLSRNKIADLCHTFIK
DGATILTHAYSRVVLRVLEAAVAAKKRFSVYVTESQPDLSGKKMAKALCHLNVPVTVVLD
AAVGYIMEKADLVIVGAEGVVENGGIINKIGTNQMAVCAKAQNKPFYVVAESFKFVRLFP
LNQQDVPDKFKYKADTLKVAQTGQDLKEEHPWVDYTAPSLITLLFTDLGVLTPSAVSDEL
IKLYL

Sequence of entity 5 (I, J), FASTA

>6O9Z_5 Translation initiation factor eIF-2B subunit gamma (chains I, J)
MEFQAVVMAVGGGSRMTDLTSSIPKPLLPVGNKPLIWYPLNLLERVGFEEVIVVTTRDVQ
KALCAEFKMKMKPDIVCIPDDADMGTADSLRYIYPKLKTDVLVLSCDLITDVALHEVVDL
FRAYDASLAMLMRKGQDSIEPVPGQKGKKKAVEQRDFIGVDSTGKRLLFMANEADLDEEL
VIKGSILQKHPRIRFHTGLVDAHLYCLKKYIVDFLMENGSITSIRSELIPYLVRKQFSSA
SSQQGQEEKEEDLKKKELKSLDIYSFIKEANTLNLAPYDACWNACRGDRWEDLSRSQVRC
YVHIMKEGLCSRVSTLGLYMEANRQVPKLLSALCPEEPPVHSSAQIVSKHLVGVDSLIGP
ETQIGEKSSIKRSVIGSSCLIKDRVTITNCLLMNSVTVEEGSNIQGSVICNNAVIEKGAD
IKDCLIGSGQRIEAKAKRVNEVIVGNDQLMEI

Sequence of entity 6 (L, M), FASTA

>6O9Z_6 Eukaryotic translation initiation factor 2 subunit 1 (chains L, M)
MDYKDDDDKPGLSCRFYQHKFPEVEDVVMVNVRSIAEMGAYVSLLEYNNIEGMILLSELS
RRRIRSINKLIRIGRNECVVVIRVDKEKGYIDLSKRRVSPEEAIKCEDKFTKSKTVYSIL
RHVAEVLEYTKDEQLESLFQRTAWVFDDKYKRPGYGAYDAFKHAVSDPSILDSLDLNEDE
REVLINNINRRLTPQAVKIRADIEVACYGYEGIDAVKEALRAGLNCSTENMPIKINLIAP
PRYVMTTTTLERTEGLSVLSQAMAVIKEKIEEKRGVFNVQMEPKVVTDTDETELARQMER
LERENAEVDGDDDAEEMEAKAED

Primary citation

eIF2B-catalyzed nucleotide exchange and phosphoregulation by the integrated stress response. Kenner, L.R., Anand, A.A., Nguyen, H.C. et al. Science (2019) 364:491-495. DOI 10.1126/science.aaw2922 · 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…
7RLO 2.6 Å, Structure of the human eukaryotic translation initiation factor 2B (eIF2B) in complex…
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…

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