8PHJ: CA4-bound Cami1

Name: PDB 8PHJ: cA4-bound Cami1 in complex with 70S ribosome
Published: 2023-12-13
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

cA4-bound Cami1 in complex with 70S ribosome. Determined by electron microscopy at 3.67 Å resolution. Released 13 Dec 2023.

Method: Electron microscopy
Resolution: 3.67 Å
Organisms: Escherichia coli, synthetic construct, Allochromatium vinosum
Chains: 61
Atoms: 152,518
Mol. weight: 2344.05 kDa
Ligands: ZN, MG
Released: 13 Dec 2023

Explore 8PHJ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8PHJ contains 306 α-helices and 354 β-strands across 54 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 0: 1 helix, 4 β-strands

Element	Residues	Length	Sheet
β-strand	7-13	7	1
β-strand	20-25	6	1
α-helix	33-34	2
β-strand	35-40	6	1
β-strand	45-52	8	1

Chain 1: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	9-16	8
α-helix	18-21	4
α-helix	25-37	13

Chain 2: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	3-6	4
β-strand	15-16	2	10
β-strand	22-24	3	10
α-helix	25-26	2
α-helix	38-43	6
β-strand	48-49	2	10
α-helix	55-61	7

Chain 3: 1 helix, 4 β-strands

Element	Residues	Length	Sheet
β-strand	2-4	3	14
β-strand	14-19	6	14
β-strand	22-27	6	14
α-helix	31-33	3
β-strand	35-37	3	14

Chain 4: 2 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	10-15	6	17
β-strand	21-26	6	17
β-strand	32-33	2	17
α-helix	42-45	4
α-helix	57-63	7

Chain 5: 7 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	5-20	16
β-strand	25-29	5	20
α-helix	35-47	13
β-strand	52-53	2	20
α-helix	57-63	7
α-helix	70-72	3
β-strand	81-83	3	20
α-helix	92-102	11
β-strand	107-113	7	20
β-strand	116-118	3	20
α-helix	120-122	3
α-helix	124-128	5

Chain 6: 7 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	10-11	2	22
α-helix	25-29	5
α-helix	35-46	12
α-helix	50	1
β-strand	57-61	5	22
β-strand	67-71	5	22
α-helix	73-75	3
α-helix	76-83	8
β-strand	100-101	2	23
α-helix	103-113	11
α-helix	122-135	14
β-strand	139-140	2	23

Chain B: 9 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	6-12	7
β-strand	16-19	4	45
α-helix	20-22	3
α-helix	25-30	6
β-strand	31-34	4	45
β-strand	38-41	4	45
α-helix	43-62	20
β-strand	67-70	4	46
α-helix	77-85	9
β-strand	90-92	3	46
α-helix	104-123	20
α-helix	133-148	16
β-strand	160-164	5	46
α-helix	170-179	10
β-strand	183-187	5	46
β-strand	198-201	4	46
α-helix	207-226	20

46 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
Large ribosomal subunit protein bL33	0	protein	55	Escherichia coli	P0A7N9 (AlphaFold model)
Large ribosomal subunit protein bL34	1	protein	46	Escherichia coli	P0A7P5 (AlphaFold model)
Large ribosomal subunit protein bL35	2	protein	65	Escherichia coli	P0A7Q1 (AlphaFold model)
Large ribosomal subunit protein bL36A	3	protein	38	Escherichia coli	P0A7Q6 (AlphaFold model)
Large ribosomal subunit protein bL31A	4	protein	70	Escherichia coli	P0A7M9
Large ribosomal subunit protein uL10	5	protein	165	Escherichia coli	P0A7J3
Large ribosomal subunit protein uL11	6	protein	142	Escherichia coli	P0A7J7
fMet-tRNA(fMet)	7, 8	RNA	77	Escherichia coli
mRNA	9	RNA	31	synthetic construct
16S rRNA	A	RNA	1542	Escherichia coli
Small ribosomal subunit protein uS2	B	protein	241	Escherichia coli	P0A7V0
Small ribosomal subunit protein uS3	C	protein	233	Escherichia coli	P0A7V3

47 more molecules are not listed.

Sequence of entity 1 (0), FASTA

>8PHJ_1 Large ribosomal subunit protein bL33 (chains 0)
MAKGIREKIKLVSSAGTGHFYTTTKNKRTKPEKLELKKFDPVVRQHVIYKEAKIK

Sequence of entity 2 (1), FASTA

>8PHJ_2 Large ribosomal subunit protein bL34 (chains 1)
MKRTFQPSVLKRNRSHGFRARMATKNGRQVLARRRAKGRARLTVSK

Sequence of entity 3 (2), FASTA

>8PHJ_3 Large ribosomal subunit protein bL35 (chains 2)
MPKIKTVRGAAKRFKKTGKGGFKHKHANLRHILTKKATKRKRHLRPKAMVSKGDLGLVIA
CLPYA

Sequence of entity 4 (3), FASTA

>8PHJ_4 Large ribosomal subunit protein bL36A (chains 3)
MKVRASVKKLCRNCKIVKRDGVIRVICSAEPKHKQRQG

Sequence of entity 5 (4), FASTA

>8PHJ_5 Large ribosomal subunit protein bL31A (chains 4)
MKKDIHPKYEEITASCSCGNVMKIRSTVGHDLNLDVCSKCHPFFTGKQRDVATGGRVDRF
NKRFNIPGSK

Sequence of entity 6 (5), FASTA

>8PHJ_6 Large ribosomal subunit protein uL10 (chains 5)
MALNLQDKQAIVAEVSEVAKGALSAVVADSRGVTVDKMTELRKAGREAGVYMRVVRNTLL
RRAVEGTPFECLKDAFVGPTLIAYSMEHPGAAARLFKEFAKANAKFEVKAAAFEGELIPA
SQIDRLATLPTYEEAIARLMATMKEASAGKLVRTLAAVRDAKEAA

Sequence of entity 7 (6), FASTA

>8PHJ_7 Large ribosomal subunit protein uL11 (chains 6)
MAKKVQAYVKLQVAAGMANPSPPVGPALGQQGVNIMEFCKAFNAKTDSIEKGLPIPVVIT
VYADRSFTFVTKTPPAAVLLKKAAGIKSGSGKPNKDKVGKISRAQLQEIAQTKAADMTGA
DIEAMTRSIEGTARSMGLVVED

Sequence of entity 8 (7, 8), FASTA

>8PHJ_8 fMet-tRNA(fMet) (chains 7, 8)
CGCGGGGUGGAGCAGCCUGGUAGCUCGUCGGGCUCAUAACCCGAAGAUCGUCGGUUCAAA
UCCGGCCCCCGCAACCA

Sequence of entity 9 (9), FASTA

>8PHJ_9 mRNA (chains 9)
GGGCAAGGAGGUAAAAAUGUAGAAAAACAAU

Sequence of entity 10 (A), FASTA

>8PHJ_10 16S rRNA (chains A)
AAAUUGAAGAGUUUGAUCAUGGCUCAGAUUGAACGCUGGCGGCAGGCCUAACACAUGCAA
GUCGAACGGUAACAGGAAGAAGCUUGCUUCUUUGCUGACGAGUGGCGGACGGGUGAGUAA
UGUCUGGGAAACUGCCUGAUGGAGGGGGAUAACUACUGGAAACGGUAGCUAAUACCGCAU
AACGUCGCAAGACCAAAGAGGGGGACCUUCGGGCCUCUUGCCAUCGGAUGUGCCCAGAUG
GGAUUAGCUAGUAGGUGGGGUAACGGCUCACCUAGGCGACGAUCCCUAGCUGGUCUGAGA
GGAUGACCAGCCACACUGGAACUGAGACACGGUCCAGACUCCUACGGGAGGCAGCAGUGG
GGAAUAUUGCACAAUGGGCGCAAGCCUGAUGCAGCCAUGCCGCGUGUAUGAAGAAGGCCU
UCGGGUUGUAAAGUACUUUCAGCGGGGAGGAAGGGAGUAAAGUUAAUACCUUUGCUCAUU
GACGUUACCCGCAGAAGAAGCACCGGCUAACUCCGUGCCAGCAGCCGCGGUAAUACGGAG
GGUGCAAGCGUUAAUCGGAAUUACUGGGCGUAAAGCGCACGCAGGCGGUUUGUUAAGUCA
GAUGUGAAAUCCCCGGGCUCAACCUGGGAACUGCAUCUGAUACUGGCAAGCUUGAGUCUC
GUAGAGGGGGGUAGAAUUCCAGGUGUAGCGGUGAAAUGCGUAGAGAUCUGGAGGAAUACC
GGUGGCGAAGGCGGCCCCCUGGACGAAGACUGACGCUCAGGUGCGAAAGCGUGGGGAGCA
AACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGAUGUCGACUUGGAGGUUGUGCC
CUUGAGGCGUGGCUUCCGGAGCUAACGCGUUAAGUCGACCGCCUGGGGAGUACGGCCGCA
AGGUUAAAACUCAAAUGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAU
UCGAUGCAACGCGAAGAACCUUACCUGGUCUUGACAUCCACGGAAGUUUUCAGAGAUGAG
AAUGUGCCUUCGGGAACCGUGAGACAGGUGCUGCAUGGCUGUCGUCAGCUCGUGUUGUGA
AAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUAUCCUUUGUUGCCAGCGGUCCGGC
CGGGAACUCAAAGGAGACUGCCAGUGAUAAACUGGAGGAAGGUGGGGAUGACGUCAAGUC
AUCAUGGCCCUUACGACCAGGGCUACACACGUGCUACAAUGGCGCAUACAAAGAGAAGCG
ACCUCGCGAGAGCAAGCGGACCUCAUAAAGUGCGUCGUAGUCCGGAUUGGAGUCUGCAAC
UCGACUCCAUGAAGUCGGAAUCGCUAGUAAUCGUGGAUCAGAAUGCCACGGUGAAUACGU
UCCCGGGCCUUGUACACACCGCCCGUCACACCAUGGGAGUGGGUUGCAAAAGAAGUAGGU
AGCUUAACCUUCGGGAGGGCGCUUACCACUUUGUGAUUCAUGACUGGGGUGAAGUCGUAA
CAAGGUAACCGUAGGGGAACCUGCGGUUGGAUCACCUCCUUA

Sequence of entity 11 (B), FASTA

>8PHJ_11 Small ribosomal subunit protein uS2 (chains B)
MATVSMRDMLKAGVHFGHQTRYWNPKMKPFIFGARNKVHIINLEKTVPMFNEALAELNKI
ASRKGKILFVGTKRAASEAVKDAALSCDQFFVNHRWLGGMLTNWKTVRQSIKRLKDLETQ
SQDGTFDKLTKKEALMRTRELEKLENSLGGIKDMGGLPDALFVIDADHEHIAIKEANNLG
IPVFAIVDTNSDPDGVDFVIPGNDDAIRAVTLYLGAVAATVREGRSQDLASQAEESFVEA
E

Sequence of entity 12 (C), FASTA

>8PHJ_12 Small ribosomal subunit protein uS3 (chains C)
MGQKVHPNGIRLGIVKPWNSTWFANTKEFADNLDSDFKVRQYLTKELAKASVSRIVIERP
AKSIRVTIHTARPGIVIGKKGEDVEKLRKVVADIAGVPAQINIAEVRKPELDAKLVADSI
TSQLERRVMFRRAMKRAVQNAMRLGAKGIKVEVSGRLGGAEIARTEWYREGRVPLHTLRA
DIDYNTSEAHTTYGVIGVKVWIFKGEILGGMAAVEQPEKPAAQPKKQQRKGRK

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2
MG	Magnesium ion	Mg	241

Primary citation

Ribosomal stalk-captured CARF-RelE ribonuclease inhibits translation following CRISPR signaling. Mogila, I., Tamulaitiene, G., Keda, K. et al. Science (2023) 382:1036-1041. DOI 10.1126/science.adj2107 · PubMed

Other PDB entries of the same protein (UniProt P0A7N9 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8B0X 1.55 Å, Translating 70S ribosome in the unrotated state (P and E, tRNAs)
9Q87 1.55 Å, Principles of ion binding to RNA inferred from the analysis of a 1.55 Angstrom…
8CGK 1.64 Å, Lincomycin and Avilamycin bound to the 50S subunit
8CGV 1.66 Å, Tiamulin bound to the 50S subunit
8CEU 1.83 Å, Retapamulin and Capreomycin bound to the 50S subunit
8FTO 1.85 Å, E. coli 70S ribosome with an improved MS2 tag inserted in H98
8CAM 1.86 Å, Evernimicin bound to the 50S subunit
9GHE 1.87 Å, Staphylococcus aureus FusB bound to the small subunit of the Escherichia coli 70S…
9T0Y 1.87 Å, E. coli 70S ribosome from delta-9 strain
9T6M 1.87 Å, E. coli 70S ribosome from delta-10 strain
9SYH 1.89 Å, E. coli 70S ribosome from deltaRlmE strain
9D89 1.95 Å, E. coli 50S ribosomal subunit in complex with PrAMP rumicidin-2 (focused refinement)

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