3JAM: 40S-eIF1A-eIF1 complex from yeast

Name: PDB 3JAM: CryoEM structure of 40S-eIF1A-eIF1 complex from yeast
Published: 2015-08-12
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: translation

CryoEM structure of 40S-eIF1A-eIF1 complex from yeast. Determined by electron microscopy at 3.46 Å resolution. Released 12 Aug 2015.

Method: Electron microscopy
Resolution: 3.46 Å
Organisms: Kluyveromyces lactis, Saccharomyces cerevisiae
Chains: 37
Atoms: 77,850
Mol. weight: 1208.67 kDa
Ligands: MG, ZN
Released: 12 Aug 2015

Explore 3JAM in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3JAM contains 200 α-helices and 261 β-strands across 36 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: 4 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	19	1
β-strand	20-21	2	4
α-helix	22-23	2
β-strand	30-31	2	4
β-strand	37-43	7	5
α-helix	50-56	7
β-strand	57	1	60
β-strand	66-72	7	5
α-helix	75-80	6

Chain A: 6 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	11-20	10
β-strand	37-40	4	2
β-strand	46-48	3	2
α-helix	50-66	17
α-helix	70-72	3
β-strand	73-77	5	3
α-helix	80-92	13
β-strand	96-99	4	3
β-strand	120-123	4	3
α-helix	130-137	8
β-strand	143-145	3	3
β-strand	159	1	3
α-helix	168-185	18

Chain b: 4 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	12-17	6
α-helix	19	1
β-strand	32-36	5	7
α-helix	37	1
β-strand	43-47	5	7
β-strand	64-65	2	8
α-helix	71	1
β-strand	72-73	2	8
β-strand	78-81	4	7

Chain B: 9 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	23-26	4
β-strand	27-33	7	6
β-strand	42-49	8	6
β-strand	65-69	5	6
α-helix	71-74	4
α-helix	77-79	3
β-strand	82-93	12	6
β-strand	95-105	11	6
α-helix	107-113	7
β-strand	120-128	9	6
β-strand	134-142	9	6
α-helix	155-157	3
α-helix	158-175	18
α-helix	181-188	8
α-helix	192-201	10
β-strand	208-211	4	6
β-strand	215-219	5	6
α-helix	225-229	5

Chain c: 0 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	8-19	12	12
β-strand	25-32	8	12
β-strand	41-45	5	12
β-strand	53-56	4	12

Chain C: 10 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	45-52	8
α-helix	58-63	6
α-helix	71-77	7
β-strand	82-94	13	9
β-strand	99-110	12	9
β-strand	115-123	9	9
α-helix	126-140	15
β-strand	142-143	2	9
β-strand	146-147	2	10
β-strand	158-159	2	10
β-strand	163-167	5	11
β-strand	170-176	7	11
α-helix	177-178	2
β-strand	183-184	2	11
α-helix	187-196	10
β-strand	201-206	6	11
α-helix	212-225	14
α-helix	232-234	3
α-helix	241-243	3
α-helix	244-247	4

Chain d: 3 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	30-31	2	17
α-helix	33-35	3
β-strand	38-39	2	17
α-helix	40-45	6
α-helix	47-50	4
β-strand	53-54	2	75

Chain D: 7 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	7-28	22
β-strand	34-41	8	13
β-strand	46-52	7	13
α-helix	55-59	5
α-helix	65-77	13
β-strand	84-89	6	13
α-helix	98-111	14
α-helix	115-129	15
β-strand	133-139	7	14
β-strand	150-155	6	14
α-helix	163-167	5
β-strand	168-177	10	14
β-strand	180-189	10	14
β-strand	207	1	15
α-helix	208-213	6
β-strand	223-224	2	16

28 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
18S rRNA	2	RNA	1799	Kluyveromyces lactis
uS2	A	protein	254	Kluyveromyces lactis	Q6CN12 (AlphaFold model)
eS1	B	protein	255	Kluyveromyces lactis	Q6CWD0 (AlphaFold model)
uS5	C	protein	259	Kluyveromyces lactis	Q6CKL3 (AlphaFold model)
uS3	D	protein	237	Kluyveromyces lactis	Q6CRK7 (AlphaFold model)
eS4	E	protein	261	Kluyveromyces lactis	Q6CWJ2
uS7	F	protein	227	Kluyveromyces lactis	Q6CRA3
eS6	G	protein	236	Kluyveromyces lactis	Q6CM04
eS7	H	protein	190	Kluyveromyces lactis	Q6CTD6
eS8	I	protein	201	Kluyveromyces lactis	Q6CMG3
uS4	J	protein	188	Kluyveromyces lactis	Q6CM18
eS10	K	protein	106	Kluyveromyces lactis	Q6CVZ5

25 more molecules are not listed.

Sequence of entity 1 (2), FASTA

>3JAM_1 18S rRNA (chains 2)
UAUCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUCU
AAGUAUAAGCAAUUUAUACAGUGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUCGUUUAU
UUGAUAGUUCCUUUACUACAUGGAUAUCUGUGGUAAUUCUAGAGCUAAUACAUGCUUAAA
AUCUCGACCCUUUGGAAGAGAUGUAUUUAUUAGAUAAAAAAUCAAUGUCUUCGGACUCCU
UGAUGAUUCAUAAUAACUUUUCGAAUCGCAUGGCCUUGUGCUGGCGAUGGUUCAUUCAAA
UUUCUGCCCUAUCAACUUUCGAUGGUAGGAUAGUGGCCUACCAUGGUUUCAACGGGUAAC
GGGGAAUAAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAA
GGCAGCAGGCGCGCAAAUUACCCAAUCCUAAUUCAGGGAGGUAGUGACAAUAAAUAACGA
UACAGGGCCCAUUCGGGUCUUGUAAUUGGAAUGAGUACAAUGUAAAUACCUUAACGAGGA
ACAACUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAGUAGCGUAUA
UUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGAACUUUGGGUCUGGUUGUCCGGUCCGA
CUUUAUGUCGCGCACUGGUUUUUCAACCGGAUCUUUCCUUCUGGCUAACCUGUACUCCUU
GUGGGUGCAGGCGAACCAGGACUUUUACUUUGAAAAAAUUAGAGUGUUCAAAGCAGGCGA
AAGCUCGAAUAUAUUAGCAUGGAAUAAUGGAAUAGGACGUUUGGUUCUAUUUUGUUGGUU
UCUAGGACCAUCGUAAUGAUUAAUAGGGACGGUCGGGGGCAUCAGUAUUCAAUUGUCAGA
GGUGAAAUUCUUGGAUUUAUUGAAGACUAACUACUGCGAAAGCAUUUGCCAAGGACGUUU
UCAUUAAUCAAGAACGAAAGUUAGGGGAUCGAAGAUGAUCAGAUACCGUCGUAGUCUUAA
CCAUAAACUAUGCCGACUAGGGAUCGGGUGGUGUUUUUCUUAUGACCCACUCGGCACCUU
ACGAGAAAUCAAAGUCUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAG
GAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGG
GAAACUCACCAGGUCCAGACACAAUAAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUUU
GUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGCUUAAUUGCGAU
AACGAACGAGACCUUAACCUACUAAAUAGGGUUGCUGGCACUUGCCGGUUGACUCUUCUU
AGAGGGACUAUCGGUUUCAAGCCGAUGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCC
UUAGACGUUCUGGGCCGCACGCGCGCUACACUGACGGAGCCAGCGAGUACAACCUUGGCC
GAGAGGUCUGGGUAAUCUUGUGAAACUCCGUCGUGCUGGGGAUAGAGCAUUGUAAUUAUU
GCUCUUCAACGAGGAAUUCCUAGUAAGCGCAAGUCAUCAGCUUGCGUUGAUUACGUCCCU
GCCCUUUGUACACACCGCCCGUCGCUAGUACCGAUUGAAUGGCUUAGUGAGGCCUCAGGA
UUUGCUUAGAGAAGGGGGCAACUCCAUCUCAGAGCGAAGAAUCUGGUCAAACUUGGUCAU
UUAGAGGAACUAAAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAUUA

Sequence of entity 2 (A), FASTA

>3JAM_2 uS2 (chains A)
MSLPSTFDLTSEDAQLLLAARVHLGAKNVQVHQEPYVYKARPDGVNVINVGKTWEKIVLA
ARIIAAIPNPEDVVAISSRTYGQRAVLKYAAHTGATPIAGRFTPGSFTNYITRSFKEPRL
VIVTDPRSDAQAIKESSYVNIPVIALTDLDSPSEYVDVAIPCNNRGKHSIGLIWYLLARE
VLRLRGALPDRTQPWAIMPDLYFYRNPEEIEQQTAEEEAVASGEQTEEAVDATEEQTEAA
EWAEEGQAQEEEWN

Sequence of entity 3 (B), FASTA

>3JAM_3 eS1 (chains B)
MAVGKNKRLSKGKKGLKKRVVDPFTRKEWYDIKAPSTFENRNVGKTLVNKSVGLKNASDS
LKGRVVEVCLADLQGSEDHSFRKVKLRVDEVQGKNLLTNFHGMDFTTDKLRSMVRKWQTL
IEANVTVKTSDDYVLRIFAIAFTRKQANQVKRTSYAQSSHIRQIRKVISEILTREVQNST
LAQLTSKLIPEVINKEIENATKDIFPLQNVHIRKVKLLKQPKFDLGSLLSLHGEASAEEK
GKKVAGFKDEILETV

Sequence of entity 4 (C), FASTA

>3JAM_4 uS5 (chains C)
MSAPQAQGQQAPRRGGFGGANRGGRGGRRGGRRDQEEKGWVPVTKLGRLVKAGKISSIEE
IFLHSLPVKEFQIIDQLLPNLKDEVMNIKPVQKQTRAGQRTRFKAVVVVGDSNGHVGLGI
KTAKEVAGAIRAGIIIAKLSVIPIRRGYWGTNLGQPHSLATKTSGKCGSVSVRLIPAPRG
SGIVASPAVKKLMQLAGVEDVYTSSTGSTRTLENTLKAAFVAIGNTYGFLTPNLWEVQAL
TPSPMDVYADYATASKKKL

Sequence of entity 5 (D), FASTA

>3JAM_5 uS3 (chains D)
MVAIISKKRKLVADGVFYAELNEFFTRELAEEGYSGVEVRVTPTKTEIIIRATKVQDVVG
ENGRRINELTLLIEKRFKYKRGTIALYAERVHDRGLSAVAQAESMKFKLLNGLAIRRAAY
GVVRYVMESGAKGCEVVISGKLRAARAKSMKFADGFLIHSGQPVNDFIETATRHVLLRQG
VLGIKVKIMKDPSRNTSGPKALPDAVTIIEPKEEEPVLEPSVKDYRPTEPVEAAESA

Sequence of entity 6 (E), FASTA

>3JAM_6 eS4 (chains E)
MARGPKKHLKRLAAPHHWMLDKLSGCYAPRPSAGPHKLRESLPLIVFLRNRLKYALNGRE
VKAILMQRHVKVDGKVRTDTTFPAGFMDVITLEATNENFRLVYDVKGRFAVHRITDEEAS
YKLAKVKKVQLGKKGIPYVVTHDGRTIRYPDPNIKVNDTVKVDLATGTITDFIKFDTGKL
VYVTGGRNLGRVGTIVHRERHEGGFDLVHIKDSLENTFVTRLNNVFVIGEPGRPWISLPK
GKGIKLTISEERDRRRAQHGL

Sequence of entity 7 (F), FASTA

>3JAM_7 uS7 (chains F)
MSEHEAQVEVEVQEDFEVVQEFVPVELATTIPVEIQQAQQEIKLFNKWSFEDVEVKDASL
VDYIQISKPIYVAHTAGRYANKRFRKAQCPIVERLTNSLMMNGRNNGKKLKAVRIVKHTL
EIINVLTDQNPLQVVVDAIINSGPREDTTRVGGGGAARRQAVDVSPLRRVNQSIALLTIG
AREAAFRNIKTIAETLAEELINAAKGSSTSYAIKKKDELERVAKSNR

Sequence of entity 8 (G), FASTA

>3JAM_8 eS6 (chains G)
MKLNISYPINGTQKCIEIDDEHRVRVFYDKRIGQEVDGESVGDEFKGYVFKIAGGNDKQG
FPMKQGVLLPTRVKLLLAKGHSCYRPRRNGERKRKSVRGAIVGPDLAVLALIITKKGEQE
IEGITNDTVPKRLGPKRANNIRKFFGLTKEDDVRDYVIRREVTKGDKSYTKAPKIQRLVT
PQRLQRKRQQKSLKIKNAQAQREAAAEYAQLLAKRLSERKAEKAEVRKRRASSLKA

Sequence of entity 9 (H), FASTA

>3JAM_9 eS7 (chains H)
MSDPQAKILSQAPTELELQVAQAFIDLENNSPELKADLRALQFKSIREIEVAGGKKALAV
FVPVPSLAAYHKVQIKLTRELEKKFQDRHVIFLAERRILPKPSRKSRQTQKRPRSRTLTA
VHDKILEDLVFPTEIVGKRVRYLVGGNKIQKILLNSKDVQHIDNKLESFQAVYNKLTGKQ
IVFEIPSETH

Sequence of entity 10 (I), FASTA

>3JAM_10 eS8 (chains I)
MGISRDSRHKRAATGAKRAQFRKKRKFELGRQAANTKIGTKRIHPVRTRGGNQKFRALRI
ETGNFSWASEGVARKTRITGVVYHPSNNELVRTNTLTKAAIVQIDATPFRQWYESHYGQS
LGKKKNTKAEEETATTSKNTERKWAARAAEAKIEHAVDSQFGAGRLYAAISSRPGQSGRC
DGYILEGEELAFYLRRLTAKK

Sequence of entity 11 (J), FASTA

>3JAM_11 uS4 (chains J)
MPRAPRTYSKTYSTPKRPYESARLDAELKLAGEYGLKNKREIYRISFQLSKIRRAARDLL
TRDEKDPKRLFEGNALIRRLVRIGVLSEDKKKLDYVLALKVEDFLERRLQTQVYKLGLAK
SVHHARVLISQRHIAVGKQIVNIPSFMVRLESEKHIDFARTSPFGGARPGRVARKRAAAA
GGEEADEE

Sequence of entity 12 (K), FASTA

>3JAM_12 eS10 (chains K)
MLIPKEDRKKIYQHLFQEGVLVAKKDFNQPKHEEIDTKNLFVIKALQSLTSKGFVKTQFS
WQYYYYTLTEEGVVYLREYLNLPEHIFPATYLAGQSGDQRPQGKKY

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	80
ZN	Zinc ion	Zn	3

Primary citation

Conformational Differences between Open and Closed States of the Eukaryotic Translation Initiation Complex. Llacer, J.L., Hussain, T., Marler, L. et al. Mol Cell (2015) 59:399-412. DOI 10.1016/j.molcel.2015.06.033 · PubMed

Other PDB entries of the same protein (UniProt Q6CN12 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6FYY 3.02 Å, Structure of a partial yeast 48S preinitiation complex with eIF5 N-terminal domain…
8RW1 3.35 Å, Structure of a yeast 48S-AUC preinitiation complex in closed conformation
8S8D 3.45 Å, Structure of a yeast 48S-AUC preinitiation complex in closed conformation (model…
6FYX 3.5 Å, Structure of a partial yeast 48S preinitiation complex with eIF5 N-terminal domain…
5IT7 3.6 Å, Structure of the Kluyveromyces lactis 80S ribosome in complex with the cricket paralysis…
6UZ7 3.6 Å, K.lactis 80S ribosome with p/PE tRNA and eIF5B
3J80 3.75 Å, CryoEM structure of 40S-eIF1-eIF1A preinitiation complex
5IT9 3.8 Å, Structure of the yeast Kluyveromyces lactis small ribosomal subunit in complex with the…
8S8E 3.85 Å, Structure of a yeast 48S-AUC preinitiation complex in closed conformation (model…
8S8F 3.95 Å, Structure of a yeast 48S-AUC preinitiation complex in closed conformation (model…
3J81 4.0 Å, CryoEM structure of a partial yeast 48S preinitiation complex
8S8G 4.0 Å, Structure of a yeast 48S-AUC preinitiation complex in closed conformation (model…

Browse structure collections

About this viewer

MolViewer shows 3JAM directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.