5GAD: RNC-SRP-SR complex early state

Name: PDB 5GAD: RNC-SRP-SR complex early state
Published: 2016-01-27
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

RNC-SRP-SR complex early state. Determined by electron microscopy at 3.7 Å resolution. Released 27 Jan 2016.

Method: Electron microscopy
Resolution: 3.7 Å
Organism: Escherichia coli
Chains: 37
Atoms: 98,006
Mol. weight: 1528.37 kDa
Ligands: MG, ZN, GNP
Released: 27 Jan 2016

Explore 5GAD in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5GAD contains 178 α-helices and 228 β-strands across 33 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: 2 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	5-9	5	3
α-helix	18-27	10
β-strand	35-38	4	3
α-helix	42-51	10
β-strand	55-58	4	3

Chain b: 1 helix, 4 β-strands

Element	Residues	Length	Sheet
α-helix	10-17	8
β-strand	29-30	2	4
β-strand	37-38	2	4
β-strand	48-49	2	5
β-strand	52-53	2	5

Chain c: 0 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	7-13	7	15
β-strand	20-25	6	15
β-strand	35-40	6	15
β-strand	45-50	6	15

Chain C: 9 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	6
α-helix	11-13	3
β-strand	17-19	3	6
α-helix	25-26	2
α-helix	31-33	3
β-strand	34-35	2	7
β-strand	43	1	8
β-strand	49	1	8
β-strand	54	1	9
β-strand	62-63	2	7
β-strand	65	1	10
β-strand	76-83	8	10
β-strand	90-96	7	10
β-strand	101-105	5	10
β-strand	107	1	11
β-strand	115-116	2	10
β-strand	118	1	12
β-strand	129-131	3	12
α-helix	132-134	3
α-helix	136	1
β-strand	140-142	3	12
β-strand	144	1	13
β-strand	154	1	13
β-strand	162-168	7	12
β-strand	171-175	5	12
β-strand	181-185	5	12
β-strand	189-192	4	12
β-strand	195	1	11
α-helix	198-202	5
β-strand	204	1	6
α-helix	208-213	6
β-strand	216	1	9
α-helix	222-224	3
β-strand	245	1	14
β-strand	251	1	14
α-helix	263-266	4
β-strand	267-269	3	12

Chain d: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	9-16	8
α-helix	18-22	5
α-helix	25-37	13

Chain D: 7 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	4-15	12	16
β-strand	21-28	8	16
β-strand	32-38	7	17
α-helix	40-43	4
β-strand	47-51	5	17
α-helix	62-71	10
β-strand	80-83	4	17
β-strand	95-96	2	17
α-helix	98-101	4
β-strand	106-112	7	16
α-helix	113-115	3
β-strand	118-119	2	18
α-helix	121-125	5
α-helix	127-129	3
α-helix	155-156	2
β-strand	163-164	2	18
β-strand	169-181	13	16
β-strand	186-190	5	16
β-strand	200-205	6	16

Chain e: 5 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	8-13	6
β-strand	15-16	2	21
β-strand	22-24	3	21
α-helix	25-26	2
α-helix	38-44	7
β-strand	48-49	2	21
α-helix	50-51	2
α-helix	55-61	7

Chain E: 9 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	2-4	3	19
β-strand	11-13	3	19
α-helix	16-19	4
α-helix	25-38	14
α-helix	68-69	2
α-helix	98-114	17
β-strand	118-121	4	20
α-helix	131-141	11
β-strand	146-150	5	20
α-helix	155-160	6
β-strand	167-171	5	20
α-helix	172-174	3
α-helix	177-182	6
β-strand	185-189	5	20
α-helix	190-199	10

25 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
Esrp 4.5S RNA	1	RNA	113	Escherichia coli
tRNA CCAend	2	RNA	3	Escherichia coli
23S rRNA	A	RNA	2903	Escherichia coli
5S rRNA	B	RNA	120	Escherichia coli
50S ribosomal protein L2	C	protein	273	Escherichia coli	P60422 (AlphaFold model)
50S ribosomal protein L3	D	protein	209	Escherichia coli	P60438 (AlphaFold model)
50S ribosomal protein L4	E	protein	201	Escherichia coli	P60723 (AlphaFold model)
50S ribosomal protein L5	F	protein	179	Escherichia coli	P62399 (AlphaFold model)
50S ribosomal protein L6	G	protein	177	Escherichia coli	P0AG55
50S ribosomal protein L9	H	protein	149	Escherichia coli	P0A7R1
50S ribosomal protein L10	I	protein	165	Escherichia coli	P0A7J3
50S ribosomal protein L11	J	protein	142	Escherichia coli	P0A7J7

25 more molecules are not listed.

Sequence of entity 1 (1), FASTA

>5GAD_1 ESRP 4.5S RNA (chains 1)
GGGGGCUCUGUUGGUUCUCCCGCAACGCUACUCUGUUUACCAGGUCAGGUCCGGAAGGAA
GCAGCCAAGGCAGAUGACGCGUGUGCCGGGAUGUAGCUGGCAGGGCCCCCACC

Sequence of entity 2 (2), FASTA

>5GAD_2 tRNA CCAend (chains 2)
CCA

Sequence of entity 3 (A), FASTA

>5GAD_3 23S rRNA (chains A)
GGUUAAGCGACUAAGCGUACACGGUGGAUGCCCUGGCAGUCAGAGGCGAUGAAGGACGUG
CUAAUCUGCGAUAAGCGUCGGUAAGGUGAUAUGAACCGUUAUAACCGGCGAUUUCCGAAU
GGGGAAACCCAGUGUGUUUCGACACACUAUCAUUAACUGAAUCCAUAGGUUAAUGAGGCG
AACCGGGGGAACUGAAACAUCUAAGUACCCCGAGGAAAAGAAAUCAACCGAGAUUCCCCC
AGUAGCGGCGAGCGAACGGGGAGCAGCCCAGAGCCUGAAUCAGUGUGUGUGUUAGUGGAA
GCGUCUGGAAAGGCGCGCGAUACAGGGUGACAGCCCCGUACACAAAAAUGCACAUGCUGU
GAGCUCGAUGAGUAGGGCGGGACACGUGGUAUCCUGUCUGAAUAUGGGGGGACCAUCCUC
CAAGGCUAAAUACUCCUGACUGACCGAUAGUGAACCAGUACCGUGAGGGAAAGGCGAAAA
GAACCCCGGCGAGGGGAGUGAAAAAGAACCUGAAACCGUGUACGUACAAGCAGUGGGAGC
ACGCUUAGGCGUGUGACUGCGUACCUUUUGUAUAAUGGGUCAGCGACUUAUAUUCUGUAG
CAAGGUUAACCGAAUAGGGGAGCCGAAGGGAAACCGAGUCUUAACUGGGCGUUAAGUUGC
AGGGUAUAGACCCGAAACCCGGUGAUCUAGCCAUGGGCAGGUUGAAGGUUGGGUAACACU
AACUGGAGGACCGAACCGACUAAUGUUGAAAAAUUAGCGGAUGACUUGUGGCUGGGGGUG
AAAGGCCAAUCAAACCGGGAGAUAGCUGGUUCUCCCCGAAAGCUAUUUAGGUAGCGCCUC
GUGAAUUCAUCUCCGGGGGUAGAGCACUGUUUCGGCAAGGGGGUCAUCCCGACUUACCAA
CCCGAUGCAAACUGCGAAUACCGGAGAAUGUUAUCACGGGAGACACACGGCGGGUGCUAA
CGUCCGUCGUGAAGAGGGAAACAACCCAGACCGCCAGCUAAGGUCCCAAAGUCAUGGUUA
AGUGGGAAACGAUGUGGGAAGGCCCAGACAGCCAGGAUGUUGGCUUAGAAGCAGCCAUCA
UUUAAAGAAAGCGUAAUAGCUCACUGGUCGAGUCGGCCUGCGCGGAAGAUGUAACGGGGC
UAAACCAUGCACCGAAGCUGCGGCAGCGACGCUUAUGCGUUGUUGGGUAGGGGAGCGUUC
UGUAAGCCUGCGAAGGUGUGCUGUGAGGCAUGCUGGAGGUAUCAGAAGUGCGAAUGCUGA
CAUAAGUAACGAUAAAGCGGGUGAAAAGCCCGCUCGCCGGAAGACCAAGGGUUCCUGUCC
AACGUUAAUCGGGGCAGGGUGAGUCGACCCCUAAGGCGAGGCCGAAAGGCGUAGUCGAUG
GGAAACAGGUUAAUAUUCCUGUACUUGGUGUUACUGCGAAGGGGGGACGGAGAAGGCUAU
GUUGGCCGGGCGACGGUUGUCCCGGUUUAAGCGUGUAGGCUGGUUUUCCAGGCAAAUCCG
GAAAAUCAAGGCUGAGGCGUGAUGACGAGGCACUACGGUGCUGAAGCAACAAAUGCCCUG
CUUCCAGGAAAAGCCUCUAAGCAUCAGGUAACAUCAAAUCGUACCCCAAACCGACACAGG
UGGUCAGGUAGAGAAUACCAAGGCGCUUGAGAGAACUCGGGUGAAGGAACUAGGCAAAAU
GGUGCCGUAACUUCGGGAGAAGGCACGCUGAUAUGUAGGUGAGGUCCCUCGCGGAUGGAG
CUGAAAUCAGUCGAAGAUACCAGCUGGCUGCAACUGUUUAUUAAAAACACAGCACUGUGC
AAACACGAAAGUGGACGUAUACGGUGUGACGCCUGCCCGGUGCCGGAAGGUUAAUUGAUG
GGGUUAGCGCAAGCGAAGCUCUUGAUCGAAGCCCCGGUAAACGGCGGCCGUAACUAUAAC
GGUCCUAAGGUAGCGAAAUUCCUUGUCGGGUAAGUUCCGACCUGCACGAAUGGCGUAAUG
AUGGCCAGGCUGUCUCCACCCGAGACUCAGUGAAAUUGAACUCGCUGUGAAGAUGCAGUG
UACCCGCGGCAAGACGGAAAGACCCCGUGAACCUUUACUAUAGCUUGACACUGAACAUUG
AGCCUUGAUGUGUAGGAUAGGUGGGAGGCUUUGAAGUGUGGACGCCAGUCUGCAUGGAGC
CGACCUUGAAAUACCACCCUUUAAUGUUUGAUGUUCUAACGUUGACCCGUAAUCCGGGUU
GCGGACAGUGUCUGGUGGGUAGUUUGACUGGGGCGGUCUCCUCCUAAAGAGUAACGGAGG
AGCACGAAGGUUGGCUAAUCCUGGUCGGACAUCAGGAGGUUAGUGCAAUGGCAUAAGCCA
GCUUGACUGCGAGCGUGACGGCGCGAGCAGGUGCGAAAGCAGGUCAUAGUGAUCCGGUGG
UUCUGAAUGGAAGGGCCAUCGCUCAACGGAUAAAAGGUACUCCGGGGAUAACAGGCUGAU
ACCGCCCAAGAGUUCAUAUCGACGGCGGUGUUUGGCACCUCGAUGUCGGCUCAUCACAUC
CUGGGGCUGAAGUAGGUCCCAAGGGUAUGGCUGUUCGCCAUUUAAAGUGGUACGCGAGCU
GGGUUUAGAACGUCGUGAGACAGUUCGGUCCCUAUCUGCCGUGGGCGCUGGAGAACUGAG
GGGGGCUGCUCCUAGUACGAGAGGACCGGAGUGGACGCAUCACUGGUGUUCGGGUUGUCA
UGCCAAUGGCACUGCCCGGUAGCUAAAUGCGGAAGAGAUAAGUGCUGAAAGCAUCUAAGC
ACGAAACUUGCCCCGAGAUGAGUUCUCCCUGACCCUUUAAGGGUCCUGAAGGAACGUUGA
AGACGACGACGUUGAUAGGCCGGGUGUGUAAGCGCAGCGAUGCGUUGAGCUAACCGGUAC
UAAUGAACCGUGAGGCUUAACCU

Sequence of entity 4 (B), FASTA

>5GAD_4 5S rRNA (chains B)
UGCCUGGCGGCCGUAGCGCGGUGGUCCCACCUGACCCCAUGCCGAACUCAGAAGUGAAAC
GCCGUAGCGCCGAUGGUAGUGUGGGGUCUCCCCAUGCGAGAGUAGGGAACUGCCAGGCAU

Sequence of entity 5 (C), FASTA

>5GAD_5 50S ribosomal protein L2 (chains C)
MAVVKCKPTSPGRRHVVKVVNPELHKGKPFAPLLEKNSKSGGRNNNGRITTRHIGGGHKQ
AYRIVDFKRNKDGIPAVVERLEYDPNRSANIALVLYKDGERRYILAPKGLKAGDQIQSGV
DAAIKPGNTLPMRNIPVGSTVHNVEMKPGKGGQLARSAGTYVQIVARDGAYVTLRLRSGE
MRKVEADCRATLGEVGNAEHMLRVLGKAGAARWRGVRPTVRGTAMNPVDHPHGGGEGRNF
GKHPVTPWGVQTKGKKTRSNKRTDKFIVRRRSK

Sequence of entity 6 (D), FASTA

>5GAD_6 50S ribosomal protein L3 (chains D)
MIGLVGKKVGMTRIFTEDGVSIPVTVIEVEANRVTQVKDLANDGYRAIQVTTGAKKANRV
TKPEAGHFAKAGVEAGRGLWEFRLAEGEEFTVGQSISVELFADVKKVDVTGTSKGKGFAG
TVKRWNFRTQDATHGNSLSHRVPGSIGQNQTPGKVFKGKKMAGQMGNERVTVQSLDVVRV
DAERNLLLVKGAVPGATGSDLIVKPAVKA

Sequence of entity 7 (E), FASTA

>5GAD_7 50S ribosomal protein L4 (chains E)
MELVLKDAQSALTVSETTFGRDFNEALVHQVVVAYAAGARQGTRAQKTRAEVTGSGKKPW
RQKGTGRARSGSIKSPIWRSGGVTFAARPQDHSQKVNKKMYRGALKSILSELVRQDRLIV
VEKFSVEAPKTKLLAQKLKDMALEDVLIITGELDENLFLAARNLHKVDVRDATGIDPVSL
IAFDKVVMTADAVKQVEEMLA

Sequence of entity 8 (F), FASTA

>5GAD_8 50S ribosomal protein L5 (chains F)
MAKLHDYYKDEVVKKLMTEFNYNSVMQVPRVEKITLNMGVGEAIADKKLLDNAAADLAAI
SGQKPLITKARKSVAGFKIRQGYPIGCKVTLRGERMWEFFERLITIAVPRIRDFRGLSAK
SFDGRGNYSMGVREQIIFPEIDYDKVDRVRGLDITITTTAKSDEEGRALLAAFDFPFRK

Sequence of entity 9 (G), FASTA

>5GAD_9 50S ribosomal protein L6 (chains G)
MSRVAKAPVVVPAGVDVKINGQVITIKGKNGELTRTLNDAVEVKHADNTLTFGPRDGYAD
GWAQAGTARALLNSMVIGVTEGFTKKLQLVGVGYRAAVKGNVINLSLGFSHPVDHQLPAG
ITAECPTQTEIVLKGADKQVIGQVAADLRAYRRPEPYKGKGVRYADEVVRTKEAKKK

Sequence of entity 10 (H), FASTA

>5GAD_10 50S ribosomal protein L9 (chains H)
MQVILLDKVANLGSLGDQVNVKAGYARNFLVPQGKAVPATKKNIEFFEARRAELEAKLAE
VLAAANARAEKINALETVTIASKAGDEGKLFGSIGTRDIADAVTAAGVEVAKSEVRLPNG
VLRTTGEHEVSFQVHSEVFAKVIVNVVAE

Sequence of entity 11 (I), FASTA

>5GAD_11 50S ribosomal protein L10 (chains I)
MALNLQDKQAIVAEVSEVAKGALSAVVADSRGVTVDKMTELRKAGREAGVYMRVVRNTLL
RRAVEGTPFECLKDAFVGPTLIAYVTEHPGAAARLFKEFAKANAKFEVKAAAFEGELIPA
SQIDRLATLPTYEEAIARLMATMKEASAGKLVRTLAAVRDAKEAA

Sequence of entity 12 (J), FASTA

>5GAD_12 50S ribosomal protein L11 (chains J)
MAKKVQAYVKLQVAAGMANPSPPVGPALGQQGVNIMEFCKAFNAKTDSIEKGLPIPVVIT
VYADRSFTFVTKTPPAAVLLKKAAGIKSGSGKPNKDKVGKISRAQLQEIAQTKAADMTGA
DIEAMTRSIEGTARSMGLVVED

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	433
ZN	Zinc ion	Zn	1
GNP	Phosphoaminophosphonic acid-guanylate ester	C10 H17 N6 O13 P3	2

Primary citation

Structures of the E. coli translating ribosome with SRP and its receptor and with the translocon. Jomaa, A., Boehringer, D., Leibundgut, M. et al. Nat Commun (2016) 7:10471-10471. DOI 10.1038/ncomms10471 · PubMed

Other PDB entries of the same protein (UniProt P60422 (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
8E30 1.91 Å, E. coli 50S ribosome bound to compound streptogramin A analog 3142

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