1K8A: Co-crystal structure of Carbomycin A

Co-crystal structure of Carbomycin A bound to the 50S ribosomal subunit of Haloarcula marismortui. Determined by X-ray diffraction at 3.0 Å resolution. Released 19 Jul 2002.

Method: X-ray diffraction
Resolution: 3.0 Å
Organism: Haloarcula marismortui
Chains: 30
Atoms: 98,560
Mol. weight: 1459.05 kDa
Ligands: CAI, MG, CD
Released: 19 Jul 2002

Explore 1K8A in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1K8A contains 190 α-helices and 193 β-strands across 28 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: 3 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	11-14	4
α-helix	20-33	14
β-strand	37	1	1
β-strand	47-51	5	1
β-strand	54-57	4	1
β-strand	63-65	3	1
α-helix	74-81	8

Chain 2: 3 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	5-7	3
β-strand	16-18	3	2
β-strand	25-28	4	2
β-strand	33-34	2	2
α-helix	45-46	2
α-helix	49-51	3

Chain 3: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	5-17	13
α-helix	20-22	3
α-helix	23-28	6

Chain 4: 5 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	2-4	3	13
β-strand	6-11	6	14
β-strand	16-24	9	14
α-helix	26-30	5
α-helix	35-43	9
α-helix	50-53	4
α-helix	63	1
β-strand	64	1	15
α-helix	65	1
β-strand	67-71	5	14
β-strand	77-78	2	14
β-strand	84	1	15
β-strand	89-91	3	13

Chain C: 13 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	2-4	3
α-helix	5-10	6
α-helix	14-16	3
α-helix	20-22	3
α-helix	29-31	3
β-strand	39-48	10	3
β-strand	53-60	8	3
β-strand	65-68	4	3
α-helix	70	1
β-strand	71	1	4
β-strand	75	1	1
β-strand	79-81	3	3
β-strand	82	1	5
β-strand	93-95	3	5
α-helix	100	1
β-strand	104-106	3	5
β-strand	108	1	6
β-strand	118	1	6
β-strand	126-130	5	5
β-strand	136-139	4	5
β-strand	145-148	4	5
β-strand	153-156	4	5
α-helix	158	1
β-strand	159	1	4
α-helix	164-166	3
α-helix	172-179	8
α-helix	191-193	3
α-helix	196-198	3
β-strand	214-215	2	7
α-helix	219-220	2
β-strand	227-228	2	7

Chain D: 11 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	17-19	3
β-strand	37-38	2	8
β-strand	41-53	13	9
β-strand	68-75	8	9
β-strand	79-90	12	10
β-strand	93-101	9	10
α-helix	109-111	3
α-helix	121-134	14
β-strand	137-145	9	10
α-helix	148-150	3
α-helix	159-160	2
β-strand	161-165	5	10
β-strand	166-167	2	8
α-helix	171-184	14
β-strand	187-188	2	10
α-helix	190-192	3
β-strand	199-205	7	9
α-helix	206-208	3
β-strand	211-212	2	11
α-helix	214-217	4
α-helix	225-228	4
β-strand	255-256	2	11
β-strand	261-275	15	9
α-helix	279-280	2
β-strand	284	1	12
β-strand	288	1	12
β-strand	292-298	7	9
β-strand	308-313	6	9
β-strand	327-330	4	9

Chain E: 14 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	16
β-strand	12-17	6	16
α-helix	20-23	4
α-helix	25-26	2
α-helix	28-40	13
α-helix	43-45	3
β-strand	59	1	17
β-strand	72-73	2	17
β-strand	76-77	2	17
α-helix	104-117	14
α-helix	121-126	6
β-strand	138-140	3	16
α-helix	142-146	5
α-helix	150-159	10
α-helix	163-169	7
β-strand	173-174	2	18
α-helix	178-182	5
β-strand	186-187	2	18
β-strand	193-196	4	16
α-helix	202-205	4
β-strand	211-214	4	16
α-helix	220-223	4
α-helix	225-227	3
β-strand	233-236	4	16
α-helix	237-243	7

Chain F: 8 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	17-25	9	19
α-helix	38-45	8
β-strand	50-51	2	19
β-strand	58	1	20
β-strand	62	1	20
β-strand	71-75	5	19
α-helix	78-87	10
α-helix	88-90	3
β-strand	98	1	19
β-strand	104-106	3	19
β-strand	129-135	7	19
α-helix	140-143	4
α-helix	150-152	3
α-helix	153-155	3
α-helix	157-158	2
α-helix	159-167	9

20 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 rRNA	A	RNA	2922	Haloarcula marismortui
5S rRNA	B	RNA	122	Haloarcula marismortui
Ribosomal protein L2	C	protein	239	Haloarcula marismortui	P20276 (AlphaFold model)
Ribosomal protein L3	D	protein	337	Haloarcula marismortui	P20279 (AlphaFold model)
Ribosomal protein L4	E	protein	246	Haloarcula marismortui	P12735 (AlphaFold model)
Ribosomal protein L5	F	protein	176	Haloarcula marismortui	P14124 (AlphaFold model)
Ribosomal protein L6	G	protein	177	Haloarcula marismortui	P14135
Ribosomal protein L7AE	H	protein	119	Haloarcula marismortui	P12743
Ribosomal protein L10	I	protein	348	Haloarcula marismortui	P15825
Ribosomal protein L10E	J	protein	167	Haloarcula marismortui	P60617
Ribosomal protein L13	K	protein	145	Haloarcula marismortui	P29198
Ribosomal protein L14	L	protein	132	Haloarcula marismortui	P22450

18 more molecules are not listed.

Sequence of entity 1 (A), FASTA

>1K8A_1 23S RRNA (chains A)
UUGGCUACUAUGCCAGCUGGUGGAUUGCUCGGCUCAGGCGCUGAUGAAGGACGUGCCAAG
CUGCGAUAAGCCAUGGGGAGCCGCACGGAGGCGAAGAACCAUGGAUUUCCGAAUGAGAAU
CUCUCUAACAAUUGCUUCGCGCAAUGAGGAACCCCGAGAACUGAAACAUCUCAGUAUCGG
GAGGAACAGAAAACGCAAUGUGAUGUCGUUAGUAACCGCGAGUGAACGCGAUACAGCCCA
AACCGAAGCCCUCACGGGCAAUGUGGUGUCAGGGCUACCUCUCAUCAGCCGACCGUCUCG
ACGAAGUCUCUUGGAACAGAGCGUGAUACAGGGUGACAACCCCGUACUCGAGACCAGUAC
GACGUGCGGUAGUGCCAGAGUAGCGGGGGUUGGAUAUCCCUCGCGAAUAACGCAGGCAUC
GACUGCGAAGGCUAAACACAACCUGAGACCGAUAGUGAACAAGUAGUGUGAACGAACGCU
GCAAAGUACCCUCAGAAGGGAGGCGAAAUAGAGCAUGAAAUCAGUUGGCGAUCGAGCGAC
AGGGCAUACAAGGUCCCUCGACGAAUGACCGACGCGCGAGCGUCCAGUAAGACUCACGGG
AAGCCGAUGUUCUGUCGUACGUUUUGAAAAACGAGCCAGGGAGUGUGUCUGCAUGGCAAG
UCUAACCGGAGUAUCCGGGGAGGCACAGGGAAACCGACAUGGCCGCAGGGCUUUGCCCGA
GGGCCGCCGUCUUCAAGGGCGGGGAGCCAUGUGGACACGACCCGAAUCCGGACGAUCUAC
GCAUGGACAAGAUGAAGCGUGCCGAAAGGCACGUGGAAGUCUGUUAGAGUUGGUGUCCUA
CAAUACCCUCUCGUGAUCUAUGUGUAGGGGUGAAAGGCCCAUCGAGUCCGGCAACAGCUG
GUUCCAAUCGAAACAUGUCGAAGCAUGACCUCCGCCGAGGUAGUCUGUGAGGUAGAGCGA
CCGAUUGGUGUGUCCGCCUCCGAGAGGAGUCGGCACACCUGUCAAACUCCAAACUUACAG
ACGCCGUUUGACGCGGGGAUUCCGGUGCGCGGGGUAAGCCUGUGUACCAGGAGGGGAACA
ACCCAGAGAUAGGUUAAGGUCCCCAAGUGUGGAUUAAGUGUAAUCCUCUGAAGGUGGUCU
CGAGCCCUAGACAGCCGGGAGGUGAGCUUAGAAGCAGCUACCCUCUAAGAAAAGCGUAAC
AGCUUACCGGCCGAGGUUUGAGGCGCCCAAAAUGAUCGGGACUCAAAUCCACCACCGAGA
CCUGUCCGUACCACUCAUACUGGUAAUCGAGUAGAUUGGCGCUCUAAUUGGAUGGAAGUA
GGGGUGAAAACUCCUAUGGACCGAUUAGUGACGAAAAUCCUGGCCAUAGUAGCAGCGAUA
GUCGGGUGAGAACCCCGACGGCCUAAUGGAUAAGGGUUCCUCAGCACUGCUGAUCAGCUG
AGGGUUAGCCGGUCCUAAGUCAUACCGCAACUCGACUAUGACGAAAUGGGAAACGGGUUA
AUAUUCCCGUGCCACUAUGCAGUGAAAGUUGACGCCCUGGGGUCGAUCACGCUGGGCAUU
CGCCCAGUCGAACCGUCCAACUCCGUGGAAGCCGUAAUGGCAGGAAGCGGACGAACGGCG
GCAUAGGGAAACGUGAUUCAACCUGGGGCCCAUGAAAAGACGAGCAUAGUGUCCGUACCG
AGAACCGACACAGGUGUCCAUGGCGGCGAAAGCCAAGGCCUGUCGGGAGCAACCAACGUU
AGGGAAUUCGGCAAGUUAGUCCCGUACCUUCGGAAGAAGGGAUGCCUGCUCCGGAACGGA
GCAGGUCGCAGUGACUCGGAAGCUCGGACUGUCUAGUAACAACAUAGGUGACCGCAAAUC
CGCAAGGACUCGUACGGUCACUGAAUCCUGCCCAGUGCAGGUAUCUGAACACCUCGUACA
AGAGGACGAAGGACCUGUCAACGGCGGGGGUAACUAUGACCCUCUUAAGGUAGCGUAGUA
CCUUGCCGCAUCAGUAGCGGCUUGCAUGAAUGGAUUAACCAGAGCUUCACUGUCCCAACG
UUGGGCCCGGUGAACUGUACAUUCCAGUGCGGAGUCUGGAGACACCCAGGGGGAAGCGAA
GACCCUAUGGAGCUUUACUGCAGGCUGUCGCUGAGACGUGGUCGCCGAUGUGCAGCAUAG
GUAGGAGACACUACACAGGUACCCGCGCUAGCGGGCCACCGAGUCAACAGUGAAAUACUA
CCCGUCGGUGACUGCGACUCUCACUCCGGGAGGAGGACACCGAUAGCCGGGCAGUUUGAC
UGGGGCGGUACGCGCUCGAAAAGAUAUCGAGCGCGCCCUAUGGCUAUCUCAGCCGGGACA
GAGACCCGGCGAAGAGUGCAAGAGCAAAAGAUAGCUUGACAGUGUUCUUCCCAACGAGGA
ACGCUGACGCGAAAGCGUGGUCUAGCGAACCAAUUAGCCUGCUUGAUGCGGGCAAUUGAU
GACAGAAAAGCUACCCUAGGGAUAACAGAGUCGUCACUCGCAAGAGCACAUAUCGACCGA
GUGGCUUGCUACCUCGAUGUCGGUUCCCUCCAUCCUGCCCGUGCAGAAGCGGGCAAGGGU
GAGGUUGUUCGCCUAUUAAAGGAGGUCGUGAGCUGGGUUUAGACCGUCGUGAGACAGGUC
GGCUGCUAUCUACUGGGUGUGUAAUGGUGUCUGACAAGAACGACCGUAUAGUACGAGAGG
AACUACGGUUGGUGGCCACUGGUGUACCGGUUGUUCGAGAGAGCACGUGCCGGGUAGCCA
CGCCACACGGGGUAAGAGCUGAACGCAUCUAAGCUCGAAACCCACUUGGAAAAGAGACAC
CGCCGAGGUCCCGCGUACAAGACGCGGUCGAUAGACUCGGGGUGUGCGCGUCGAGGUAAC
GAGACGUUAAGCCCACGAGCACUAACAGACCAAAGCCAUCAU

Sequence of entity 2 (B), FASTA

>1K8A_2 5S RRNA (chains B)
UUAGGCGGCCACAGCGGUGGGGUUGCCUCCCGUACCCAUCCCGAACACGGAAGAUAAGCC
CACCAGCGUUCCGGGGAGUACUGGAGUGCGCGAGCCUCUGGGAAACCCGGUUCGCCGCCA
CC

Sequence of entity 3 (C), FASTA

>1K8A_3 RIBOSOMAL PROTEIN L2 (chains C)
GRRIQGQRRGRGTSTFRAPSHRYKADLEHRKVEDGDVIAGTVVDIEHDPARSAPVAAVEF
EDGDRRLILAPEGVGVGDELQVGVDAEIAPGNTLPLAEIPEGVPVCNVESSPGDGGKFAR
ASGVNAQLLTHDRNVAVVKLPSGEMKRLDPQCRATIGVVGGGGRTDKPFVKAGNKHHKMK
ARGTKWPNVRGVAMNAVDHPFGGGGRQHPGKPKSISRNAPPGRKVGDIASKRTGRGGNE

Sequence of entity 4 (D), FASTA

>1K8A_4 RIBOSOMAL PROTEIN L3 (chains D)
PQPSRPRKGSLGFGPRKRSTSETPRFNSWPSDDGQPGVQGFAGYKAGMTHVVLVNDEPNS
PREGMEETVPVTVIETPPMRAVALRAYEDTPYGQRPLTEVWTDEFHSELDRTLDVPEDHD
PDAAEEQIRDAHEAGDLGDLRLITHTVPDAVPSVPKKKPDVMETRVGGGSVSDRLDHALD
IVEDGGEHAMNDIFRAGEYADVAGVTKGKGTQGPVKRWGVQKRKGKHARQGWRRRIGNLG
PWNPSRVRSTVPQQGQTGYHQRTELNKRLIDIGEGDEPTVDGGFVNYGEVDGPYTLVKGS
VPGPDKRLVRFRPAVRPNDQPRLDPEVRYVSNESNQG

Sequence of entity 5 (E), FASTA

>1K8A_5 RIBOSOMAL PROTEIN L4 (chains E)
MQATIYDLDGNTDGEVDLPDVFETPVRSDLIGKAVRAAQANRKQDYGSDEYAGLRTPAES
FGSGRGQAHVPKLDGRARRVPQAVKGRSAHPPKTEKDRSLDLNDKERQLAVRSALAATAD
ADLVADRGHEFDRDEVPVVVSDDFEDLVKTQEVVSLLEALDVHADIDRADETKIKAGQGS
ARGRKYRRPASILFVTSDEPSTAARNLAGADVATASEVNTEDLAPGGAPGRLTVFTESAL
AEVAER

Sequence of entity 6 (F), FASTA

>1K8A_6 RIBOSOMAL PROTEIN L5 (chains F)
SSESESGGDFHEMREPRIEKVVVHMGIGHGGRDLANAEDILGEITGQMPVRTKAKRTVGE
FDIREGDPIGAKVTLRDEMAEEFLQTALPLAELATSQFDDTGNFSFGVEEHTEFPSQEYD
PSIGIYGLDVTVNLVRPGYRVAKRDKASRSIPTKHRLNPADAVAFIESTYDVEVSE

Sequence of entity 7 (G), FASTA

>1K8A_7 RIBOSOMAL PROTEIN L6 (chains G)
PRVELEIPEDVDAEQDHLDITVEGDNGSVTRRLWYPDIDVSVDGDTVVIESDEDNAKTMS
TIGTFQSHIENMFHGVTEGWEYGMEVFYSHFPMQVNVEGDEVVIENFLGEKAPRRTTIHG
DTDVEIDGEELTVSGPDIEAVGQTAADIEQLTRINDKDVRVFQDGVYITRKPNRGDA

Sequence of entity 8 (H), FASTA

>1K8A_8 RIBOSOMAL PROTEIN L7AE (chains H)
PVYVDFDVPADLEDDALEALEVARDTGAVKKGTNETTKSIERGSAELVFVAEDVQPEEIV
MHIPELADEKGVPFIFVEQQDDLGHAAGLEVGSAAAAVTDAGAAATVLEEIADKVEELR

Sequence of entity 9 (I), FASTA

>1K8A_9 RIBOSOMAL PROTEIN L10 (chains I)
MSAESERKTETIPEWKQEEVDAIVEMIESYESVGVVNIAGIPSRQLQDMRRDLHGTAELR
VSRNTLLERALDDVDDGLEDLNGYITGQVGLIGTDDNPFSLFQELEASKTPAPIGAGEVA
PNDIVIPEGDTGVDPGPFVGELQSVGADARIQEGSIQVLSDSTVLDTGEEVSQELSNVLN
ELGIEPKEVGLDLRAVFADGVLFEPEELELDIDEYRSDIQAAAGRAFNLSVNADYPTATT
APTMLQSDRGNAKSLALQAAIEDPEVVPDLVSKADAQVRALASQIDDEEALPEELQGVEA
DVATEEPTDDQDDDTASEDDADADDAAEEADDDDDDDEDAGDALGAMF

Sequence of entity 10 (J), FASTA

>1K8A_10 RIBOSOMAL PROTEIN L10E (chains J)
KPGAMYRNSSKPAYTRREYISGIPGKKIAQFDMGNNGAGPTYPAQVELVVEKPVQIRHNA
LEAARVAANRYVQNSGAAANYKFRIRKFPFHVIRENKAAAAAAAAAAADGMRAPFGKPVG
TAARVHGANHIFIAWVNPDPNVEEAWRRAKMKVTPTINIDSSPAGNA

Sequence of entity 11 (K), FASTA

>1K8A_11 RIBOSOMAL PROTEIN L13 (chains K)
MSVAEFDADVIVDARDCIMGRVASQVAEQALDGETVAVVNAERAVITGREEQIVEKYEKR
VDIGNDNGYFYPKRPDGIFKRTIRGMLPHKKQRGREAFESVRVYLGNPYDEDGEVLDGTS
LDRLSNIKFVTLGEISETLGANKTW

Sequence of entity 12 (L), FASTA

>1K8A_12 RIBOSOMAL PROTEIN L14 (chains L)
MEALGADVTQGLEKGSLITCADNTGARELKVISVHGYSGTKNRHPKAGLGDKITVSVTKG
TPEMRRQVLEAVVVRQRKPIRRPDGTRVKFEDNAAVIVDENEDPRGTELKGPIAREVAQR
FGSVASAATMIV

Ligands and cofactors

ID	Name	Formula	Copies
CAI	Carbomycin a	C42 H67 N O16	1
MG	Magnesium ion	Mg	119
CD	Cadmium ion	Cd	5

Water and common crystallization additives (NA, CL, K) are not listed.

Primary citation

The structures of four macrolide antibiotics bound to the large ribosomal subunit. Hansen, J.L., Ippolito, J.A., Ban, N. et al. Mol Cell (2002) 10:117-128. DOI 10.1016/S1097-2765(02)00570-1 · PubMed

Other PDB entries of the same protein (UniProt P20276 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1VQ8 2.2 Å, The structure of CCDA-PHE-CAP-BIO and the antibiotic sparsomycin bound to the large…
1VQO 2.2 Å, The structure of CCPMN bound to the large ribosomal subunit haloarcula marismortui
1VQP 2.25 Å, The structure of the transition state analogue "RAP" bound to the large ribosomal…
1VQK 2.3 Å, The structure of CCDA-PHE-CAP-BIO bound to the a site of the ribosomal subunit of…
1VQL 2.3 Å, The structure of the transition state analogue "DCSN" bound to the large ribosomal…
1VQM 2.3 Å, The structure of the transition state analogue "DAN" bound to the large ribosomal…
1FFK 2.4 Å, Crystal structure of the large ribosomal subunit from haloarcula marismortui at 2.4 Å…
1JJ2 2.4 Å, Fully Refined Crystal Structure of the Haloarcula marismortui Large Ribosomal Subunit at…
1S72 2.4 Å, Refined crystal structure of the haloarcula marismortui large ribosomal subunit at 2.4 Å…
1VQ9 2.4 Å, The structure of CCA-PHE-CAP-BIO and the antibiotic sparsomycin bound to the large…
1VQN 2.4 Å, The structure of CC-HPMN AND CCA-PHE-CAP-BIO bound to the large ribosomal subunit of…
1YHQ 2.4 Å, Crystal Structure Of Azithromycin Bound To The G2099A Mutant 50S Ribosomal Subunit Of…

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1K8A is part of these collections:

The ribosome and protein synthesis

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