6N1D: 50S ribosomal protein L1

X-ray Crystal complex showing Spontaneous Ribosomal Translocation of mRNA and tRNAs into a Chimeric Hybrid State. Determined by X-ray diffraction at 3.2 Å resolution. Released 3 Apr 2019.

Method: X-ray diffraction
Resolution: 3.2 Å
Organisms: Thermus thermophilus HB27, Thermus thermophilus, Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
Chains: 111
Atoms: 295,025
Mol. weight: 4451.77 kDa
Ligands: SF4, MG
Released: 3 Apr 2019

Explore 6N1D in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6N1D contains 408 α-helices and 650 β-strands across 98 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 AL01: 8 helices, 0 β-strands

Element	Residues	Length
α-helix	11-14	4
α-helix	24-34	11
α-helix	84-86	3
α-helix	102-106	5
α-helix	121-127	7
α-helix	147-152	6
α-helix	184-186	3
α-helix	190-197	8

Chain AL02: 4 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	24
β-strand	17	1	25
β-strand	18	1	24
β-strand	36-37	2	26
β-strand	54	1	27
β-strand	62-63	2	26
β-strand	73	1	28
β-strand	77-83	7	29
β-strand	92-97	6	29
β-strand	102-106	5	29
β-strand	108	1	30
β-strand	116-117	2	29
β-strand	119	1	28
β-strand	130-132	3	28
β-strand	142-146	5	28
β-strand	153-155	3	28
β-strand	164-169	6	31
β-strand	172-176	5	31
β-strand	182-186	5	31
β-strand	190-193	4	28
β-strand	196	1	30
α-helix	201-203	3
β-strand	205	1	25
α-helix	210-213	4
β-strand	217	1	27
α-helix	223-225	3
α-helix	265-269	5
β-strand	270	1	31

Chain AL03: 5 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	4-10	7	36
β-strand	13-16	4	37
β-strand	19-22	4	37
β-strand	24-27	4	36
β-strand	31-32	2	38
β-strand	33-36	4	39
β-strand	46-53	8	39
α-helix	63-68	6
β-strand	75-82	8	39
β-strand	90-91	2	38
α-helix	93-95	3
β-strand	101-107	7	36
α-helix	108-110	3
β-strand	113-114	2	40
α-helix	116-120	5
β-strand	144	1	41
β-strand	147	1	41
β-strand	158-159	2	40
β-strand	164-171	8	36
β-strand	175-176	2	36
β-strand	181-184	4	36
β-strand	195-200	6	36
α-helix	201	1

Chain AL04: 6 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	8-13	6	44
β-strand	16-21	6	44
α-helix	30-43	14
β-strand	53	1	45
β-strand	88	1	45
α-helix	103-119	17
β-strand	125-126	2	44
α-helix	137-144	8
β-strand	154-156	3	46
α-helix	161-168	8
β-strand	173-174	2	46
α-helix	183-188	6
β-strand	192-193	2	46
β-strand	194-195	2	44
α-helix	201-205	5

Chain AL05: 6 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	6-10	5
α-helix	11-15	5
α-helix	16-22	7
β-strand	34-40	7	49
α-helix	53-55	3
β-strand	69-70	2	49
β-strand	77	1	50
β-strand	82	1	50
β-strand	90-94	5	49
α-helix	96-106	11
β-strand	132	1	49
β-strand	135	1	51
β-strand	155	1	51
β-strand	156-161	6	49
α-helix	168-176	9

Chain AL06: 2 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	18	1	55
β-strand	25	1	55
β-strand	42-45	4	56
β-strand	50-53	4	56
α-helix	59-78	20
β-strand	86-87	2	57
β-strand	88	1	58
β-strand	96-98	3	59
β-strand	103-105	3	59
β-strand	114-115	2	59
β-strand	122-123	2	60
β-strand	131-132	2	57
β-strand	133-134	2	60
α-helix	139-149	11
β-strand	163	1	58

Chain AL09: 6 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	2-5	4	69
β-strand	19-20	2	69
α-helix	23-25	3
α-helix	26-30	5
β-strand	36-38	3	69
α-helix	41-57	17
α-helix	63-72	10
β-strand	78-79	2	70
β-strand	92	1	71
α-helix	94-100	7
α-helix	101-105	5
β-strand	114-115	2	72
β-strand	120	1	71
β-strand	127-130	4	72
β-strand	138-141	4	72
β-strand	143-144	2	70

Chain AL13: 5 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	36-40	5	80
β-strand	45	1	81
α-helix	46-57	12
β-strand	74-78	5	80
β-strand	84	1	81
α-helix	89-91	3
β-strand	94-98	5	82
β-strand	105-109	5	82
α-helix	110-116	7
α-helix	120-126	7
α-helix	136-139	4
β-strand	143-144	2	80
β-strand	159	1	80

90 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
16S rRNA	A16S, B16S	RNA	1518	Thermus thermophilus HB27
23S rRNA	A23S, B23S	RNA	2881	Thermus thermophilus HB27
5s rRNA	A5S, B5S	RNA	119	Thermus thermophilus HB27
50S ribosomal protein L1	AL01, BL01	protein	228	Thermus thermophilus	Q72GV9 (AlphaFold model)
50S ribosomal protein L2	AL02, BL02	protein	276	Thermus thermophilus HB27	Q72I07 (AlphaFold model)
50S ribosomal protein L3	AL03, BL03	protein	206	Thermus thermophilus HB27	Q72I04 (AlphaFold model)
50S ribosomal protein L4	AL04, BL04	protein	205	Thermus thermophilus HB27	Q72I05 (AlphaFold model)
50S ribosomal protein L5	AL05, BL05	protein	181	Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)	Q72I16
50S ribosomal protein L6	AL06, BL06	protein	180	Thermus thermophilus HB27	Q72I19
50S ribosomal protein L9	AL09, BL09	protein	148	Thermus thermophilus HB27	Q72GV5
50S ribosomal protein L13	AL13, BL13	protein	140	Thermus thermophilus HB27	Q72IN1
50S ribosomal protein L14	AL14, BL14	protein	122	Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)	Q72I14

44 more molecules are not listed.

Sequence of entity 1 (A16S, B16S), FASTA

>6N1D_1 16S rRNA (chains A16S, B16S)
GUUGGAGAGUUUGAUCCUGGCUCAGGGUGAACGCUGGCGGCGUGCCUAAGACAUGCAAGU
CGUGCGGGCCGCGGGGUUUUACUCCGUGGUCAGCGGCGGACGGGUGAGUAACGCGUGGGU
GACCUACCCGGAAGAGGGGGACAACCCGGGGAAACUCGGGCUAAUCCCCCAUGUGGACCC
GCCCCUUGGGGUGUGUCCAAAGGGCUUUGCCCGCUUCCGGAUGGGCCCGCGUCCCAUCAG
CUAGUUGGUGGGGUAAUGGCCCACCAAGGCGACGACGGGUAGCCGGUCUGAGAGGAUGGC
CGGCCACAGGGGCACUGAGACACGGGCCCCACUCCUACGGGAGGCAGCAGUUAGGAAUCU
UCCGCAAUGGGCGCAAGCCUGACGGAGCGACGCCGCUUGGAGGAAGAAGCCCUUCGGGGU
GUAAACUCCUGAACCCGGGACGAAACCCCCGAGGAGGGGACUGACGGUACCGGGGUAAUA
GCGCCGGCCAACUCCGUGCCAGCAGCCGCGGUAAUACGGAGGGCGCGAGCGUUACCCGGA
UUCACUGGGCGUAAAGGGCGUGUAGGCGGCCUGGGGCGUCCCAUGUGAAAGACCACGGCU
CAACCGUGGGGGAGCGUGGGAUACGCUCAGGCUAGACGGUGGGAGAGGGUGGUGGAAUUC
CCGGAGUAGCGGUGAAAUGCGCAGAUACCGGGAGGAACGCCGAUGGCGAAGGCAGCCACC
UGGUCCACCCGUGACGCUGAGGCGCGAAAGCGUGGGGAGCAAACCGGAUUAGAUACCCGG
GUAGUCCACGCCCUAAACGAUGCGCGCUAGGUCUCUGGGUCUCCUGGGGGCCGAAGCUAA
CGCGUUAAGCGCGCCGCCUGGGGAGUACGGCCGCAAGGCUGAAACUCAAAGGAAUUGACG
GGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGAAGCAACGCGAAGAACCUUACC
AGGCCUUGACAUGCUAGGGAACCCGGGUGAAAGCCUGGGGUGCCCCGCGAGGGGAGCCCU
AGCACAGGUGCUGCAUGGCCGUCGUCAGCUCGUGCCGUGAGGUGUUGGGUUAAGUCCCGC
AACGAGCGCAACCCCCGCCGUUAGUUGCCAGCGGUUCGGCCGGGCACUCUAACGGGACUG
CCCGCGAAAGCGGGAGGAAGGAGGGGACGACGUCUGGUCAGCAUGGCCCUUACGGCCUGG
GCGACACACGUGCUACAAUGCCCACUACAAAGCGAUGCCACCCGGCAACGGGGAGCUAAU
CGCAAAAAGGUGGGCCCAGUUCGGAUUGGGGUCUGCAACCCGACCCCAUGAAGCCGGAAU
CGCUAGUAAUCGCGGAUCAGCCAUGCCGCGGUGAAUACGUUCCCGGGCCUUGUACACACC
GCCCGUCACGCCAUGGGAGCGGGCUCUACCCGAAGUCGCCGGGAGCCUACGGGCAGGCGC
CGAGGGUAGGGCCCGUGACUGGGGCGAAGUCGUAACAAGGUAGCUGUACCGGAAGGUGCG
GCUGGAUCACCUCCUUUC

Sequence of entity 2 (A23S, B23S), FASTA

>6N1D_2 23S rRNA (chains A23S, B23S)
AGAUGGUAAGGGCCCACGGUGGAUGCCUCGGCACCCGAGCCGAUGAAGGACGUGGCUACC
UGCGAUAAGCCAGGGGGAGCCGGUAGCGGGCGUGGAUCCCUGGAUGUCCGAAUGGGGGAA
CCCGGCCGGCGGGAACGCCGGUCACCGCGCUUUUUGCGCGGGGGGAACCUGGGGAACUGA
AACAUCUCAGUACCCAGAGGAGAGGAAAGAGAAAUCGACUCCCUGAGUAGCGGCGAGCGA
AAGGGGACCAGCCUAAACCGUCCGGCUUGUCCGGGCGGGGUCGUGGGGCCCUCGGACACC
GAAUCCCCAGCCUAGCCGAAGCUGUUGGGAAGCAGCGCCAGAGAGGGUGAAAGCCCCGUA
GGCGAAAGGUGGGGGGAUAGGUGAGGGUACCCGAGUACCCCGUGGUUCGUGGAGCCAUGG
GGGAAUCUGGGCGGACCACCGCCUAAGGCUAAGUACUCCGGGUGACCGAUAGCGCACCAG
UACCGUGAGGGAAAGGUGAAAAGAACCCCGGGAGGGGAGUGAAAUAGAGCCUGAAACCGU
GGGCUUACAAGCAGUCACGGCCCCGCAAGGGGUUGUGGCGUGCCUAUUGAAGCAUGAGCC
GGCGACUCACGGUCGUGGGCGAGCUUAAGCCGUUGAGGCGGAGGCGUAGGGAAACCGAGU
CCGAACAGGGCGUCUAGUCCGCGGCCGUGGACCCGAAACCGGGCGAGCUAGCCCUGGCCA
GGGUGAAGCUGGGGUGAGACCCAGUGGAGGCCCGAACCGGUGGGGGAUGCAAACCCCUCG
GAUGAGCUGGGGCUAGGAGUGAAAAGCUAACCGAGCCCGGAGAUAGCUGGUUCUCCCCGA
AAUGACUUUAGGGUCAGCCUCAGGCGCUGACUGGGGCCUGUAGAGCACUGAUAGGGCUAG
GGGGCCCACCAGCCUACCAAACCCUGUCAAACUCCGAAGGGUCCCAGGUGGAGCCUGGGA
GUGAGGGCGCGAGCGAUAACGUCCGCGUCCGAGCGCGGGAACAACCGAGACCGCCAGCUA
AGGCCCCCAAGUCUGGGCUAAGUGGUAAAGGAUGUGGCGCCGCGAAGACAGCCAGGAGGU
UGGCUUAGAAGCAGCCAUCCUUUAAAGAGUGCGUAAUAGCUCACUGGUCGAGUGGCGCCG
CGCCGAAAAUGAUCGGGGCCUAAGCCCAGCGCCGAAGCUGCGGGUCUGGGGGAUGACCCC
AGGCGGUAGGGGAGCGUUCCCGAUGCCGAUGAAGGCCGACCCGCGAGGGCGGCUGGAGGU
AAGGGAAGUGCGAAUGCCGGCAUGAGUAACGAUAAAGAGGGUGAGAAUCCCUCUCGCCGU
AAGCCCAAGGGUUCCUACGCAAUGGUCGUCAGCGUAGGGUUAGGCGGGACCUAAGGUGAA
GCCGAAAGGCGUAGCCGAAGGGCAGCCGGUUAAUAUUCCGGCCCUUCCCGCAGGUGCGAU
GGGGGGACGCUCUAGGCUAGGGGGACCGGAGCCAUGGACGAGCCCGGCCAGAAGCGCAGG
GUGGGAGGUAGGCAAAUCCGCCUCCCAAAAGCUCUGCGUGGUGGGGAAGCCCGUACGGGU
GACAACCCCCCGAAGCCAGGGAGCCAAGAAAAGCCUCUAAGCACAACCUGCGGGAACCCG
UACCGCAAACCGACACAGGUGGGCGGGUGCAAGAGCACUCAGGCGCGCGGGAGAACCCUC
GCCAAGGAACUCUGCAAGUUGGCCCCGUAACUUCGGGAGAAGGGGUGCUCCCUGGGGUGA
UGAGCUCCGGGGAGCCGCAGUGAACAGGCUCUGGCGACUGUUUACCAAAAACACAGCUCU
CUGCGAACUCGUAAGAGGAGGUAUAGGGAGCGACGCUUGCCCGGUGCCGGAAGGUCAAGG
GGAGGGGUGCAAGCCCCGAACCGAAGCCCCGGUGAACGGCGGCCGUAACUAUAACGGUCC
UAAGGUAGCGAAAUUCCUUGUCGGGUAAGUUCCGACCUGCACGAAAAGCGUAACGACCGG
AGCGCUGUCUCGGCGAGGGACCCGGUGAAAUUGAACUGGCCGUGAAGAUGCGGCCUACCC
GUGGCAGGACGAAAAGACCCCGUGGAGCUUUACUGCAGCCUGGUGUUGGCUCUUGGUCGC
GCCUGCGUAGGAUAGGUGGGAGCCUGUGAACCCCCGCCUCCGGGUGGGGGGGAGGCGCCG
GUGAAAUACCACCCUGGCGCGGCUGGGGGCCUAACCCUCGGAUGGGGGGACAGCGCUUGG
CGGGCAGUUUGACUGGGGCGGUCGCCUCCUAAAAGGUAACGGAGGCGCCCAAAGGUCCCC
UCAGGCGGGACGGAAAUCCGCCGGAGAGCGCAAGGGUAGAAGGGGGCCUGACUGCGAGGC
CUGCAAGCCGAGCAGGGGCGAAAGCCGGGCCUAGUGAACCGGUGGUCCCGUGUGGAAGGG
CCAUCGAUCAACGGAUAAAAGUUACCCCGGGGAUAACAGGCUGAUCUCCCCCGAGCGUCC
ACAGCGGCGGGGAGGUUUGGCACCUCGAUGUCGGCUCGUCGCAUCCUGGGGCUGAAGAAG
GUCCCAAGGGUUGGGCUGUUCGCCCAUUAAAGCGGCACGCGAGCUGGGUUCAGAACGUCG
UGAGACAGUUCGGUCUCUAUCCGCCACGGGCGCAGGAGGCUUGAGGGGGGCUCUUCCUAG
UACGAGAGGACCGGAAGGGACGCACCUCUGGUUUCCCAGCUGUCCCUCCAGGGGCAUAAG
CUGGGUAGCCAUGUGCGGAAGGGAUAACCGCUGAAAGCAUCUAAGCGGGAAGCCCGCCCC
AAGAUGAGGCCUCCCACGGCGUCAAGCCGGUAAGGACCCGGGAAGACGACCCGGUGGAUG
GGCCGGGGGUGUAAGCGCCGCGAGGCGUUGAGCCGACCGGUCCCAAUCGUCCGAGGUCUA
G

Sequence of entity 3 (A5S, B5S), FASTA

>6N1D_3 5s rRNA (chains A5S, B5S)
UCCCCCGUGCCCAUAGCGGCGUGGAACCACCCGUUCCCAUUCCGAACACGGAAGUGAAAC
GCGCCAGCGCCGAUGGUACUGGGCGGGCGACCGCCUGGGAGAGUAGGUCGGUGCGGGGG

Sequence of entity 4 (AL01, BL01), FASTA

>6N1D_4 50S ribosomal protein L1 (chains AL01, BL01)
PKHGKRYRALLEKVDPNKVYTIDEAARLVKELATAKFDETVEVHAKLGIDPRRSDQNVRG
TVSLPHGLGKQVRVLAIAKGEKIKEAEEAGADYVGGEEIIQKILDGWMDFDAVVATPDVM
GAVGSKLGRILGPRGLLPNPKAGTVGFNIGEIIREIKAGRIEFRNDKTGAIHAPVGKASF
PPEKLADNIRAFIRALEAHKPEGAKGTFLRSVYVTTTMGPSVRINPHS

Sequence of entity 5 (AL02, BL02), FASTA

>6N1D_5 50S ribosomal protein L2 (chains AL02, BL02)
MAVKKFKPYTPSRRFMTVADFSEITKTEPEKSLVKPLKKTGGRNNQGRITVRFRGGGHKR
LYRIIDFKRWDKVGIPAKVAAIEYDPNRSARIALLHYVDGEKRYIIAPDGLQVGQQVVAG
PDAPIQVGNALPLRFIPVGTVVHAVELEPKKGAKLARAAGTSAQIQGREGDYVILRLPSG
ELRKVHGECYATVGAVGNADHKNIVLGKAGRSRWLGRRPHVRGAAMNPVDHPHGGGEGRA
PRGRPPASPWGWQTKGLKTRKRRKPSSRFIIARRKK

Sequence of entity 6 (AL03, BL03), FASTA

>6N1D_6 50S ribosomal protein L3 (chains AL03, BL03)
MKGILGVKVGMTRIFRDDRAVPVTVILAGPCPVVQRRTPEKDGYTAVQLGFLPQNPKRVN
RPLKGHFAKAGVEPVRILREIRDFNPEGDTVTVEIFKPGERVDVTGTSKGRGFAGVMKRW
NFAGGPDSHGAHKIHRHPGSIGNRKTPGRVYKGKKMAGHYGAERVTVMNLEVVDVIPEEN
LLLVKGAVPGPNGGLVIVRETKKAAK

Sequence of entity 7 (AL04, BL04), FASTA

>6N1D_7 50S ribosomal protein L4 (chains AL04, BL04)
MYQIPVLSPSGRRELAADLPAEINPHLLWEVVRWQLAKRRRGTASTKTRGEVAYSGRKIW
PQKHTGRARHGDIGAPIFVGGGVVFGPKPRDYSYTLPKKVRKKGLAMAVADRAREGKLLL
VEAFAGVNGKTKEFLAWAKEAGLDGSESVLLVTGNELVRRAARNLPWVVTLAPEGLNVYD
IVRTERLVMDLDAWEVFQNRIGGEA

Sequence of entity 8 (AL05, BL05), FASTA

>6N1D_8 50S ribosomal protein L5 (chains AL05, BL05)
PLDLALKRKYYEEVRPELIRRFGYQNVWEVPRLEKVVINQGLGEAKEDARILEKAAQELA
LITGQKPAVTRAKKSISNFKLRKGMPIGLRVTLRRDRMWIFLEKLLNVALPRIRDFRGLN
PNSFDGRGNYNLGLREQLIFPEITYDMVDALRGMDIAVVTTAETDEEARALLELLGFPFR
K

Sequence of entity 9 (AL06, BL06), FASTA

>6N1D_9 50S ribosomal protein L6 (chains AL06, BL06)
MSRIGRLPIPVPKGVSVEVAPGRVKVKGPKGELEVPVSPEMRVVVEEGVVRVERPSDERR
HKSLHGLTRTLIANAVKGVSEGYSKELLIKGIGYRARLVGRALELTVGFSHPVVVEPPEG
ITFEVPEPTRVRVSGIDKQKVGQVAANIRAIRKPSAYHEKGIYYAGEPVRLKPGKAGAKK

Sequence of entity 10 (AL09, BL09), FASTA

>6N1D_10 50S ribosomal protein L9 (chains AL09, BL09)
MKVILLEPLENLGDVGQVVDVKPGYARNYLLPRGLAVLATESNLKALEARIRAQAKRLAE
RKAEAERLKEILENLTLTIPVRAGETKIYGSVTAKDIAEALSRQHGITIDPKRLALEKPI
KELGEYVLTYKPHPEVPIQLKVSVVAQE

Sequence of entity 11 (AL13, BL13), FASTA

>6N1D_11 50S ribosomal protein L13 (chains AL13, BL13)
MKTYVPKQVEPRWVLIDAEGKTLGRLATKIATLLRGKHRPDWTPNVAMGDFVVVVNADKI
RVTGKKLEQKIYTRYSGYPGGLKKIPLEKMLATHPERVLEHAVKGMLPKGPLGRRLFKRL
KVYAGPDHPHQAQRPEKLEV

Sequence of entity 12 (AL14, BL14), FASTA

>6N1D_12 50S ribosomal protein L14 (chains AL14, BL14)
MIQPQTYLEVADNTGARKIMCIRVLKGSNAKYATVGDVIVASVKEAIPRGAVKEGDVVKA
VVVRTKKEVKRPDGSAIRFDDNAAVIINNQLEPRGTRVFGPVARELREKGFMKIVSLAPE
VL

Ligands and cofactors

ID	Name	Formula	Copies
SF4	Iron/sulfur cluster	Fe4 S4	2
MG	Magnesium ion	Mg	359

Primary citation

Spontaneous ribosomal translocation of mRNA and tRNAs into a chimeric hybrid state. Zhou, J., Lancaster, L., Donohue, J.P. et al. Proc Natl Acad Sci U S A (2019) 116:7813-7818. DOI 10.1073/pnas.1901310116 · PubMed

Other PDB entries of the same protein (UniProt Q72GV9 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4V9K 3.5 Å, 70S ribosome translocation intermediate GDPNP-I containing elongation factor EFG/GDPNP,…
4V9L 3.5 Å, 70S Ribosome translocation intermediate FA-3.6A containing elongation factor EFG/FUSIDIC…
4W29 3.8 Å, 70S ribosome translocation intermediate containing elongation factor EFG/GDP/fusidic…
4V9J 3.86 Å, 70S ribosome translocation intermediate GDPNP-II containing elongation factor EFG/GDPNP,…
4V9M 4.0 Å, 70S Ribosome translocation intermediate FA-4.2A containing elongation factor EFG/FUSIDIC…

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