6O81: PDB entry 6O81

Name: PDB 6O81: Electron cryo-microscopy of the eukaryotic translation initiation factor 2B bound to 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 translation initiation factor 2 from Homo sapiens. Determined by electron microscopy at 3.21 Å resolution. Released 15 May 2019.

Method: Electron microscopy
Resolution: 3.21 Å
Organism: Homo sapiens
Chains: 16
Atoms: 33,693
Mol. weight: 703.64 kDa
Ligands: C7B
Released: 15 May 2019

Explore 6O81 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6O81 contains 209 α-helices and 256 β-strands across 16 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: 22 helices, 37 β-strands

Element	Residues	Length	Sheet
β-strand	44-48	5	1
β-strand	69	1	2
β-strand	74	1	2
α-helix	75-86	12
β-strand	90-95	6	1
α-helix	99-106	8
β-strand	119	1	1
β-strand	122-124	3	1
α-helix	131-141	11
β-strand	148	1	3
β-strand	149-152	4	1
β-strand	155-157	3	4
α-helix	162-174	13
β-strand	181-187	7	3
β-strand	201-205	5	3
β-strand	211-217	7	3
β-strand	223-224	2	5
α-helix	229-233	5
β-strand	238-241	4	3
β-strand	244-246	3	3
β-strand	251-252	2	3
α-helix	255-262	8
α-helix	269-278	10
α-helix	286	1
β-strand	287-292	6	3
β-strand	297-299	3	4
α-helix	303-314	12
α-helix	331-333	3
β-strand	336-337	2	6
α-helix	339-341	3
β-strand	343-344	2	6
β-strand	355-356	2	7
β-strand	360-362	3	6
β-strand	367-368	2	8
β-strand	373-375	3	7
β-strand	377-378	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	424	1	7
β-strand	429-431	3	6
β-strand	436-437	2	8
β-strand	447-449	3	6
β-strand	458	1	6
α-helix	550-566	17
α-helix	571-585	15
α-helix	589-606	18
α-helix	614-627	14
α-helix	629-635	7
α-helix	639-655	17
α-helix	657-662	6
α-helix	663-670	8
α-helix	678-686	9
α-helix	693-698	6
α-helix	701-714	14

Chain C: 17 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	9-23	15
α-helix	31-47	17
α-helix	54-71	18
α-helix	77-97	21
α-helix	129-145	17
α-helix	148-154	7
α-helix	155-157	3
β-strand	164-168	5	17
α-helix	172-181	10
β-strand	188-192	5	17
α-helix	193-194	2
α-helix	200-207	8
β-strand	214-217	4	17
α-helix	222-225	4
β-strand	231-234	4	17
β-strand	238-239	2	18
β-strand	245-248	4	18
α-helix	251-260	10
β-strand	265-268	4	17
α-helix	271-273	3
β-strand	274	1	18
β-strand	288	1	19
α-helix	301-303	3
β-strand	306	1	20
β-strand	311	1	19
β-strand	313-316	4	18
α-helix	318-320	3
β-strand	323-326	4	17
β-strand	329-331	3	17
α-helix	336-343	8
α-helix	346-349	4

Chains d and e: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	4-15	12

Chain D: 17 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	127-145	19
α-helix	147-153	7
α-helix	154-157	4
β-strand	164-168	5	21
α-helix	172-181	10
β-strand	188-192	5	21
α-helix	200-207	8
β-strand	214-217	4	21
α-helix	219-221	3
α-helix	222-226	5
β-strand	231-234	4	21
β-strand	238-239	2	22
β-strand	245-248	4	22
α-helix	251-260	10
β-strand	265-268	4	21
β-strand	274	1	22
β-strand	288	1	23
α-helix	291-293	3
α-helix	301-303	3
β-strand	306-308	3	24
β-strand	311	1	23
β-strand	313-316	4	22
α-helix	318-320	3
β-strand	323-326	4	21
β-strand	329-331	3	21
α-helix	336-343	8
α-helix	346-348	3

Chain E: 21 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	169-173	5
α-helix	175-177	3
α-helix	178-180	3
β-strand	185	1	25
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	24
α-helix	340-352	13
β-strand	357-362	6	24
α-helix	369-377	9
β-strand	383-387	5	24
α-helix	391-394	4
β-strand	400-404	5	24
β-strand	407-408	2	26
β-strand	414-415	2	26
β-strand	416-417	2	27
α-helix	421-429	9
β-strand	434-437	4	24
α-helix	440-442	3
β-strand	443	1	26
β-strand	457	1	25
α-helix	460-462	3
α-helix	476-478	3
β-strand	482-484	3	21
β-strand	487	1	25
β-strand	489-490	2	27
β-strand	499-502	4	24
β-strand	505-507	3	24
α-helix	509-511	3
α-helix	512-517	6

Chain F: 20 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	169-173	5
α-helix	175-177	3
α-helix	178-180	3
β-strand	185	1	28
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	20
α-helix	340-351	12
β-strand	357-362	6	20
α-helix	369-377	9
β-strand	383-387	5	20
α-helix	391-394	4
β-strand	400-404	5	20
β-strand	407-408	2	29
β-strand	414-415	2	29
β-strand	416-417	2	30
α-helix	421-429	9
β-strand	434-437	4	20
α-helix	440-442	3
β-strand	443	1	29
β-strand	457	1	28
α-helix	460-462	3
β-strand	482-484	3	17
β-strand	487	1	28
β-strand	489-490	2	30
β-strand	499-502	4	20
β-strand	505-507	3	20
α-helix	509-511	3
α-helix	512-517	6

Chains G and H: 15 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	5-15	11
α-helix	22-37	16
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	31
α-helix	132-143	12
β-strand	148-153	6	31
α-helix	161-169	9
β-strand	175-178	4	31
α-helix	179	1
β-strand	192-196	5	31
β-strand	199-200	2	32
β-strand	206-208	3	32
α-helix	212-221	10
β-strand	226-229	4	31
α-helix	232-234	3
β-strand	235	1	32
β-strand	274-276	3	32
α-helix	278-280	3
β-strand	283-286	4	31
β-strand	289-291	3	31
α-helix	295-303	9

Chains I and J: 10 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	35
α-helix	37-45	9
β-strand	51-54	4	35
α-helix	63-67	5
β-strand	75-78	4	35
α-helix	86-92	7
α-helix	94-96	3
β-strand	100-104	5	35
α-helix	115-123	9
β-strand	128-133	6	35
β-strand	156-161	6	3
β-strand	166	1	35
β-strand	167-172	6	3
β-strand	182-183	2	5
α-helix	184-189	6
β-strand	192-196	5	3
β-strand	200-201	2	35
β-strand	207	1	35
α-helix	209-217	9
α-helix	224-227	4
α-helix	230-235	6
β-strand	263-268	6	35
α-helix	282-291	10

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
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	315	Homo sapiens	P05198
Eukaryotic translation initiation factor 2 subunit 3	S, T	protein	472	Homo sapiens	P41091
Translation initiation factor eiF2 beta-subunit	d, e	protein	14	Homo sapiens

Sequence of entity 1 (A, B), FASTA

>6O81_1 Translation initiation factor eIF-2B subunit epsilon (chains A, B)
MAAPVVAPPGVVVSRANKRSGAGPGGSGGGGARGAEEEPPPPLQAVLVADSFDRRFFPIS
KDQPRVLLPLANVALIDYTLEFLTATGVQETFVFCCWKAAQIKEHLLKSKWCRPTSLNVV
RIITSELYRSLGDVLRDVDAKALVRSDFLLVYGDVISNINITRALEEHRLRRKLEKNVSV
MTMIFKESSPSHPTRCHEDNVVVAVDSTTNRVLHFQKTQGLRRFAFPLSLFQGSSDGVEV
RYDLLDCHISICSPQVAQLFTDNFDYQTRDDFVRGLLVNEEILGNQIHMHVTAKEYGARV
SNLHMYSAVCADVIRRWVYPLTPEANFTDSTTQSCTHSRHNIYRGPEVSLGHGSILEENV
LLGSGTVIGSNCFITNSVIGPGCHIGDNVVLDQTYLWQGVRVAAGAQIHQSLLCDNAEVK
ERVTLKPRSVLTSQVVVGPNITLPEGSVISLHPPDAEEDEDDGEFSDDSGADQEKDKVKM
KGYNPAEVGAAGKGYLWKAAGMNMEEEEELQQNLWGLKINMEEESESESEQSMDSEEPDS
RGGSPQMDDIKVFQNEVLGTLQKGKEENISCDNLVLEINSLKYAYNISLKEVMQVLSHVV
LEFPLQQMDSPLDSSRYCALLLPLLKAWSPVFRNYIKRAADHLEALAAIEDFFLEHEALG
ISMAKVLMAFYQLEILAGETILSWFSQRDTTDKGQQLRKNQQLQRFIQWLKEAEEESSED
D

Sequence of entity 2 (C, D), FASTA

>6O81_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

>6O81_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

>6O81_4 Translation initiation factor eIF-2B subunit alpha (chains G, H)
MDDKELIEYFKSQMKEDPDMASAVAAIRTLLEFLKRDKGETIQGLRANLTSAIETLCGVD
SSVAVSSGGELFLRFISLASLEYSDYSKCKKIMIERGELFLRRISLSRNKIADLCHTFIK
DGATILTHAYSRVVLRVLEAAVAAKKRFSVYVTESQPDLSGKKMAKALCHLNVPVTVVLD
AAVGYIMEKADLVIVGAEGVVENGGIINKIGTNQMAVCAKAQNKPFYVVAESFKFVRLFP
LNQQDVPDKFKYKADTLKVAQTGQDLKEEHPWVDYTAPSLITLLFTDLGVLTPSAVSDEL
IKLYL

Sequence of entity 5 (I, J), FASTA

>6O81_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

>6O81_6 Eukaryotic translation initiation factor 2 subunit 1 (chains L, M)
MPGLSCRFYQHKFPEVEDVVMVNVRSIAEMGAYVSLLEYNNIEGMILLSELSRRRIRSIN
KLIRIGRNECVVVIRVDKEKGYIDLSKRRVSPEEAIKCEDKFTKSKTVYSILRHVAEVLE
YTKDEQLESLFQRTAWVFDDKYKRPGYGAYDAFKHAVSDPSILDSLDLNEDEREVLINNI
NRRLTPQAVKIRADIEVACYGYEGIDAVKEALRAGLNCSTENMPIKINLIAPPRYVMTTT
TLERTEGLSVLSQAMAVIKEKIEEKRGVFNVQMEPKVVTDTDETELARQMERLERENAEV
DGDDDAEEMEAKAED

Sequence of entity 7 (S, T), FASTA

>6O81_7 Eukaryotic translation initiation factor 2 subunit 3 (chains S, T)
MAGGEAGVTLGQPHLSRQDLTTLDVTKLTPLSHEVISRQATINIGTIGHVAHGKSTVVKA
ISGVHTVRFKNELERNITIKLGYANAKIYKLDDPSCPRPECYRSCGSSTPDEFPTDIPGT
KGNFKLVRHVSFVDCPGHDILMATMLNGAAVMDAALLLIAGNESCPQPQTSEHLAAIEIM
KLKHILILQNKIDLVKESQAKEQYEQILAFVQGTVAEGAPIIPISAQLKYNIEVVCEYIV
KKIPVPPRDFTSEPRLIVIRSFDVNKPGCEVDDLKGGVAGGSILKGVLKVGQEIEVRPGI
VSKASEGKLMCKPKFSKIVSLFAEHNDLQYAAPGGLIGVGTKIDPTLCRADRMVGQVLGA
VGALPEIFTELEISYFLLRRLLGVRTEGDKKAAKVQKLSKNEVLMVNIGSLSTGGRVSAV
KADLGKIVLTNPVCTEVGEKIALSRRVEKHWRLIGWGQIRRGVTIKPTVDDD

Sequence of entity 8 (d, e), FASTA

>6O81_8 Translation initiation factor eiF2 beta-subunit (chains d, e)
XXXXXXXXXXXXXX

Ligands and cofactors

ID	Name	Formula	Copies
C7B	2-(4-chloranylphenoxy)-~{N}-[4-[2-(4-chloranylphenoxy)ethanoylamino]cyclohexyl]…	C22 H24 Cl2 N2 O4	1

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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