4V4J: 50S ribosomal protein L1

Name: PDB 4V4J: Interactions and Dynamics of the Shine-Dalgarno Helix in the 70S Ribosome.
Published: 2014-07-09
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

Interactions and Dynamics of the Shine-Dalgarno Helix in the 70S Ribosome. Determined by X-ray diffraction at 3.83 Å resolution. Released 9 Jul 2014.

Method: X-ray diffraction
Resolution: 3.83 Å
Organism: Thermus thermophilus
Chains: 54
Atoms: 147,125
Mol. weight: 2224.55 kDa
Released: 9 Jul 2014

Explore 4V4J in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4V4J contains 179 α-helices and 260 β-strands across 47 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: 3 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	8-11	4
β-strand	15-16	2	3
β-strand	22-23	2	3
β-strand	24	1	4
β-strand	47	1	4
α-helix	53-56	4
α-helix	57-60	4

Chain A: 5 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	9-12	4
β-strand	21-22	2	1
α-helix	23-27	5
α-helix	30-33	4
β-strand	46-48	3	2
α-helix	183-189	7
α-helix	191-195	5
β-strand	210-213	4	2
β-strand	225-226	2	1

Chain b: 0 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	16-17	2	9
β-strand	24-26	3	9
β-strand	33-34	2	9

Chain B: 2 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	76	1	5
β-strand	96	1	6
β-strand	97	1	5
β-strand	102	1	6
β-strand	141-145	5	7
β-strand	146-147	2	8
β-strand	151-153	3	8
β-strand	163-164	2	7
β-strand	176	1	7
β-strand	182	1	7
β-strand	191-193	3	7
α-helix	200-203	4
α-helix	210-212	3
β-strand	271	1	7

Chain c: 12 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	32-35	4	29
β-strand	40-42	3	29
α-helix	44-62	19
β-strand	68-71	4	30
α-helix	78-81	4
α-helix	84-87	4
β-strand	92-93	2	30
α-helix	105-112	8
α-helix	114-123	10
α-helix	132-134	3
α-helix	135-138	4
α-helix	139-143	5
α-helix	144-148	5
α-helix	152-154	3
β-strand	161-164	4	30
α-helix	172-177	6
β-strand	184-186	3	30
β-strand	199-200	2	30
α-helix	208-223	16

Chain C: 1 helix, 12 β-strands

Element	Residues	Length	Sheet
β-strand	7	1	10
β-strand	8-13	6	11
β-strand	22-26	5	11
β-strand	27	1	12
α-helix	93-95	3
β-strand	101-102	2	13
β-strand	105-107	3	14
β-strand	164-166	3	14
β-strand	170-171	2	13
β-strand	175-176	2	12
β-strand	181-182	2	12
β-strand	195	1	10
β-strand	197	1	14

Chain d: 8 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	8-11	4
α-helix	12-16	5
α-helix	29-39	11
α-helix	48-50	3
β-strand	52-54	3	34
β-strand	57	1	35
β-strand	66	1	35
β-strand	67-70	4	34
α-helix	73-75	3
α-helix	85-94	10
β-strand	102-105	4	34
α-helix	113-126	14
α-helix	130-143	14
β-strand	150	1	36
β-strand	153	1	36
β-strand	166	1	36
β-strand	182-189	8	36
β-strand	196-203	8	36

Chain D: 7 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	16-18	3
α-helix	25-38	14
α-helix	98-112	15
α-helix	131-135	5
β-strand	150-151	2	15
α-helix	156-162	7
α-helix	178-182	5
β-strand	187-188	2	15
α-helix	191-194	4

39 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
23S large subunit ribosomal RNA	w	RNA	2889	Thermus thermophilus
5S large subunit ribosomal RNA	x	RNA	120	Thermus thermophilus
50S ribosomal protein L1	A	protein	229	Thermus thermophilus	Q5SLP7 (AlphaFold model)
50S ribosomal protein L2	B	protein	276	Thermus thermophilus	P60405 (AlphaFold model)
50S ribosomal protein L3	C	protein	206	Thermus thermophilus	Q5SHN8 (AlphaFold model)
50S ribosomal protein L4	D	protein	205	Thermus thermophilus	Q5SHN9 (AlphaFold model)
50S ribosomal protein L5	E	protein	182	Thermus thermophilus	Q5SHQ0
50S ribosomal protein L6	F	protein	180	Thermus thermophilus	P0DOY8
50S ribosomal protein L9	G	protein	148	Thermus thermophilus	Q5SLQ1
50S ribosomal protein L13	H	protein	140	Thermus thermophilus	P60488
50S ribosomal protein L14	I	protein	122	Thermus thermophilus	Q5SHP8
50S ribosomal protein L15	J	protein	150	Thermus thermophilus	Q5SHQ7

42 more molecules are not listed.

Sequence of entity 1 (w), FASTA

>4V4J_1 23S LARGE SUBUNIT RIBOSOMAL RNA (chains w)
GGUCAAGAUGGUAAGGGCCCACGGUGGAUGCCUCGGCACCCGAGCCGAUGAAGGACGUGG
CUACCUGCGAUAAGCCAGGGGGAGCCGGUAGCGGGCGUGGAUCCCUGGAUGUCCGAAUGG
GGGAACCCGGCCGGCGGGAACGCCGGUCACCGCGCUUUUUGCGCGGGGGGAACCUGGGGA
ACUGAAACAUCUCAGUACCCAGAGGAGAGGAAAGAGAAAUCGACUCCCUGAGUAGCGGCG
AGCGAAAGGGGACCAGCCUAAACCGUCCGGCUUGUCCGGGCGGGGUCGUGGGGCCCUCGG
ACACCGAAUCCCCAGCCUAGCCGAAGCUGUUGGGAAGCAGCGCCAGAGAGGGUGAAAGCC
CCGUAGGCGAAAGGUGGGGGGAUAGGUGAGGGUACCCGAGUACCCCGUGGUUCGUGGAGC
CAUGGGGGAAUCUGGGCGGACCACCGCCUAAGGCUAAGUACUCCGGGUGACCGAUAGCGC
ACCAGUACCGUGAGGGAAAGGUGAAAAGAACCCCGGGAGGGGAGUGAAAUAGAGCCUGAA
ACCGUGGGCUUACAAGCAGUCACGGCCCCGCAAGGGGUUGUGGCGUGCCUAUUGAAGCAU
GAGCCGGCGACUCACGGUCGUGGGCGAGCUUAAGCCGUUGAGGCGGAGGCGUAGGGAAAC
CGAGUCCGAACAGGGCGUCUAGUCCGCGGCCGUGGACCCGAAACCGGGCGAGCUAGCCCU
GGCCAGGGUGAAGCUGGGGUGAGACCCAGUGGAGGCCCGAACCGGUGGGGGAUGCAAACC
CCUCGGAUGAGCUGGGGCUAGGAGUGAAAAGCUAACCGAGCCCGGAGAUAGCUGGUUCUC
CCCGAAAUGACUUUAGGGUCAGCCUCAGGCGCUGACUGGGGCCUGUAGAGCACUGAUAGG
GCUAGGGGGCCCACCAGCCUACCAAACCCUGUCAAACUCCGAAGGGUCCCAGGUGGAGCC
UGGGAGUGAGGGCGCGAGCGAUAACGUCCGCGUCCGAGCGCGGGAACAACCGAGACCGCC
AGCUAAGGCCCCCAAGUCUGGGCUAAGUGGUAAAGGAUGUGGCGCCGCGAAGACAGCCAG
GAGGUUGGCUUAGAAGCAGCCAUCCUUUAAAGAGUGCGUAAUAGCUCACUGGUCGAGUGG
CGCCGCGCCGAAAAUGAUCGGGGCUCAAGCCCAGCGCCGAAGCUGCGGGUCUGGGGGAUG
ACCCCAGGCGGUAGGGGAGCGUUCCCGAUGCCGAUGAAGGCCGACCCGCGAGGGCGGCUG
GAGGUAAGGGAAGUGCGAAUGCCGGCAUGAGUAACGAUAAAGAGGGUGAGAAUCCCUCUC
GCCGUAAGCCCAAGGGUUCCUACGCAAUGGUCGUCAGCGUAGGGUUAGGCGGGACCUAAG
GUGAAGCCGAAAGGCGUAGCCGAAGGGCAGCCGGUUAAUAUUCCGGCCCUUCCCGCAGGU
GCGAUGGGGGGACGCUCUAGGCUAGGGGGACCGGAGCCAUGGACGAGCCCGGCCAGAAGC
GCAGGGUGGGAGGUAGGCAAAUCCGCCUCCCAAAAGCUCUGCGUGGUGGGGAAGCCCGUA
CGGGUGACAACCCCCCGAAGCCAGGGAGCCAAGAAAAGCCUCUAAGCACAACCUGCGGGA
ACCCGUACCGCAAACCGACACAGGUGGGCGGGUGCAAGAGCACUCAGGCGCGCGGGAGAA
CCCUCGCCAAGGAACUCUGCAAGUUGGCCCCGUAACUUCGGGAGAAGGGGUGCUCCCUGG
GGUGAUGAGCUCCGGGGAGCCGCAGUGAACAGGCUCUGGCGACUGUUUACCAAAAACACA
GCUCUCUGCGAACUCGUAAGAGGAGGUAUAGGGAGCGACGCUUGCCCGGUGCCGGAAGGU
CAAGGGGAGGGGUGCAAGCCCCGAACCGAAGCCCCGGUGAACGGCGGCCGUAACUAUAAC
GGUCCUAAGGUAGCGAAAUUCCUUGUCGGGUAAGUUCCGACCUGCACGAAAAGCGUAACG
ACCGGAGCGCUGUCUCGGCGAGGGACCCGGUGAAAUUGAACUGGCCGUGAAGAUGCGGCC
UACCCGUGGCAGGACGAAAAGACCCCGUGGAGCUUUACUGCAGCCUGGUGUUGGCUCUUG
GUCGCGCCUGCGUAGGAUAGGUGGGAGCCUGUGAACCCCCGCCUCCGGGUGGGGGGGAGG
CGCCGGUGAAAUACCACCCUGGCGCGGCUGGGGGCCUAACCCUCGGAUGGGGGGACAGCG
CUUGGCGGGCAGUUUGACUGGGGCGGUCGCCUCCUAAAAGGUAACGGAGGCGCCCAAAGG
UCCCCUCAGGCGGGACGGAAAUCCGCCGGAGAGCGCAAGGGUAGAAGGGGGCCUGACUGC
GAGGCCUGCAAGCCGAGCAGGGGCGAAAGCCGGGCCUAGUGAACCGGUGGUCCCGUGUGG
AAGGGCCAUCGAUCAACGGAUAAAAGUUACCCCGGGGAUAACAGGCUGAUCUCCCCCGAG
CGUCCACAGCGGCGGGGAGGUUUGGCACCUCGAUGUCGGCUCGUCGCAUCCUGGGGCUGA
AGAAGGUCCCAAGGGUUGGGCUGUUCGCCCAUUAAAGCGGCACGCGAGCUGGGUUCAGAA
CGUCGUGAGACAGUUCGGUCUCUAUCCGCCACGGGCGCAGGAGGCUUGAGGGGGGCUCUU
CCUAGUACGAGAGGACCGGAAGGGACGCACCUCUGGUUUCCCAGCUGUCCCUCCAGGGGC
AUAAGCUGGGUAGCCAUGUGCGGAAGGGAUAACCGCUGAAAGCAUCUAAGCGGGAAGCCC
GCCCCAAGAUGAGGCCUCCCACGGCGUCAAGCCGGUAAGGACCCGGGAAGACGACCCGGU
GGAUGGGCCGGGGGUGUAAGCGCCGCGAGGCGUUGAGCCGACCGGUCCCAAUCGUCCGAG
GUCUUGACC

Sequence of entity 2 (x), FASTA

>4V4J_2 5S LARGE SUBUNIT RIBOSOMAL RNA (chains x)
UCCCCCGUGCCCAUAGCGGCGUGGAACCACCCGUUCCCAUUCCGAACACGGAAGUGAAAC
GCGCCAGCGCCGAUGGUACUGGGCGGGCGACCGCCUGGGAGAGUAGGUCGGUGCGGGGGA

Sequence of entity 3 (A), FASTA

>4V4J_3 50S ribosomal protein L1 (chains A)
MPKHGKRYRALLEKVDPNKIYTIDEAAHLVKELATAKFDETVEVHAKLGIDPRRSDQNVR
GTVSLPHGLGKQVRVLAIAKGEKIKEAEEAGADYVGGEEIIQKILDGWMDFDAVVATPDV
MGAVGSKLGRILGPRGLLPNPKAGTVGFNIGEIIREIKAGRIEFRNDKTGAIHAPVGKAS
FPPEKLADNIRAFIRALEAHKPEGAKGTFLRSVYVTTTMGPSVRINPHS

Sequence of entity 4 (B), FASTA

>4V4J_4 50S ribosomal protein L2 (chains B)
MAVKKFKPYTPSRRFMTVADFSEITKTEPEKSLVKPLKKTGGRNNQGRITVRFRGGGHKR
LYRIIDFKRWDKVGIPAKVAAIEYDPNRSARIALLHYVDGEKRYIIAPDGLQVGQQVVAG
PDAPIQVGNALPLRFIPVGTVVHAVELEPKKGAKLARAAGTSAQIQGREGDYVILRLPSG
ELRKVHGECYATVGAVGNADHKNIVLGKAGRSRWLGRRPHVRGAAMNPVDHPHGGGEGRA
PRGRPPASPWGWQTKGLKTRKRRKPSSRFIIARRKK

Sequence of entity 5 (C), FASTA

>4V4J_5 50S ribosomal protein L3 (chains C)
MKGILGVKVGMTRIFRDDRAVPVTVILAGPCPVVQRRTPEKDGYTAVQLGFLPQNPKRVN
RPLKGHFAKAGVEPVRILREIRDFNPEGDTVTVEIFKPGERVDVTGTSKGRGFAGVMKRW
NFAGGPDSHGAHKIHRHPGSIGNRKTPGRVYKGKKMAGHYGAERVTVMNLEVVDVIPEEN
LLLVKGAVPGPNGGLVIVRETKKAAK

Sequence of entity 6 (D), FASTA

>4V4J_6 50S ribosomal protein L4 (chains D)
MYQIPVLSPSGRRELAADLPAEINPHLLWEVVRWQLAKRRRGTASTKTRGEVAYSGRKIW
PQKHTGRARHGDIGAPIFVGGGVVFGPKPRDYSYTLPKKVRKKGLAMAVADRAREGKLLL
VEAFAGVNGKTKEFLAWAKEAGLDGSESVLLVTGNELVRRAARNLPWVVTLAPEGLNVYD
IVRTERLVMDLDAWEVFQNRIGGEA

Sequence of entity 7 (E), FASTA

>4V4J_7 50S ribosomal protein L5 (chains E)
MPLDLALKRKYYEEVRPELIRRFGYQNVWEVPRLEKVVINQGLGEAKEDARILEKAAQEL
ALITGQKPAVTRAKKSISNFKLRKGMPIGLRVTLRRDRMWIFLEKLLNVALPRIRDFRGL
NPNSFDGRGNYNLGLREQLIFPEITYDMVDALRGMDIAVVTTAETDEEARALLELLGFPF
RK

Sequence of entity 8 (F), FASTA

>4V4J_8 50S ribosomal protein L6 (chains F)
MSRIGRLPIPVPKGVSVEVAPGRVKVKGPKGELEVPVSPEMRVVVEEGVVRVERPSDERR
HKSLHGLTRTLIANAVKGVSEGYSKELLIKGIGYRARLVGRALELTVGFSHPVVVEPPEG
ITFEVPEPTRVRVSGIDKQKVGQVAANIRAIRKPSAYHEKGIYYAGEPVRLKPGKAGAKK

Sequence of entity 9 (G), FASTA

>4V4J_9 50S ribosomal protein L9 (chains G)
MKVILLEPLENLGDVGQVVDVKPGYARNYLLPRGLAVLATESNLKALEARIRAQAKRLAE
RKAEAERLKEILENLTLTIPVRAGETKIYGSVTAKDIAEALSRQHGITIDPKRLALEKPI
KELGEYVLTYKPHPEVPIQLKVSVVAQE

Sequence of entity 10 (H), FASTA

>4V4J_10 50S ribosomal protein L13 (chains H)
VKTYVPKQVEPRWVLIDAEGKTLGRLATKIATLLRGKHRPDWTPNVAMGDFVVVVNADKI
RVTGKKLEQKIYTRYSGYPGGLKKIPLEKMLATHPERVLEHAVKGMLPKGPLGRRLFKRL
KVYAGPDHPHQAQRPEKLEV

Sequence of entity 11 (I), FASTA

>4V4J_11 50S ribosomal protein L14 (chains I)
MIQPQTYLEVADNTGARKIMCIRVLKGSNAKYATVGDVIVASVKEAIPRGAVKEGDVVKA
VVVRTKKEVKRPDGSAIRFDDNAAVIINNQLEPRGTRVFGPVARELREKGFMKIVSLAPE
VL

Sequence of entity 12 (J), FASTA

>4V4J_12 50S ribosomal protein L15 (chains J)
MKLSDLRPNPGANKRRKRVGRGPGSGHGKTATRGHKGQKSRSGGLKDPRRFEGGRSTTLM
RLPKRGMQGQVPGEIKRPRYQGVNLKDLARFEGEVTPELLVRAGLLKKGYRLKILGEGEA
KPLKVVAHAFSKSALEKLKAAGGEPVLLEA

Primary citation

Interactions and dynamics of the Shine Dalgarno helix in the 70S ribosome. Korostelev, A., Trakhanov, S., Asahara, H. et al. Proc Natl Acad Sci U S A (2007) 104:16840-16843. DOI 10.1073/pnas.0707850104 · PubMed

Other PDB entries of the same protein (UniProt Q5SLP7 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3TG8 1.95 Å, Mutant ribosomal protein L1 lacking ala158 from thermus thermophilus
2OV7 2.3 Å, The first domain of the ribosomal protein L1 from Thermus thermophilus
2OUM 2.55 Å, The first domain of L1 from Thermus thermophilus
5NPM 2.7 Å, Crystal structure of mutant ribosomal protein TTHL1 lacking 8 N-terminal residues in…
4U26 2.8 Å, Crystal structure of the E. coli ribosome bound to dalfopristin and quinupristin.
4U27 2.8 Å, Crystal structure of the E. coli ribosome bound to flopristin and linopristin.
4V51 2.8 Å, Structure of the Thermus thermophilus 70S ribosome complexed with mRNA, tRNA and…
4WPO 2.8 Å, Crystal structure of the Thermus thermophilus 70S ribosome in complex with elongation…
4WQF 2.8 Å, Crystal structure of the Thermus thermophilus 70S ribosome in complex with elongation…
4WQU 2.8 Å, Crystal structure of the Thermus thermophilus 70S ribosome in complex with elongation…
4WQY 2.8 Å, Crystal structure of the Thermus thermophilus 70S ribosome in complex with elongation…
4V9H 2.86 Å, Crystal structure of the ribosome bound to elongation factor G in the guanosine…

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