6CAJ: PDB entry 6CAJ

Name: PDB 6CAJ: Electron cryo-microscopy of the eukaryotic translation initiation factor 2B from Homo sapiens
Published: 2018-04-11
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: translation

Electron cryo-microscopy of the eukaryotic translation initiation factor 2B from Homo sapiens. Determined by electron microscopy at 2.8 Å resolution. Released 11 Apr 2018.

Method: Electron microscopy
Resolution: 2.8 Å
Organism: Homo sapiens
Chains: 10
Atoms: 24,295
Mol. weight: 526.77 kDa
Ligands: C7B
Released: 11 Apr 2018

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

Secondary structure: helices and β-sheets

6CAJ contains 152 α-helices and 183 β-strands across 10 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: 13 helices, 37 β-strands

Element	Residues	Length	Sheet
β-strand	44-48	5	20
α-helix	65-67	3
β-strand	69	1	21
β-strand	74	1	21
α-helix	75-86	12
β-strand	90-94	5	20
α-helix	99-107	9
α-helix	110-112	3
β-strand	119-123	5	20
α-helix	131-141	11
β-strand	148-152	5	20
β-strand	155-157	3	22
α-helix	162-175	14
β-strand	179-187	9	20
β-strand	201-202	2	23
β-strand	203-206	4	20
β-strand	211-212	2	20
β-strand	216-217	2	23
β-strand	223-226	4	24
α-helix	229-233	5
β-strand	238-241	4	20
β-strand	244-246	3	20
β-strand	251-252	2	20
α-helix	254-262	9
α-helix	269-277	9
β-strand	286-292	7	20
β-strand	297-299	3	22
α-helix	303-314	12
β-strand	336-337	2	25
α-helix	339-341	3
β-strand	343-344	2	25
β-strand	355-356	2	26
β-strand	361-362	2	25
β-strand	367-368	2	27
β-strand	373-375	3	26
β-strand	378-379	2	25
β-strand	384-385	2	27
β-strand	390-392	3	26
β-strand	395-396	2	25
β-strand	401	1	27
β-strand	402	1	28
β-strand	407-409	3	26
β-strand	412-413	2	25
β-strand	418-419	2	28
β-strand	424	1	26
α-helix	425-426	2
β-strand	429-431	3	25
β-strand	436-437	2	28
α-helix	438	1
β-strand	447-449	3	25

Chains C and D: 20 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	76-95	20
α-helix	127-145	19
α-helix	147-153	7
α-helix	154-158	5
β-strand	164-168	5	14
α-helix	172-181	10
β-strand	188-192	5	14
α-helix	200-208	9
β-strand	214-217	4	14
α-helix	219-221	3
α-helix	222-225	4
α-helix	226-228	3
β-strand	231-234	4	14
β-strand	238-239	2	15
β-strand	245-248	4	15
α-helix	251-260	10
α-helix	263-264	2
β-strand	265-268	4	14
β-strand	274	1	15
β-strand	288	1	16
α-helix	297-299	3
α-helix	301-303	3
β-strand	306-307	2	17
β-strand	311	1	16
β-strand	313-316	4	15
α-helix	318-320	3
β-strand	323-326	4	14
β-strand	329-331	3	14
α-helix	333-335	3
α-helix	336-343	8
α-helix	346-348	3

Chains E and F: 19 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	169-172	4
β-strand	185	1	38
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	37
α-helix	340-351	12
β-strand	357-362	6	37
α-helix	369-378	10
β-strand	383-387	5	37
α-helix	388-394	7
β-strand	400-404	5	37
β-strand	405-408	4	39
β-strand	414-417	4	39
α-helix	421-429	9
α-helix	432-433	2
β-strand	434-437	4	37
α-helix	440-442	3
β-strand	443	1	39
β-strand	457	1	38
α-helix	460-462	3
β-strand	482-484	3	34
β-strand	487	1	38
β-strand	489-490	2	39
β-strand	499-502	4	37
β-strand	505-507	3	37
α-helix	509-511	3
α-helix	512-519	8

Chains G and H: 14 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	5-15	11
α-helix	22-35	14
α-helix	45-55	11
α-helix	63-76	14
α-helix	93-105	13
α-helix	107-115	9
α-helix	119-120	2
β-strand	124-127	4	32
α-helix	132-143	12
β-strand	149-153	5	32
α-helix	161-169	9
β-strand	175-178	4	32
α-helix	180-182	3
β-strand	192-195	4	32
β-strand	199-200	2	33
β-strand	206-209	4	33
α-helix	212-221	10
β-strand	226-228	3	32
β-strand	235	1	33
α-helix	248-251	4
β-strand	273-276	4	33
α-helix	278-280	3
β-strand	283-286	4	32
β-strand	289-291	3	32
α-helix	294-303	10

Chain I: 10 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	3-8	6	29
α-helix	37-45	9
β-strand	52-54	3	29
α-helix	55-56	2
α-helix	64-67	4
β-strand	76-78	3	29
α-helix	86-92	7
α-helix	94-96	3
β-strand	100-105	6	29
β-strand	110	1	30
α-helix	115-123	9
β-strand	128-131	4	29
β-strand	132-133	2	31
β-strand	157-161	5	20
β-strand	167-171	5	20
β-strand	180-183	4	24
α-helix	185-189	5
β-strand	192-196	5	20
β-strand	200-201	2	31
β-strand	207	1	29
α-helix	209-217	9
α-helix	224-226	3
β-strand	263-266	4	29
β-strand	277	1	30
α-helix	284-287	4

Chain J: 10 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	3-8	6	10
α-helix	37-45	9
β-strand	52-54	3	10
α-helix	55-56	2
α-helix	64-67	4
β-strand	76-78	3	10
α-helix	86-92	7
α-helix	94-96	3
β-strand	100-105	6	10
β-strand	110	1	11
α-helix	115-123	9
β-strand	128-133	6	10
β-strand	157-161	5	1
β-strand	167-171	5	1
β-strand	180-183	4	5
α-helix	185-189	5
β-strand	192-196	5	1
β-strand	200-201	2	10
β-strand	207	1	10
α-helix	209-217	9
α-helix	224-226	3
β-strand	263-272	10	10
β-strand	277	1	11
α-helix	284-287	4

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 gamma	I, J	protein	452	Homo sapiens	Q9NR50 (AlphaFold model)
Translation initiation factor eIF-2B subunit alpha	G, H	protein	305	Homo sapiens	Q14232 (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

Sequence of entity 1 (A, B), FASTA

>6CAJ_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 (I, J), FASTA

>6CAJ_2 Translation initiation factor eIF-2B subunit gamma (chains I, J)
MEFQAVVMAVGGGSRMTDLTSSIPKPLLPVGNKPLIWYPLNLLERVGFEEVIVVTTRDVQ
KALCAEFKMKMKPDIVCIPDDADMGTADSLRYIYPKLKTDVLVLSCDLITDVALHEVVDL
FRAYDASLAMLMRKGQDSIEPVPGQKGKKKAVEQRDFIGVDSTGKRLLFMANEADLDEEL
VIKGSILQKHPRIRFHTGLVDAHLYCLKKYIVDFLMENGSITSIRSELIPYLVRKQFSSA
SSQQGQEEKEEDLKKKELKSLDIYSFIKEANTLNLAPYDACWNACRGDRWEDLSRSQVRC
YVHIMKEGLCSRVSTLGLYMEANRQVPKLLSALCPEEPPVHSSAQIVSKHLVGVDSLIGP
ETQIGEKSSIKRSVIGSSCLIKDRVTITNCLLMNSVTVEEGSNIQGSVICNNAVIEKGAD
IKDCLIGSGQRIEAKAKRVNEVIVGNDQLMEI

Sequence of entity 3 (G, H), FASTA

>6CAJ_3 Translation initiation factor eIF-2B subunit alpha (chains G, H)
MDDKELIEYFKSQMKEDPDMASAVAAIRTLLEFLKRDKGETIQGLRANLTSAIETLCGVD
SSVAVSSGGELFLRFISLASLEYSDYSKCKKIMIERGELFLRRISLSRNKIADLCHTFIK
DGATILTHAYSRVVLRVLEAAVAAKKRFSVYVTESQPDLSGKKMAKALCHLNVPVTVVLD
AAVGYIMEKADLVIVGAEGVVENGGIINKIGTNQMAVCAKAQNKPFYVVAESFKFVRLFP
LNQQDVPDKFKYKADTLKVAQTGQDLKEEHPWVDYTAPSLITLLFTDLGVLTPSAVSDEL
IKLYL

Sequence of entity 4 (C, D), FASTA

>6CAJ_4 Translation initiation factor eIF-2B subunit beta (chains C, D)
MHHHHHHGGGSENLYFQSPGSAAKGSELSERIESFVETLKRGGGPRSSEEMARETLGLLR
QIITDHRWSNAGELMELIRREGRRMTAAQPSETTVGNMVRRVLKIIREEYGRLHGRSDES
DQQESLHKLLTSGGLNEDFSFHYAQLQSNIIEAINELLVELEGTMENIAAQALEHIHSNE
VIMTIGFSRTVEAFLKEAARKRKFHVIVAECAPFCQGHEMAVNLSKAGIETTVMTDAAIF
AVMSRVNKVIIGTKTILANGALRAVTGTHTLALAAKHHSTPLIVCAPMFKLSPQFPNEED
SFHKFVAPEEVLPFTEGDILEKVSVHCPVFDYVPPELITLFISNIGGNAPSYIYRLMSEL
YHPDDHVL

Sequence of entity 5 (E, F), FASTA

>6CAJ_5 Translation initiation factor eIF-2B subunit delta (chains E, F)
MAAVAVAVREDSGSGMKAELPPGPGAVGREMTKEEKLQLRKEKKQQKKKRKEEKGAEPET
GSAVSAAQCQVGPTRELPESGIQLGTPREKVPAGRSKAELRAERRAKQEAERALKQARKG
EQGGPPPKASPSTAGETPSGVKRLPEYPQVDDLLLRRLVKKPERQQVPTRKDYGSKVSLF
SHLPQYSRQNSLTQFMSIPSSVIHPAMVRLGLQYSQGLVSGSNARCIALLRALQQVIQDY
TTPPNEELSRDLVNKLKPYMSFLTQCRPLSASMHNAIKFLNKEITSVGSSKREEEAKSEL
RAAIDRYVQEKIVLAAQAISRFAYQKISNGDVILVYGCSSLVSRILQEAWTEGRRFRVVV
VDSRPWLEGRHTLRSLVHAGVPASYLLIPAASYVLPEVSKVLLGAHALLANGSVMSRVGT
AQLALVARAHNVPVLVCCETYKFCERVQTDAFVSNELDDPDDLQCKRGEHVALANWQNHA
SLRLLNLVYDVTPPELVDLVITELGMIPCSSVPVVLRVKSSDQ

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

Structure of the nucleotide exchange factor eIF2B reveals mechanism of memory-enhancing molecule. Tsai, J.C., Miller-Vedam, L.E., Anand, A.A. et al. Science (2018) 359. DOI 10.1126/science.aaq0939 · 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)
7L70 2.8 Å, The eukaryotic translation initiation factor 2B from Homo sapiens in its apo form

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