6HTQ: 50S ribosomal protein L2

Name: PDB 6HTQ: Stringent response control by a bifunctional RelA enzyme in the presence and absence of the ribosome
Published: 2019-10-23
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

Stringent response control by a bifunctional RelA enzyme in the presence and absence of the ribosome. Determined by electron microscopy at 4.5 Å resolution. Released 23 Oct 2019.

Method: Electron microscopy
Resolution: 4.5 Å
Organisms: Bacillus subtilis subsp. subtilis str. 168, Bacillus subtilis (strain 168)
Chains: 53
Atoms: 146,680
Mol. weight: 2190.61 kDa
Released: 23 Oct 2019

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

Secondary structure: helices and β-sheets

6HTQ contains 225 α-helices and 327 β-strands across 46 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 1: 0 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	27-29	3	103
β-strand	36-38	3	103
β-strand	43	1	104
β-strand	48-49	2	104
β-strand	52-53	2	104

Chain 2: 0 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	105
β-strand	7-9	3	106
β-strand	18-21	4	105
β-strand	31-36	6	106
β-strand	41-47	7	106

Chain 3: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	9-13	5
α-helix	26-37	12

Chain 4: 5 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	8-10	3
α-helix	15	1
β-strand	16	1	1
α-helix	17	1
β-strand	22	1	1
β-strand	23-25	3	2
α-helix	38-43	6
β-strand	47-49	3	2
α-helix	52-58	7

Chain 5: 1 helix, 4 β-strands

Element	Residues	Length	Sheet
β-strand	2-3	2	3
β-strand	15-19	5	3
β-strand	22-26	5	3
α-helix	30-32	3
β-strand	34-35	2	3

Chain b: 11 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	18	1	19
α-helix	25-30	6
β-strand	31-33	3	19
β-strand	39-41	3	19
α-helix	43-61	19
β-strand	68-70	3	20
α-helix	76-87	12
β-strand	90-92	3	20
α-helix	95-97	3
α-helix	104-122	19
α-helix	132	1
α-helix	133-137	5
α-helix	138-147	10
α-helix	149-151	3
β-strand	162-163	2	20
α-helix	170-178	9
β-strand	184-185	2	20
β-strand	186-187	2	21
β-strand	200-201	2	21
α-helix	207-223	17

Chain c: 5 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	12	1	24
β-strand	16	1	24
β-strand	20-21	2	25
α-helix	28-45	18
β-strand	53-58	6	25
β-strand	63-68	6	25
α-helix	81-94	14
β-strand	98-103	6	25
α-helix	108-110	3
α-helix	112-124	13
α-helix	129-143	15
β-strand	147-153	7	26
β-strand	154	1	27
β-strand	163	1	27
β-strand	166-170	5	26
β-strand	181-190	10	26
β-strand	193-202	10	26

Chain C: 6 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-4	2	4
β-strand	18-19	2	4
α-helix	31-33	3
β-strand	34-36	3	5
β-strand	61-63	3	5
β-strand	65	1	6
β-strand	75	1	7
β-strand	78-82	5	6
β-strand	91-94	4	6
β-strand	102-105	4	6
α-helix	106-107	2
β-strand	117	1	7
α-helix	122-124	3
β-strand	129-131	3	8
α-helix	136	1
β-strand	140-142	3	8
β-strand	162-167	6	8
β-strand	171-175	5	8
α-helix	177-179	3
β-strand	181-185	5	8
β-strand	189-192	4	8
α-helix	210-213	4
β-strand	247	1	9
β-strand	253	1	9
β-strand	270	1	8

38 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 ribosomal RNA	A	RNA	2925	Bacillus subtilis subsp. subtilis str. 168
5S ribosomal RNA	B	RNA	112	Bacillus subtilis subsp. subtilis str. 168
50S ribosomal protein L2	C	protein	272	Bacillus subtilis (strain 168)	P42919 (AlphaFold model)
50S ribosomal protein L3	D	protein	206	Bacillus subtilis (strain 168)	P42920 (AlphaFold model)
50S ribosomal protein L4	E	protein	205	Bacillus subtilis (strain 168)	P42921 (AlphaFold model)
50S ribosomal protein L5	F	protein	176	Bacillus subtilis (strain 168)	P12877 (AlphaFold model)
50S ribosomal protein L6	G	protein	175	Bacillus subtilis (strain 168)	P46898
50S ribosomal protein L13	J	protein	142	Bacillus subtilis (strain 168)	P70974
50S ribosomal protein L14	K	protein	122	Bacillus subtilis (strain 168)	P12875
50S ribosomal protein L15	L	protein	146	Bacillus subtilis (strain 168)	P19946
50S ribosomal protein L16	M	protein	135	Bacillus subtilis (strain 168)	P14577
50S ribosomal protein L17	N	protein	119	Bacillus subtilis (strain 168)	P20277

41 more molecules are not listed.

Sequence of entity 1 (A), FASTA

>6HTQ_1 23S ribosomal RNA (chains A)
GUUAAGUUAGAAAGGGCGCACGGUGGAUGCCUUGGCACUAGGAGCCGAUGAAGGACGGGA
CGAACACCGAUAUGCUUCGGGGAGCUGUAAGCAAGCUUUGAUCCGGAGAUUUCCGAAUGG
GGAAACCCACCACUCGUAAUGGAGUGGUAUCCAUAUCUGAAUUCAUAGGAUAUGAGAAGG
CAGACCCGGGGAACUGAAACAUCUAAGUACCCGGAGGAAGAGAAAGCAAAUGCGAUUCCC
UGAGUAGCGGCGAGCGAAACGGGAUCAGCCCAAACCAAGAGGCUUGCCUCUUGGGGUUGU
AGGACACUCUGUACGGAGUUACAAAGGAACGAGGUAGAUGAAGAGGUCUGGAAAGGCCCG
CCAUAGGAGGUAACAGCCCUGUAGUCAAAACUUCGUUCUCUCCUGAGUGGAUCCUGAGUA
CGGCGGAACACGUGAAAUUCCGUCGGAAUCCGGGAGGACCAUCUCCCAAGGCUAAAUACU
CCCUAGUGACCGAUAGUGAACCAGUACCGUGAGGGAAAGGUGAAAAGCACCCCGGAAGGG
GAGUGAAAGAGAUCCUGAAACCGUGUGCCUACAAGUAGUCAGAGCCCGUUAACGGGUGAU
GGCGUGCCUUUUGUAGAAUGAACCGGCGAGUUACGAUCUCGUGCAAGGUUAAGCAGAAGA
UGCGGAGCCGCAGCGAAAGCGAGUCUGAAUAGGGCGCAUGAGUACGUGGUCGUAGACCCG
AAACCAGGUGAUCUACCCAUGUCCAGGGUGAAGUUCAGGUAACACUGAAUGGAGGCCCGA
ACCCACGCACGUUGAAAAGUGCGGGGAUGAGGUGUGGGUAGGGGUGAAAUGCCAAUCGAA
CCUGGAGAUAGCUGGUUCUCUCCGAAAUAGCUUUAGGGCUAGCCUCAAGGUAAGAGUCUU
GGAGGUAGAGCACUGAUUGGACUAGGGGCCCCUACCGGGUUACCGAAUUCAGUCAAACUC
CGAAUGCCAAUGACUUAUCCUUGGGAGUCAGACUGCGAGUGAUAAGAUCCGUAGUCGAAA
GGGAAACAGCCCAGACCGCCAGCUAAGGUCCCAAAGUAUACGUUAAGUGGAAAAGGAUGU
GGAGUUGCUUAGACAACCAGGAUGUUGGCUUAGAAGCAGCCACCAUUUAAAGAGUGCGUA
AUAGCUCACUGGUCGAGUGACUCUGCGCCGAAAAUGUACCGGGGCUAAACGUAUCACCGA
AGCUGCGGACUGUUCUUCGAACAGUGGUAGGAGAGCGUUCUAAGGGCUGUGAAGCCAGAC
CGGAAGGACUGGUGGAGCGCUUAGAAGUGAGAAUGCCGGUAUGAGUAGCGAAAGAGGGGU
GAGAAUCCCCUCCACCGAAUGCCUAAGGUUUCCUGAGGAAGGCUCGUCCGCUCAGGGUUA
GUCGGGACCUAAGCCGAGGCCGAAAGGCGUAGGCGAUGGACAACAGGUUGAUAUUCCUGU
ACCACCUCCUCACCAUUUGAGCAAUGGGGGGACGCAGGAGGAUAGGGUAAGCGCGGUAUU
GGAUAUCCGCGUCCAAGCAGUUAGGCUGGGAAAUAGGCAAAUCCGUUUCCCAUAAGGCUG
AGCUGUGAUGGCGAGCGAAAUAUAGUAGCGAAGUUCCUGAUUCCACACUGCCAAGAAAAG
CCUCUAGCGAGGUGAGAGGUGCCCGUACCGCAAACCGACACAGGUAGGCGAGGAGAGAAU
CCUAAGGUGAUCGAGAGAACUCUCGUUAAGGAACUCGGCAAAAUGACCCCGUAACUUCGG
GAGAAGGGGUGCUCUGUUAGGGUGCAAGCCCGAGAGAGCCGCAGUGAAUAGGCCCAGGCG
ACUGUUUAGCAAAAACACAGGUCUCUGCGAAGCCGUAAGGCGAAGUAUAGGGGCUGACGC
CUGCCCGGUGCUGGAAGGUUAAGAGGAGCGCUUAGCGUAAGCGAAGGUGCGAAUUGAAGC
CCCAGUAAACGGCGGCCGUAACUAUAACGGUCCUAAGGUAGCGAAAUUCCUUGUCGGGUA
AGUUCCGACCCGCACGAAAGGCGCAACGAUCUGGGCACUGUCUCAACGAGAGACUCGGUG
AAAUUAUAGUACCUGUGAAGAUGCAGGUUACCCGCGACAGGACGGAAAGACCCCGUGGAG
CUUUACUGCAGCCUGAUAUUGAAUGUUGGUACAGCUUGUACAGGAUAGGUAGGAGCCUUG
GAAACCGGAGCGCCAGCUUCGGUGGAGGCAUCGGUGGGAUACUACCCUGGCUGUAUUGAC
CUUCUAACCCGCCGCCCUUAUCGGGCGGGGAGACAGUGUCAGGUGGGCAGUUUGACUGGG
GCGGUCGCCUCCUAAAAGGUAACGGAGGCGCCCAAAGGUUCCCUCAGAAUGGUUGGAAAU
CAUUCGCAGAGUGUAAAGGCACAAGGGAGCUUGACUGCGAGACCUACAAGUCGAGCAGGG
ACGAAAGUCGGGCUUAGUGAUCCGGUGGUUCCGCAUGGAAGGGCCAUCGCUCAACGGAUA
AAAGCUACCCCGGGGAUAACAGGCUUAUCUCCCCCAAGAGUCCACAUCGACGGGGAGGUU
UGGCACCUCGAUGUCGGCUCAUCGCAUCCUGGGGCUGUAGUCGGUCCCAAGGGUUGGGCU
GUUCGCCCAUUAAAGCGGUACGCGAGCUGGGUUCAGAACGUCGUGAGACAGUUCGGUCCC
UAUCCGUCGCGGGCGCAGGAAAUUUGAGAGGAGCUGUCCUUAGUACGAGAGGACCGGGAU
GGACGCACCGCUGGUGUACCAGUUGUUCUGCCAAGGGCAUCGCUGGGUAGCUAUGUGCGG
ACGGGAUAAGUGCUGAAAGCAUCUAAGCAUGAAGCCCCCCUCAAGAUGAGAUUUCCCAUU
CCGCAAGGAAGUAAGAUCCCUGAAAGAUGAUCAGGUUGAUAGGUCUGAGGUGGAAGUGUG
GCGACACAUGGAGCUGACAGAUACUAAUCGAUCGAGGACUUAACC

Sequence of entity 2 (B), FASTA

>6HTQ_2 5S ribosomal RNA (chains B)
UGGUGGCGAUAGCGAAGAGGUCACACCCGUUCCCAUACCGAACACGGAAGUUAAGCUCUU
CAGCGCCGAUGGUAGUCGGGGGUUUCCCCCUGUGAGAGUAGGACGCCGCCAA

Sequence of entity 3 (C), FASTA

>6HTQ_3 50S ribosomal protein L2 (chains C)
AIKKYKPTSNGRRGMTTSDFAEITTDKPEKSLLAPLHKKGGRNNQGKLTVRHQGGGHKRQ
YRVIDFKRDKDGIPGRVATVEYDPNRSANIALINYADGEKRYILAPKGIQVGTEIMSGPE
ADIKVGNALPLINIPVGTVVHNIELKPGKGGQLVRSAGTSAQVLGKEGKYVLVRLNSGEV
RMILSACRASIGQVGNEQHELINIGKAGRSRWKGIRPTVRGSVMNPNDHPHGGGEGRAPI
GRKSPMSPWGKPTLGFKTRKKKNKSDKFIVRR

Sequence of entity 4 (D), FASTA

>6HTQ_4 50S ribosomal protein L3 (chains D)
TKGILGRKIGMTQVFAENGDLIPVTVIEAAPNVVLQKKTAENDGYEAIQLGFDDKREKLS
NKPEKGHVAKAETAPKRFVKELRGVEMDAYEVGQEVKVEIFSAGEIVDVTGVSKGKGFQG
AIKRHGQSRGPMSHGSRYHRRPGSMGPVDPNRVFKGKLLPGRMGGEQITVQNLEIVKVDA
ERNLLLIKGNVPGAKKSLITVKSAVK

Sequence of entity 5 (E), FASTA

>6HTQ_5 50S ribosomal protein L4 (chains E)
PKVALYNQNGSTAGDIELNASVFGIEPNESVVFDAILMQRASLRQGTHKVKNRSEVRGGG
RKPWRQKGTGRARQGSIRSPQWRGGGVVFGPTPRSYSYKLPKKVRRLAIKSVLSSKVIDN
NIIVLEDLTLDTAKTKEMAAILKGLSVEKKALIVTADANEAVALSARNIPGVTVVEANGI
NVLDVVNHEKLLITKAAVEKVEEVL

Sequence of entity 6 (F), FASTA

>6HTQ_6 50S ribosomal protein L5 (chains F)
NRLKEKYNKEIAPALMTKFNYDSVMQVPKIEKIVINMGVGDAVQNAKAIDSAVEELTFIA
GQKPVVTRAKKSIAGFRLREGMPIGAKVTLRGERMYDFLDKLISVSLPRVRDFRGVSKKS
FDGRGNYTLGIKEQLIFPEIDYDKVTKVRGMDIVIVTTANTDEEARELLTQVGMPF

Sequence of entity 7 (G), FASTA

>6HTQ_7 50S ribosomal protein L6 (chains G)
SRVGKKLLEIPSDVTVTLNDNNTVAVKGPKGELTRTFHPDMEIKVEDNVLTVARPSDQKE
HRALHGTTRSLLGNMVEGVSKGFERGLELVGVGYRASKSGNKLVLNVGYSHPVEIVPEEG
IEIEVPSQTKVVVKGTDKERVGAIAANIRAVRSPEPYKGKGIRYEGEVVRRKEGK

Sequence of entity 8 (J), FASTA

>6HTQ_8 50S ribosomal protein L13 (chains J)
TPMANASTIERKWLVVDAAGKTLGRLSSEVAAILRGKHKPTYTPHVDTGDHVIIINAEKI
ELTGKKLTDKIYYRHTQHPGGLKSRTALEMRTNYPEKMLELAIKGMLPKGSLGRQMFKKL
NVYRGSEHPHEAQKPEVYELRG

Sequence of entity 9 (K), FASTA

>6HTQ_9 50S ribosomal protein L14 (chains K)
MIQQETRLKVADNSGAREVLTIKVLGGSGRKTANIGDVIVCTVKQATPGGVVKKGEVVKA
VIVRTKSGARRSDGSYISFDENACVIIRDDKSPRGTRIFGPVARELRENNFMKIVSLAPE
VI

Sequence of entity 10 (L), FASTA

>6HTQ_10 50S ribosomal protein L15 (chains L)
MKLHELKPSEGSRKTRNRVGRGIGSGNGKTAGKGHKGQNARSGGGVRPGFEGGQMPLFQR
LPKRGFTNINRKEYAVVNLDKLNGFAEGTEVTPELLLETGVISKLNAGVKILGNGKLEKK
LTVKANKFSASAKEAVEAAGGTAEVI

Sequence of entity 11 (M), FASTA

>6HTQ_11 50S ribosomal protein L16 (chains M)
MLLPKRVKYRREHRGKMRGRAKGGTEVHFGEFGIQALEASWITNRQIEAARIAMTRYMKR
GGKVWIKIFPSKPYTAKPLEVRMGSGKGAPEGWVAVVKPGKVLFEISGVSEEVAREALRL
ASHKLPIKTKFVKRE

Sequence of entity 12 (N), FASTA

>6HTQ_12 50S ribosomal protein L17 (chains N)
SYRKLGRTSAQRKAMLRDLTTDLIINERIETTETRAKELRSVVEKMITLGKRGDLHARRQ
AAAYIRNEVANEENNQDALQKLFSDIATRYEERQGGYTRIMKLGPRRGDGAPMAIIELV

Primary citation

Structural Basis for Regulation of the Opposing (p)ppGpp Synthetase and Hydrolase within the Stringent Response Orchestrator Rel. Pausch, P., Abdelshahid, M., Steinchen, W. et al. Cell Rep (2020) 32:108157-108157. DOI 10.1016/j.celrep.2020.108157 · PubMed

Other PDB entries of the same protein (UniProt P42919 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8S1P 1.96 Å, YlmH bound to PtRNA-50S
8QCQ 2.3 Å, B. subtilis ApdA-stalled ribosomal complex
9FY1 2.3 Å, Structure of CliM-stalled Bacillus subtilis 70S ribosome with release factor bound in…
9FY2 2.3 Å, Structure of CliM-stalled Bacillus subtilis 70S ribosome with empty A-site
9FY3 2.8 Å, Structure of CliM-stalled Bacillus subtilis 70S ribosome with tRNA-Tyr in the A-site
7AS8 2.9 Å, Bacillus subtilis ribosome quality control complex state B. Ribosomal 50S subunit with…
8BUU 2.9 Å, ARE-ABCF VmlR2 bound to a 70S ribosome
7AQC 2.99 Å, Structure of the bacterial RQC complex (Decoding State)
7SAE 3.0 Å, 44SR70P Class1 ribosomal particle
6TNN 3.07 Å, Mini-RNase III (Mini-III) bound to 50S ribosome with precursor 23S rRNA
6TPQ 3.07 Å, RNase M5 bound to 50S ribosome with precursor 5S rRNA
6HA1 3.1 Å, Cryo-EM structure of a 70S Bacillus subtilis ribosome translating the ErmD leader…

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