4V89: 30S ribosomal protein S2

Name: PDB 4V89: Crystal Structure of Release Factor RF3 Trapped in the GTP State on a Rotated Conformation of the Ribosome (without viomycin)
Published: 2014-07-09
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

Crystal Structure of Release Factor RF3 Trapped in the GTP State on a Rotated Conformation of the Ribosome (without viomycin). Determined by X-ray diffraction at 3.7 Å resolution. Released 9 Jul 2014.

Method: X-ray diffraction
Resolution: 3.7 Å
Organism: Escherichia coli
Chains: 58
Atoms: 146,665
Mol. weight: 2264.28 kDa
Ligands: GNP, MG
Released: 9 Jul 2014

Explore 4V89 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4V89 contains 254 α-helices and 358 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 AB: 11 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	24-29	6
β-strand	30-34	5	2
β-strand	37-40	4	2
α-helix	42-48	7
α-helix	50-61	12
β-strand	68-69	2	3
α-helix	76-79	4
β-strand	90-91	2	3
α-helix	94-96	3
α-helix	103-117	15
α-helix	131-146	16
β-strand	160-162	3	3
α-helix	166-168	3
α-helix	169-178	10
β-strand	182-185	4	3
α-helix	192-194	3
β-strand	197-199	3	3
α-helix	206-217	12

Chain AC: 7 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	6-10	5
β-strand	19-20	2	11
α-helix	25-45	21
β-strand	51-55	5	12
β-strand	56-57	2	11
β-strand	63	1	13
β-strand	66-69	4	12
α-helix	73-76	4
α-helix	81-94	14
β-strand	98	1	13
β-strand	101-104	4	12
α-helix	108-110	3
α-helix	112-124	13
α-helix	129-142	14
β-strand	147-153	7	14
β-strand	165-170	6	14
β-strand	181-189	9	14
β-strand	194-202	9	14

Chain AD: 9 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	8-14	7
α-helix	49-62	14
α-helix	68-80	13
α-helix	85-94	10
β-strand	96	1	20
α-helix	97-104	8
α-helix	110-118	9
β-strand	122-123	2	21
β-strand	128	1	21
β-strand	135	1	20
β-strand	141-144	4	21
α-helix	154-162	9
β-strand	170-171	2	21
β-strand	178-181	4	21
α-helix	184-186	3
α-helix	196-202	7

Chain AE: 5 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	12-20	9	24
β-strand	24	1	25
β-strand	27	1	25
β-strand	31-39	9	24
β-strand	45-48	4	24
β-strand	51-52	2	24
α-helix	55-67	13
β-strand	70-71	2	24
α-helix	72-73	2
β-strand	76	1	26
β-strand	79	1	26
β-strand	84-88	5	27
β-strand	91-96	6	27
β-strand	105	1	27
α-helix	111-115	5
β-strand	123-128	6	27
α-helix	132-144	13
α-helix	152-154	3

Chain AF: 3 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-4	3	34
β-strand	7-10	4	35
α-helix	12-17	6
α-helix	18-31	14
β-strand	35-36	2	34
β-strand	40-45	6	35
β-strand	57-61	5	35
β-strand	64-66	3	34
α-helix	68-80	13
β-strand	84-88	5	35

Chain AG: 11 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	8-10	3
α-helix	12-14	3
α-helix	20-29	10
α-helix	35-53	19
α-helix	60-68	9
β-strand	72-73	2	41
α-helix	85-87	3
β-strand	88-89	2	41
α-helix	90-91	2
α-helix	94-108	15
α-helix	115-127	13
α-helix	132-143	12
α-helix	147-150	4

Chain AH: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	5-18	14
β-strand	23-27	5	42
α-helix	30-41	12
β-strand	45-47	3	42
β-strand	50	1	42
β-strand	57-62	6	42
β-strand	64	1	43
β-strand	69	1	43
β-strand	74-76	3	44
β-strand	85-86	2	44
β-strand	100-105	6	44
β-strand	109-111	3	44
α-helix	112-118	7
β-strand	122-128	7	44

Chain AI: 5 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	45
β-strand	10-11	2	45
β-strand	14-21	8	45
β-strand	27-29	3	45
β-strand	61-67	7	45
α-helix	71-85	15
α-helix	86-88	3
α-helix	93-98	6
α-helix	105-106	2
α-helix	110-114	5
β-strand	119	1	46
β-strand	122	1	46

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
16S rRNA	AA	RNA	1533	Escherichia coli
30S ribosomal protein S2	AB	protein	241	Escherichia coli	P0A7V0 (AlphaFold model)
30S ribosomal protein S3	AC	protein	233	Escherichia coli	P0A7V3 (AlphaFold model)
30S ribosomal protein S4	AD	protein	206	Escherichia coli	P0A7V8 (AlphaFold model)
30S ribosomal protein S5	AE	protein	167	Escherichia coli	P0A7W1 (AlphaFold model)
30S ribosomal protein S6	AF	protein	135	Escherichia coli	P02358
30S ribosomal protein S7	AG	protein	179	Escherichia coli	P02359
30S ribosomal protein S8	AH	protein	130	Escherichia coli	P0A7W7
30S ribosomal protein S9	AI	protein	130	Escherichia coli	P0A7X3
30S ribosomal protein S10	AJ	protein	103	Escherichia coli	P0A7R5
30S ribosomal protein S11	AK	protein	129	Escherichia coli	P0A7R9
30S ribosomal protein S12	AL	protein	124	Escherichia coli	P0A7S3

43 more molecules are not listed.

Sequence of entity 1 (AA), FASTA

>4V89_1 16S rRNA (chains AA)
AAUUGAAGAGUUUGAUCAUGGCUCAGAUUGAACGCUGGCGGCAGGCCUAACACAUGCAAG
UCGAACGGUAACAGGAAGAAGCUUGCUUCUUUGCUGACGAGUGGCGGACGGGUGAGUAAU
GUCUGGGAAACUGCCUGAUGGAGGGGGAUAACUACUGGAAACGGUAGCUAAUACCGCAUA
ACGUCGCAAGACCAAAGAGGGGGACCUUCGGGCCUCUUGCCAUCGGAUGUGCCCAGAUGG
GAUUAGCUAGUAGGUGGGGUAACGGCUCACCUAGGCGACGAUCCCUAGCUGGUCUGAGAG
GAUGACCAGCCACACUGGAACUGAGACACGGUCCAGACUCCUACGGGAGGCAGCAGUGGG
GAAUAUUGCACAAUGGGCGCAAGCCUGAUGCAGCCAUGCCGCGUGUAUGAAGAAGGCCUU
CGGGUUGUAAAGUACUUUCAGCGGGGAGGAAGGGAGUAAAGUUAAUACCUUUGCUCAUUG
ACGUUACCCGCAGAAGAAGCACCGGCUAACUCCGUGCCAGCAGCCGCGGUAAUACGGAGG
GUGCAAGCGUUAAUCGGAAUUACUGGGCGUAAAGCGCACGCAGGCGGUUUGUUAAGUCAG
AUGUGAAAUCCCCGGGCUCAACCUGGGAACUGCAUCUGAUACUGGCAAGCUUGAGUCUCG
UAGAGGGGGGUAGAAUUCCAGGUGUAGCGGUGAAAUGCGUAGAGAUCUGGAGGAAUACCG
GUGGCGAAGGCGGCCCCCUGGACGAAGACUGACGCUCAGGUGCGAAAGCGUGGGGAGCAA
ACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGAUGUCGACUUGGAGGUUGUGCCC
UUGAGGCGUGGCUUCCGGAGCUAACGCGUUAAGUCGACCGCCUGGGGAGUACGGCCGCAA
GGUUAAAACUCAAAUGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAUU
CGAUGCAACGCGAAGAACCUUACCUGGUCUUGACAUCCACGGAAGUUUUCAGAGAUGAGA
AUGUGCCUUCGGGAACCGUGAGACAGGUGCUGCAUGGCUGUCGUCAGCUCGUGUUGUGAA
AUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUAUCCUUUGUUGCCAGCGGUCCGGCC
GGGAACUCAAAGGAGACUGCCAGUGAUAAACUGGAGGAAGGUGGGGAUGACGUCAAGUCA
UCAUGGCCCUUACGACCAGGGCUACACACGUGCUACAAUGGCGCAUACAAAGAGAAGCGA
CCUCGCGAGAGCAAGCGGACCUCAUAAAGUGCGUCGUAGUCCGGAUUGGAGUCUGCAACU
CGACUCCAUGAAGUCGGAAUCGCUAGUAAUCGUGGAUCAGAAUGCCACGGUGAAUACGUU
CCCGGGCCUUGUACACACCGCCCGUCACACCAUGGGAGUGGGUUGCAAAAGAAGUAGGUA
GCUUAACCUUCGGGAGGGCGCUUACCACUUUGUGAUUCAUGACUGGGGUGAAGUCGUAAC
AAGGUAACCGUAGGGGAACCUGCGGUUGGAUCA

Sequence of entity 2 (AB), FASTA

>4V89_2 30S ribosomal protein S2 (chains AB)
MATVSMRDMLKAGVHFGHQTRYWNPKMKPFIFGARNKVHIINLEKTVPMFNEALAELNKI
ASRKGKILFVGTKRAASEAVKDAALSCDQFFVNHRWLGGMLTNWKTVRQSIKRLKDLETQ
SQDGTFDKLTKKEALMRTRELEKLENSLGGIKDMGGLPDALFVIDADHEHIAIKEANNLG
IPVFAIVDTNSDPDGVDFVIPGNDDAIRAVTLYLGAVAATVREGRSQDLASQAEESFVEA
E

Sequence of entity 3 (AC), FASTA

>4V89_3 30S ribosomal protein S3 (chains AC)
MGQKVHPNGIRLGIVKPWNSTWFANTKEFADNLDSDFKVRQYLTKELAKASVSRIVIERP
AKSIRVTIHTARPGIVIGKKGEDVEKLRKVVADIAGVPAQINIAEVRKPELDAKLVADSI
TSQLERRVMFRRAMKRAVQNAMRLGAKGIKVEVSGRLGGAEIARTEWYREGRVPLHTLRA
DIDYNTSEAHTTYGVIGVKVWIFKGEILGGMAAVEQPEKPAAQPKKQQRKGRK

Sequence of entity 4 (AD), FASTA

>4V89_4 30S ribosomal protein S4 (chains AD)
MARYLGPKLKLSRREGTDLFLKSGVRAIDTKCKIEQAPGQHGARKPRLSDYGVQLREKQK
VRRIYGVLERQFRNYYKEAARLKGNTGENLLALLEGRLDNVVYRMGFGATRAEARQLVSH
KAIMVNGRVVNIASYQVSPNDVVSIREKAKKQSRVKAALELAEQREKPTWLEVDAGKMEG
TFKRKPERSDLSADINEHLIVELYSK

Sequence of entity 5 (AE), FASTA

>4V89_5 30S ribosomal protein S5 (chains AE)
MAHIEKQAGELQEKLIAVNRVSKTVKGGRIFSFTALTVVGDGNGRVGFGYGKAREVPAAI
QKAMEKARRNMINVALNNGTLQHPVKGVHTGSRVFMQPASEGTGIIAGGAMRAVLEVAGV
HNVLAKAYGSTNPINVVRATIDGLENMNSPEMVAAKRGKSVEEILGK

Sequence of entity 6 (AF), FASTA

>4V89_6 30S ribosomal protein S6 (chains AF)
MRHYEIVFMVHPDQSEQVPGMIERYTAAITGAEGKIHRLEDWGRRQLAYPINKLHKAHYV
LMNVEAPQEVIDELETTFRFNDAVIRSMVMRTKHAVTEASPMVKAKDERRERRDDFANET
ADDAEAGDSEEEEEE

Sequence of entity 7 (AG), FASTA

>4V89_7 30S ribosomal protein S7 (chains AG)
MPRRRVIGQRKILPDPKFGSELLAKFVNILMVDGKKSTAESIVYSALETLAQRSGKSELE
AFEVALENVRPTVEVKSRRVGGSTYQVPVEVRPVRRNALAMRWIVEAARKRGDKSMALRL
ANELSDAAENKGTAVKKREDVHRMAEANKAFAHYRWLSLRSFSHQAGASSKQPALGYLN

Sequence of entity 8 (AH), FASTA

>4V89_8 30S ribosomal protein S8 (chains AH)
MSMQDPIADMLTRIRNGQAANKAAVTMPSSKLKVAIANVLKEEGFIEDFKVEGDTKPELE
LTLKYFQGKAVVESIQRVSRPGLRIYKRKDELPKVMAGLGIAVVSTSKGVMTDRAARQAG
LGGEIICYVA

Sequence of entity 9 (AI), FASTA

>4V89_9 30S ribosomal protein S9 (chains AI)
MAENQYYGTGRRKSSAARVFIKPGNGKIVINQRSLEQYFGRETARMVVRQPLELVDMVEK
LDLYITVKGGGISGQAGAIRHGITRALMEYDESLRSELRKAGFVTRDARQVERKKVGLRK
ARRRPQFSKR

Sequence of entity 10 (AJ), FASTA

>4V89_10 30S ribosomal protein S10 (chains AJ)
MQNQRIRIRLKAFDHRLIDQATAEIVETAKRTGAQVRGPIPLPTRKERFTVLISPHVNKD
ARDQYEIRTHLRLVDIVEPTEKTVDALMRLDLAAGVDVQISLG

Sequence of entity 11 (AK), FASTA

>4V89_11 30S ribosomal protein S11 (chains AK)
MAKAPIRARKRVRKQVSDGVAHIHASFNNTIVTITDRQGNALGWATAGGSGFRGSRKSTP
FAAQVAAERCADAVKEYGIKNLEVMVKGPGPGRESTIRALNAAGFRITNITDVTPIPHNG
CRPPKKRRV

Sequence of entity 12 (AL), FASTA

>4V89_12 30S ribosomal protein S12 (chains AL)
MATVNQLVRKPRARKVAKSNVPALEACPQKRGVCTRVYTTTPKKPNSALRKVCRVRLTNG
FEVTSYIGGEGHNLQEHSVILIRGGRVKDLPGVRYHTVRGALDCSGVKDRKQARSKYGVK
RPKA

Ligands and cofactors

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

Primary citation

Crystal structure of release factor RF3 trapped in the GTP state on a rotated conformation of the ribosome. Zhou, J., Lancaster, L., Trakhanov, S. et al. RNA (2012) 18:230-240. DOI 10.1261/rna.031187.111 · 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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