3JBU: 30S ribosomal protein S2

Name: PDB 3JBU: Mechanisms of Ribosome Stalling by SecM at Multiple Elongation Steps
Published: 2016-01-27
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

Mechanisms of Ribosome Stalling by SecM at Multiple Elongation Steps. Determined by electron microscopy at 3.64 Å resolution. Released 27 Jan 2016.

Method: Electron microscopy
Resolution: 3.64 Å
Organism: Escherichia coli K-12
Chains: 54
Atoms: 143,334
Mol. weight: 2166.42 kDa
Released: 27 Jan 2016

Explore 3JBU in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3JBU contains 246 α-helices and 312 β-strands across 48 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: 3 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	13-18	6	97
β-strand	24-29	6	97
β-strand	33-40	8	98
α-helix	41-43	3
β-strand	45-52	8	98
α-helix	53-62	10
α-helix	64-73	10

Chain 1: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	4-7	4
α-helix	11-33	23
α-helix	40-42	3
α-helix	44-60	17

Chain 2: 3 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	5-9	5	103
α-helix	18-27	10
β-strand	35-38	4	103
α-helix	42-50	9
α-helix	52-54	3
β-strand	55-58	4	103

Chain 3: 3 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	7-9	3
α-helix	10-16	7
α-helix	17-19	3
β-strand	28-30	3	104
β-strand	37-39	3	104
β-strand	48-49	2	105
β-strand	52-53	2	105

Chain 4: 1 helix, 4 β-strands

Element	Residues	Length	Sheet
β-strand	7-13	7	106
β-strand	20-25	6	106
α-helix	33-34	2
β-strand	36-40	5	106
β-strand	45-50	6	106

Chain 6: 3 helices, 0 β-strands

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

Chain 7: 5 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	15-16	2	3
β-strand	22-24	3	3
α-helix	25-26	2
α-helix	38-42	5
β-strand	48-49	2	3
α-helix	50-51	2
α-helix	52-54	3
α-helix	55-61	7

Chain 8: 1 helix, 4 β-strands

Element	Residues	Length	Sheet
β-strand	2-4	3	7
β-strand	14-19	6	7
β-strand	22-27	6	7
α-helix	31-33	3
β-strand	35-37	3	7

40 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
30S ribosomal protein S2	B	protein	241	Escherichia coli K-12	P0A7V0 (AlphaFold model)
30S ribosomal protein S3	C	protein	233	Escherichia coli K-12	P0A7V3 (AlphaFold model)
30S ribosomal protein S4	D	protein	206	Escherichia coli K-12	P0A7V8 (AlphaFold model)
30S ribosomal protein S5	E	protein	167	Escherichia coli K-12	P0A7W1 (AlphaFold model)
30S ribosomal protein S6	F	protein	131	Escherichia coli K-12	P02358
30S ribosomal protein S7	G	protein	156	Escherichia coli K-12	P02359
30S ribosomal protein S8	H	protein	130	Escherichia coli K-12	P0A7W7
30S ribosomal protein S9	I	protein	130	Escherichia coli K-12	P0A7X3
30S ribosomal protein S10	J	protein	103	Escherichia coli K-12	P0A7R5
30S ribosomal protein S11	K	protein	129	Escherichia coli K-12	P0A7R9
30S ribosomal protein S12	L	protein	124	Escherichia coli K-12	P0A7S3
30S ribosomal protein S13	M	protein	118	Escherichia coli K-12	P0A7S9

42 more molecules are not listed.

Sequence of entity 1 (B), FASTA

>3JBU_1 30S ribosomal protein S2 (chains B)
MATVSMRDMLKAGVHFGHQTRYWNPKMKPFIFGARNKVHIINLEKTVPMFNEALAELNKI
ASRKGKILFVGTKRAASEAVKDAALSCDQFFVNHRWLGGMLTNWKTVRQSIKRLKDLETQ
SQDGTFDKLTKKEALMRTRELEKLENSLGGIKDMGGLPDALFVIDADHEHIAIKEANNLG
IPVFAIVDTNSDPDGVDFVIPGNDDAIRAVTLYLGAVAATVREGRSQDLASQAEESFVEA
E

Sequence of entity 2 (C), FASTA

>3JBU_2 30S ribosomal protein S3 (chains C)
MGQKVHPNGIRLGIVKPWNSTWFANTKEFADNLDSDFKVRQYLTKELAKASVSRIVIERP
AKSIRVTIHTARPGIVIGKKGEDVEKLRKVVADIAGVPAQINIAEVRKPELDAKLVADSI
TSQLERRVMFRRAMKRAVQNAMRLGAKGIKVEVSGRLGGAEIARTEWYREGRVPLHTLRA
DIDYNTSEAHTTYGVIGVKVWIFKGEILGGMAAVEQPEKPAAQPKKQQRKGRK

Sequence of entity 3 (D), FASTA

>3JBU_3 30S ribosomal protein S4 (chains D)
MARYLGPKLKLSRREGTDLFLKSGVRAIDTKCKIEQAPGQHGARKPRLSDYGVQLREKQK
VRRIYGVLERQFRNYYKEAARLKGNTGENLLALLEGRLDNVVYRMGFGATRAEARQLVSH
KAIMVNGRVVNIASYQVSPNDVVSIREKAKKQSRVKAALELAEQREKPTWLEVDAGKMEG
TFKRKPERSDLSADINEHLIVELYSK

Sequence of entity 4 (E), FASTA

>3JBU_4 30S ribosomal protein S5 (chains E)
MAHIEKQAGELQEKLIAVNRVSKTVKGGRIFSFTALTVVGDGNGRVGFGYGKAREVPAAI
QKAMEKARRNMINVALNNGTLQHPVKGVHTGSRVFMQPASEGTGIIAGGAMRAVLEVAGV
HNVLAKAYGSTNPINVVRATIDGLENMNSPEMVAAKRGKSVEEILGK

Sequence of entity 5 (F), FASTA

>3JBU_5 30S ribosomal protein S6 (chains F)
MRHYEIVFMVHPDQSEQVPGMIERYTAAITGAEGKIHRLEDWGRRQLAYPINKLHKAHYV
LMNVEAPQEVIDELETTFRFNDAVIRSMVMRTKHAVTEASPMVKAKDERRERRDDFANET
ADDADAGDSEE

Sequence of entity 6 (G), FASTA

>3JBU_6 30S ribosomal protein S7 (chains G)
MPRRRVIGQRKILPDPKFGSELLAKFVNILMVDGKKSTAESIVYSALETLAQRSGKSELE
AFEVALENVRPTVEVKSRRVGGSTYQVPVEVRPVRRNALAMRWIVEAARKRGDKSMALRL
ANELSDAAENKGTAVKKREDVHRMAEANKAFAHYRW

Sequence of entity 7 (H), FASTA

>3JBU_7 30S ribosomal protein S8 (chains H)
MSMQDPIADMLTRIRNGQAANKAAVTMPSSKLKVAIANVLKEEGFIEDFKVEGDTKPELE
LTLKYFQGKAVVESIQRVSRPGLRIYKRKDELPKVMAGLGIAVVSTSKGVMTDRAARQAG
LGGEIICYVA

Sequence of entity 8 (I), FASTA

>3JBU_8 30S ribosomal protein S9 (chains I)
MAENQYYGTGRRKSSAARVFIKPGNGKIVINQRSLEQYFGRETARMVVRQPLELVDMVEK
LDLYITVKGGGISGQAGAIRHGITRALMEYDESLRSELRKAGFVTRDARQVERKKVGLRK
ARRRPQFSKR

Sequence of entity 9 (J), FASTA

>3JBU_9 30S ribosomal protein S10 (chains J)
MQNQRIRIRLKAFDHRLIDQATAEIVETAKRTGAQVRGPIPLPTRKERFTVLISPHVNKD
ARDQYEIRTHLRLVDIVEPTEKTVDALMRLDLAAGVDVQISLG

Sequence of entity 10 (K), FASTA

>3JBU_10 30S ribosomal protein S11 (chains K)
MAKAPIRARKRVRKQVSDGVAHIHASFNNTIVTITDRQGNALGWATAGGSGFRGSRKSTP
FAAQVAAERCADAVKEYGIKNLEVMVKGPGPGRESTIRALNAAGFRITNITDVTPIPHNG
CRPPKKRRV

Sequence of entity 11 (L), FASTA

>3JBU_11 30S ribosomal protein S12 (chains L)
MATVNQLVRKPRARKVAKSNVPALEACPQKRGVCTRVYTTTPKKPNSALRKVCRVRLTNG
FEVTSYIGGEGHNLQEHSVILIRGGRVKDLPGVRYHTVRGALDCSGVKDRKQARSKYGVK
RPKA

Sequence of entity 12 (M), FASTA

>3JBU_12 30S ribosomal protein S13 (chains M)
MARIAGINIPDHKHAVIALTSIYGVGKTRSKAILAAAGIAEDVKISELSEGQIDTLRDEV
AKFVVEGDLRREISMSIKRLMDLGCYRGLRHRRGLPVRGQRTKTNARTRKGPRKPIKK

Primary citation

Mechanisms of ribosome stalling by SecM at multiple elongation steps. Zhang, J., Pan, X., Yan, K. et al. Elife (2015) 4. DOI 10.7554/eLife.09684 · PubMed

Other PDB entries of the same protein (UniProt P0A7V0 (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…
4ODN 1.6 Å, Structure of SlyD from Thermus thermophilus in complex with S2-plus peptide
7OXH 1.7 Å, ttSlyD with pseudo-wild-type S2 peptide
4ODP 1.75 Å, Structure of SlyD delta-IF from Thermus thermophilus in complex with S2-W23A peptide
4ODM 1.75 Å, Structure of SlyD from Thermus thermophilus in complex with S2-W23A peptide
8CGJ 1.79 Å, Streptomycin bound to the 30S body
8CF1 1.82 Å, Tetracycline bound to the 30S head
7OXJ 1.85 Å, ttSlyD with M8A pseudo-wild-type S2 peptide
8FTO 1.85 Å, E. coli 70S ribosome with an improved MS2 tag inserted in H98
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

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