5GAK: 60S ribosomal protein L23-A

Name: PDB 5GAK: Yeast 60S ribosomal subunit with A-site tRNA, P-site tRNA and eIF-5A
Published: 2016-02-24
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

Yeast 60S ribosomal subunit with A-site tRNA, P-site tRNA and eIF-5A. Determined by electron microscopy at 3.88 Å resolution. Released 24 Feb 2016.

Method: Electron microscopy
Resolution: 3.88 Å
Organism: Saccharomyces cerevisiae
Chains: 49
Atoms: 128,975
Mol. weight: 2016.97 kDa
Ligands: 3HE
Released: 24 Feb 2016

Explore 5GAK in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5GAK contains 321 α-helices and 297 β-strands across 43 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: 6 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	12-20	9
α-helix	24-30	7
β-strand	33-34	2	23
β-strand	35	1	24
α-helix	37-43	7
β-strand	47-48	2	23
α-helix	49-50	2
β-strand	57-58	2	25
β-strand	70-74	5	26
β-strand	79-82	4	26
β-strand	88	1	27
β-strand	94	1	27
β-strand	98-99	2	26
α-helix	101-103	3
β-strand	104-105	2	25
β-strand	106	1	24
α-helix	114-120	7

Chain b: 7 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	9-13	5	30
β-strand	22-29	8	30
β-strand	40-46	7	30
α-helix	49-50	2
α-helix	60-65	6
β-strand	70-76	7	30
α-helix	77-79	3
β-strand	80-86	7	30
α-helix	98-100	3
α-helix	104-122	19
α-helix	128-131	4
α-helix	133-134	2

Chain c: 6 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	3-5	3
α-helix	7-11	5
α-helix	42-45	4
β-strand	53	1	35
α-helix	65-68	4
β-strand	72-74	3	36
α-helix	84-91	8
β-strand	100	1	37
β-strand	101-103	3	38
β-strand	111-113	3	36
β-strand	124-127	4	38
β-strand	129	1	36
α-helix	132-140	9
β-strand	145-147	3	38

Chain C: 5 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	7-10	4	32
β-strand	21-27	7	32
α-helix	28	1
α-helix	38-47	10
α-helix	56-57	2
α-helix	67-68	2
β-strand	69-74	6	32
β-strand	80-84	5	32
α-helix	102-105	4

Chain d: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	3-5	3
α-helix	15-17	3
α-helix	37-53	17

Chain D: 5 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	9-14	6
α-helix	21-34	14
β-strand	37-38	2	39
β-strand	45-47	3	39
β-strand	48	1	40
β-strand	54-56	3	40
β-strand	63-65	3	40
α-helix	76-78	3
α-helix	79-86	8
α-helix	88-90	3

Chain e: 5 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	11-20	10
β-strand	22-25	4	55
α-helix	27-35	9
β-strand	41-45	5	55
α-helix	50-57	8
β-strand	67-70	4	55
α-helix	74-80	7
β-strand	89-94	6	55
α-helix	100-102	3

Chain E: 10 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	6-10	5
α-helix	28-32	5
α-helix	34-37	4
β-strand	41-49	9	47
α-helix	50-51	2
β-strand	58-64	7	47
β-strand	71-77	7	47
α-helix	78	1
β-strand	79	1	48
β-strand	83	1	40
β-strand	87-90	4	47
β-strand	101-103	3	47
α-helix	104-106	3
β-strand	112-114	3	47
β-strand	116	1	49
β-strand	126	1	49
β-strand	134-140	7	47
α-helix	142-144	3
β-strand	145-149	5	47
β-strand	155-159	5	47
β-strand	163-166	4	47
α-helix	168	1
β-strand	169	1	48
α-helix	182-189	8
β-strand	224-225	2	50
α-helix	230	1
β-strand	237-238	2	50

35 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
25S rRNA	1	RNA	3396	Saccharomyces cerevisiae
60S ribosomal protein L23-A	X	protein	137	Saccharomyces cerevisiae	P0CX41 (AlphaFold model)
5S rRNA	3	RNA	121	Saccharomyces cerevisiae
60S ribosomal protein L24-A	Y	protein	155	Saccharomyces cerevisiae	P04449 (AlphaFold model)
5.8S rRNA	4	RNA	158	Saccharomyces cerevisiae
60S ribosomal protein L25	Z	protein	142	Saccharomyces cerevisiae	P04456 (AlphaFold model)
The A-site tRNA was modeled based on an E. coli tRNA-Lys	A	RNA	76	Saccharomyces cerevisiae
60S ribosomal protein L26-A	a	protein	127	Saccharomyces cerevisiae	P05743 (AlphaFold model)
P-site tRNA	B	RNA	77	Saccharomyces cerevisiae
60S ribosomal protein L27-A	b	protein	136	Saccharomyces cerevisiae	P0C2H6
60S ribosomal protein L42-A	C	protein	106	Saccharomyces cerevisiae	P0CX27
60S ribosomal protein L28	c	protein	149	Saccharomyces cerevisiae	P02406

37 more molecules are not listed.

Sequence of entity 1 (1), FASTA

>5GAK_1 25S rRNA (chains 1)
GUUUGACCUCAAAUCAGGUAGGAGUACCCGCUGAACUUAAGCAUAUCAAUAAGCGGAGGA
AAAGAAACCAACCGGGAUUGCCUUAGUAACGGCGAGUGAAGCGGCAAAAGCUCAAAUUUG
AAAUCUGGUACCUUCGGUGCCCGAGUUGUAAUUUGGAGAGGGCAACUUUGGGGCCGUUCC
UUGUCUAUGUUCCUUGGAACAGGACGUCAUAGAGGGUGAGAAUCCCGUGUGGCGAGGAGU
GCGGUUCUUUGUAAAGUGCCUUCGAAGAGUCGAGUUGUUUGGGAAUGCAGCUCUAAGUGG
GUGGUAAAUUCCAUCUAAAGCUAAAUAUUGGCGAGAGACCGAUAGCGAACAAGUACAGUG
AUGGAAAGAUGAAAAGAACUUUGAAAAGAGAGUGAAAAAGUACGUGAAAUUGUUGAAAGG
GAAGGGCAUUUGAUCAGACAUGGUGUUUUGUGCCCUCUGCUCCUUGUGGGUAGGGGAAUC
UCGCAUUUCACUGGGCCAGCAUCAGUUUUGGUGGCAGGAUAAAUCCAUAGGAAUGUAGCU
UGCCUCGGUAAGUAUUAUAGCCUGUGGGAAUACUGCCAGCUGGGACUGAGGACUGCGACG
UAAGUCAAGGAUGCUGGCAUAAUGGUUAUAUGCCGCCCGUCUUGAAACACGGACCAAGGA
GUCUAACGUCUAUGCGAGUGUUUGGGUGUAAAACCCAUACGCGUAAUGAAAGUGAACGUA
GGUUGGGGCCUCGCAAGAGGUGCACAAUCGACCGAUCCUGAUGUCUUCGGAUGGAUUUGA
GUAAGAGCAUAGCUGUUGGGACCCGAAAGAUGGUGAACUAUGCCUGAAUAGGGUGAAGCC
AGAGGAAACUCUGGUGGAGGCUCGUAGCGGUUCUGACGUGCAAAUCGAUCGUCGAAUUUG
GGUAUAGGGGCGAAAGACUAAUCGAACCAUCUAGUAGCUGGUUCCUGCCGAAGUUUCCCU
CAGGAUAGCAGAAGCUCGUAUCAGUUUUAUGAGGUAAAGCGAAUGAUUAGAGGUUCCGGG
GUCGAAAUGACCUUGACCUAUUCUCAAACUUUAAAUAUGUAAGAAGUCCUUGUUACUUAA
UUGAACGUGGACAUUUGAAUGAAGAGCUUUUAGUGGGCCAUUUUUGGUAAGCAGAACUGG
CGAUGCGGGAUGAACCGAACGUAGAGUUAAGGUGCCGGAAUACACGCUCAUCAGACACCA
CAAAAGGUGUUAGUUCAUCUAGACAGCCGGACGGUGGCCAUGGAAGUCGGAAUCCGCUAA
GGAGUGUGUAACAACUCACCGGCCGAAUGAACUAGCCCUGAAAAUGGAUGGCGCUCAAGC
GUGUUACCUAUACUCUACCGUCAGGGUUGAUAUGAUGCCCUGACGAGUAGGCAGGCGUGG
AGGUCAGUGACGAAGCCUAGACCGUAAGGUCGGGUCGAACGGCCUCUAGUGCAGAUCUUG
GUGGUAGUAGCAAAUAUUCAAAUGAGAACUUUGAAGACUGAAGUGGGGAAAGGUUCCACG
UCAACAGCAGUUGGACGUGGGUUAGUCGAUCCUAAGAGAUGGGGAAGCUCCGUUUCAAAG
GCCUGAUUUUAUGCAGGCCACCAUCGAAAGGGAAUCCGGUUAAGAUUCCGGAACCUGGAU
AUGGAUUCUUCACGGUAACGUAACUGAAUGUGGAGACGUCGGCGCGAGCCCUGGGAGGAG
UUAUCUUUUCUUCUUAACAGCUUAUCACCCCGGAAUUGGUUUAUCCGGAGAUGGGGUCUU
AUGGCUGGAAGAGGCCAGCACCUUUGCUGGCUCCGGUGCGCUUGUGACGGCCCGUGAAAA
UCCACAGGAAGGAAUAGUUUUCAUGCCAGGUCGUACUGAUAACCGCAGCAGGUCUCCAAG
GUGAACAGCCUCUAGUUGAUAGAAUAAUGUAGAUAAGGGAAGUCGGCAAAAUAGAUCCGU
AACUUCGGGAUAAGGAUUGGCUCUAAGGGUCGGGUAGUGAGGGCCUUGGUCAGACGCAGC
GGGCGUGCUUGUGGACUGCUUGGUGGGGCUUGCUCUGCUAGGCGGACUACUUGCGUGCCU
UGUUGUAGACGGCCUUGGUAGGUCUCUUGUAGACCGUCGCUUGCUACAAUUAACGAUCAA
CUUAGAACUGGUACGGACAAGGGGAAUCUGACUGUCUAAUUAAAACAUAGCAUUGCGAUG
GUCAGAAAGUGAUGUUGACGCAAUGUGAUUUCUGCCCAGUGCUCUGAAUGUCAAAGUGAA
GAAAUUCAACCAAGCGCGGGUAAACGGCGGGAGUAACUAUGACUCUCUUAAGGUAGCCAA
AUGCCUCGUCAUCUAAUUAGUGACGCGCAUGAAUGGAUUAACGAGAUUCCCACUGUCCCU
AUCUACUAUCUAGCGAAACCACAGCCAAGGGAACGGGCUUGGCAGAAUCAGCGGGGAAAG
AAGACCCUGUUGAGCUUGACUCUAGUUUGACAUUGUGAAGAGACAUAGAGGGUGUAGAAU
AAGUGGGAGCUUCGGCGCCAGUGAAAUACCACUACCUUUAUAGUUUCUUUACUUAUUCAA
UGAAGCGGAGCUGGAAUUCAUUUUCCACGUUCUAGCAUUCAAGGUCCCAUUCGGGGCUGA
UCCGGGUUGAAGACAUUGUCAGGUGGGGAGUUUGGCUGGGGCGGCACAUCUGUUAAACGA
UAACGCAGAUGUCCUAAGGGGGGCUCAUGGAGAACAGAAAUCUCCAGUAGAACAAAAGGG
UAAAAGCCCCCUUGAUUUUGAUUUUCAGUGUGAAUACAAACCAUGAAAGUGUGGCCUAUC
GAUCCUUUAGUCCCUCGGAAUUUGAGGCUAGAGGUGCCAGAAAAGUUACCACAGGGAUAA
CUGGCUUGUGGCAGUCAAGCGUUCAUAGCGACAUUGCUUUUUGAUUCUUCGAUGUCGGCU
CUUCCUAUCAUACCGAAGCAGAAUUCGGUAAGCGUUGGAUUGUUCACCCACUAAUAGGGA
ACGUGAGCUGGGUUUAGACCGUCGUGAGACAGGUUAGUUUUACCCUACUGAUGAAUGUUA
CCGCAAUAGUAAUUGAACUUAGUACGAGAGGAACAGUUCAUUCGGAUAAUUGGUUUUUGC
GGCUGUCUGAUCAGGCAUUGCCGCGAAGCUACCAUCCGCUGGAUUAUGGCUGAACGCCUC
UAAGUCAGAAUCCAUGCUAGAACGCGGUGAUUUCUUUGCUCCACACAAUAUAGAUGGAUA
CGAAUAAGGCGUCCUUGUGGCGUCGCUGAACCAUAGCAGGCUAGCAACGGUGCACUUGGC
GGAAAGGCCUUGGGUGCUUGCUGGCGAAUUGCAAUGUCAUUUUGCGUGGGGAUAAAUCAU
UUGUAUACGACUUAGAUGUACAACGGGGUAUUGUAAGCAGUAGAGUAGCCUUGUUGUUAC
GAUCUGCUGAGAUUAAGCCUUUGUUGUCUGAUUUGU

Sequence of entity 2 (X), FASTA

>5GAK_2 60S ribosomal protein L23-A (chains X)
MSGNGAQGTKFRISLGLPVGAIMNCADNSGARNLYIIAVKGSGSRLNRLPAASLGDMVMA
TVKKGKPELRKKVMPAIVVRQAKSWRRRDGVFLYFEDNAGVIANPKGEMKGSAITGPVGK
ECADLWPRVASNSGVVV

Sequence of entity 3 (3), FASTA

>5GAK_3 5S rRNA (chains 3)
GGUUGCGGCCAUAUCUACCAGAAAGCACCGUUUCCCGUCCGAUCAACUGUAGUUAAGCUG
GUAAGAGCCUGACCGAGUAGUGUAGUGGGUGACCAUACGCGAAACUCAGGUGCUGCAAUC
U

Sequence of entity 4 (Y), FASTA

>5GAK_4 60S ribosomal protein L24-A (chains Y)
MKVEIDSFSGAKIYPGRGTLFVRGDSKIFRFQNSKSASLFKQRKNPRRIAWTVLFRKHHK
KGITEEVAKKRSRKTVKAQRPITGASLDLIKERRSLKPEVRKANREEKLKANKEKKKAEK
AARKAEKAKSAGTQSSKFSKQQAKGAFQKVAATSR

Sequence of entity 5 (4), FASTA

>5GAK_5 5.8S rRNA (chains 4)
AAACUUUCAACAACGGAUCUCUUGGUUCUCGCAUCGAUGAAGAACGCAGCGAAAUGCGAU
ACGUAAUGUGAAUUGCAGAAUUCCGUGAAUCAUCGAAUCUUUGAACGCACAUUGCGCCCC
UUGGUAUUCCAGGGGGCAUGCCUGUUUGAGCGUCAUUU

Sequence of entity 6 (Z), FASTA

>5GAK_6 60S ribosomal protein L25 (chains Z)
MAPSAKATAAKKAVVKGTNGKKALKVRTSATFRLPKTLKLARAPKYASKAVPHYNRLDSY
KVIEQPITSETAMKKVEDGNILVFQVSMKANKYQIKKAVKELYEVDVLKVNTLVRPNGTK
KAYVRLTADYDALDIANRIGYI

Sequence of entity 7 (A), FASTA

>5GAK_7 The A-site tRNA was modeled based on an E. coli tRNA-Lys (chains A)
GGGUCGUUAGCUCAGUUGGUAGAGCAGUUGACUUUUAAUCAAUUGGUCGCAGGUUCGAAU
CCUGCACGACCCACCA

Sequence of entity 8 (a), FASTA

>5GAK_8 60S ribosomal protein L26-A (chains a)
MAKQSLDVSSDRRKARKAYFTAPSSQRRVLLSAPLSKELRAQYGIKALPIRRDDEVLVVR
GSKKGQEGKISSVYRLKFAVQVDKVTKEKVNGASVPINLHPSKLVITKLHLDKDRKALIQ
RKGGKLE

Sequence of entity 9 (B), FASTA

>5GAK_9 P-site tRNA (chains B)
GGAGCGGUAGUUCAGUCGGUUAGAAUACCUGCCUGUCACGCAGGGGGUCGCGGGUUCGAG
UCCCGUCCGUUCCGCCA

Sequence of entity 10 (b), FASTA

>5GAK_10 60S ribosomal protein L27-A (chains b)
MAKFLKAGKVAVVVRGRYAGKKVVIVKPHDEGSKSHPFGHALVAGIERYPLKVTKKHGAK
KVAKRTKIKPFIKVVNYNHLLPTRYTLDVEAFKSVVSTETFEQPSQREEAKKVVKKAFEE
RHQAGKNQWFFSKLRF

Sequence of entity 11 (C), FASTA

>5GAK_11 60S ribosomal protein L42-A (chains C)
MVNVPKTRKTYCKGKTCRKHTQHKVTQYKAGKASLFAQGKRRYDRKQSGFGGQTKPVFHK
KAKTTKKVVLRLECVKCKTRAQLTLKRCKHFELGGEKKQKGQALQF

Sequence of entity 12 (c), FASTA

>5GAK_12 60S ribosomal protein L28 (chains c)
MPSRFTKTRKHRGHVSAGKGRIGKHRKHPGGRGMAGGQHHHRINMDKYHPGYFGKVGMRY
FHKQQAHFWKPVLNLDKLWTLIPEDKRDQYLKSASKETAPVIDTLAAGYGKILGKGRIPN
VPVIVKARFVSKLAEEKIRAAGGVVELIA

Ligands and cofactors

ID	Name	Formula	Copies
3HE	4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2…	C15 H23 N O4	1

Primary citation

Structure of the hypusinylated eukaryotic translation factor eIF-5A bound to the ribosome. Schmidt, C., Becker, T., Heuer, A. et al. Nucleic Acids Res (2016) 44:1944-1951. DOI 10.1093/nar/gkv1517 · PubMed

Other PDB entries of the same protein (UniProt P0CX41 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9PN5 1.75 Å, Composite map of hypomethylated 80S ribosome treated with hygromycin B
8CCS 1.97 Å, 80S S. cerevisiae ribosome with ligands in hybrid-1 pre-translocation (PRE-H1) complex
8CDR 2.04 Å, Translocation intermediate 2 (TI-2) of 80S S. cerevisiae ribosome with ligands and eEF2…
8CEH 2.05 Å, Translocation intermediate 4 (TI-4) of 80S S. cerevisiae ribosome with ligands and eEF2…
8P8N 2.15 Å, Mouse RPL39 integrated into the yeast 60S ribosomal subunit
8PFR 2.15 Å, Mouse RPL39L integrated into the yeast 60S ribosomal subunit
8EVT 2.2 Å, Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome…
8T2Y 2.2 Å, Hypomethylated yeast 80S bound with cycloheximide, P-site tRNA, and A-site tRNA,…
8P8U 2.23 Å, Yeast 60S ribosomal subunit
8CGN 2.28 Å, Non-rotated 80S S. cerevisiae ribosome with ligands
8ZHC 2.3 Å, pre-frameshift complex of yeast 80S ribosome with eRF1 and mRNA of WNV
7UOO 2.34 Å, Nucleoplasmic pre-60S intermediate of the Nog2 containing pre-rotation state

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