4V4A: Wild Type Ribosome from E. Coli 70S Ribosome

Name: PDB 4V4A: Crystal Structure of the Wild Type Ribosome from E. Coli 70S Ribosome.
Published: 2014-07-09
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

Crystal Structure of the Wild Type Ribosome from E. Coli 70S Ribosome. Determined by X-ray diffraction at 9.5 Å resolution. Released 9 Jul 2014.

Method: X-ray diffraction
Resolution: 9.5 Å
Organism: Escherichia coli
Chains: 53
Atoms: 118,711
Mol. weight: 2141.52 kDa
Released: 9 Jul 2014

Explore 4V4A in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4V4A contains 103 α-helices and 108 β-strands across 19 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	12-14	3
α-helix	26-31	6
β-strand	32-36	5	1
β-strand	39-42	4	1
α-helix	44-62	19
β-strand	69-71	3	2
α-helix	75-86	12
β-strand	92-93	2	2
α-helix	105-121	17
α-helix	126-128	3
α-helix	134-148	15
β-strand	162-164	3	2
α-helix	171-180	10
β-strand	184-188	5	2
α-helix	194-196	3
β-strand	199-202	4	2
α-helix	208-224	17
α-helix	236-239	4

Chain AC: 8 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	7-11	5
α-helix	29-46	18
β-strand	52-56	5	3
β-strand	67-70	4	3
α-helix	73-77	5
α-helix	83-92	10
β-strand	102-105	4	3
α-helix	109-111	3
α-helix	113-126	14
α-helix	130-142	13
β-strand	148-153	6	4
α-helix	157-159	3
β-strand	166	1	4
β-strand	169-170	2	4
β-strand	182-187	6	4
β-strand	198-203	6	4

Chain AD: 15 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	9-14	6
α-helix	39	1
α-helix	47-49	3
α-helix	53-67	15
α-helix	72-84	13
α-helix	89-98	10
β-strand	100	1	5
α-helix	101-107	7
α-helix	114-122	9
β-strand	126	1	6
β-strand	127	1	7
β-strand	132	1	7
β-strand	139	1	5
β-strand	145	1	8
α-helix	147	1
β-strand	148	1	6
α-helix	149	1
α-helix	150-153	4
α-helix	156-164	9
β-strand	176-177	2	9
β-strand	182-183	2	9
β-strand	184	1	8
α-helix	188-190	3
α-helix	191-193	3
α-helix	200-206	7

Chain AE: 4 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	7-14	8	10
β-strand	19-20	2	11
β-strand	23-24	2	11
β-strand	28-35	8	10
β-strand	40-48	9	10
α-helix	51-63	13
β-strand	66-68	3	10
β-strand	72	1	12
β-strand	75	1	12
β-strand	80-84	5	13
β-strand	87-93	7	13
β-strand	100-101	2	13
α-helix	104-112	9
β-strand	118-124	7	13
α-helix	128-141	14
α-helix	145-151	7

Chain AF: 2 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-3	2	14
β-strand	4-10	7	15
α-helix	16-33	18
β-strand	39-52	14	15
β-strand	55-64	10	15
β-strand	66-67	2	14
α-helix	69-81	13
β-strand	85-92	8	15
β-strand	98-99	2	16

Chain AG: 8 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	8-15	8
α-helix	21-30	10
α-helix	36-52	17
α-helix	58-69	12
β-strand	73-76	4	17
β-strand	79	1	18
β-strand	84	1	18
β-strand	87-90	4	17
α-helix	93-108	16
α-helix	116-129	14
α-helix	133-144	12
α-helix	151-154	4

Chain AH: 5 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	5-18	14
β-strand	25-27	3	19
α-helix	30-41	12
β-strand	47-53	7	19
β-strand	56-62	7	19
β-strand	65	1	20
α-helix	75-77	3
β-strand	78	1	20
β-strand	83-85	3	21
β-strand	94-95	2	21
α-helix	103-106	4
β-strand	109-114	6	21
β-strand	117-120	4	21
α-helix	121-126	6
β-strand	131-137	7	21

Chain AI: 8 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	22
β-strand	9	1	22
β-strand	14-19	6	22
β-strand	26-28	3	22
β-strand	32	1	22
α-helix	33-36	4
α-helix	43-45	3
α-helix	48-52	5
β-strand	61-66	6	22
α-helix	70-88	19
α-helix	90-92	3
α-helix	93-96	4
α-helix	109-111	3
α-helix	122-124	3

11 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
16S ribosomal RNA	AA	RNA	1537	Escherichia coli
30S ribosomal protein S2	AB	protein	234	Escherichia coli
30S ribosomal protein S3	AC	protein	206	Escherichia coli
30S ribosomal protein S4	AD	protein	208	Escherichia coli
30S ribosomal protein S5	AE	protein	150	Escherichia coli
30S ribosomal protein S6	AF	protein	101	Escherichia coli
30S ribosomal protein S7	AG	protein	155	Escherichia coli
30S ribosomal protein S8	AH	protein	138	Escherichia coli
30S ribosomal protein S9	AI	protein	127	Escherichia coli
30S ribosomal protein S10	AJ	protein	98	Escherichia coli
30S ribosomal protein S11	AK	protein	119	Escherichia coli
30S ribosomal protein S12	AL	protein	124	Escherichia coli

41 more molecules are not listed.

Sequence of entity 1 (AA), FASTA

>4V4A_1 16S RIBOSOMAL RNA (chains AA)
UGGAGAGUUUGAUCCUGGCUCAGGGUGAACGCUGGCGGCGUGCCUAAGACAUGCAAGUCG
UGCGGAUACGCGCGGCCCCUUGGGGCCGUGCGUCAGCGGCGGACGGGUGAGUAACGCGUG
GGUGACCUACCCGGAAGAGGGGGACAACCCGGGGAAACUCGGGCUAAUCCCCCAUGUGGA
CGCAAGUCCAAAGGGGGAAGCCUUCGGGUCCCCCGCUUCCGGAUGGGCCCGCGUCCCAUC
AGCUAGUUGGUGGGGUAAUGGCCCACCAAGGCGACGACGGGUAGCCGGUCUGAGAGGAUG
GCCGGCCACAGGGGCACUGAGACACGGGCCCCACUCCUACGGGAGGCAGCAGUUAGGAAU
CUUCCGCAAUGGGCGCAAGCCUGACGGAGCGACGCCGCUUGGAGGAAGAAGCCCUUCGGG
GUGUAAACUCCUGAACCCGGGACGAAACCAGGGCCACUCAUACUGGCUCUGACUGACGGU
ACCGGGGUAAUAGCGCCGGCCAACUCCGUGCCAGCAGCCGCGGUAAUACGGAGGGCGCGA
GCGUUACCCGGAUUCACUGGGCGUAAAGGGCGUGUAGGCGGCCUGGGGCGUCCCAUGUGA
AAGACCACGGCUCAACCGUGGGGGAGCGUGGGAUACGCUCAGGCUAGACGGUGGGAGAGG
GUGGUGGAAUUCCCGGAGUAGCGGUGAAAUGCGCAGAUACCGGGAGGAACGCCGAUGGCG
AAGGCAGCCACCUGGUCCACCCGUGACGCUGAGGCGCGAAAGCGUGGGGAGCAAACCGGA
UUAGAUACCCGGGUAGUCCACGCCCUAAACGAUGCGCGCUAGGUCUCUGGCGGCUCAACC
GCUGGGGGCCGAAGCUAACGCGUUAAGCGCGCCGCCUGGGGAGUACGGCCGCAAGGCUGA
AACUCAAAGGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGAAGC
AACGCGAAGAACCUUACCAGGCCUUGACAUGCUAGGGAACCCGGGUGAAAGCCUGGGGUG
CCUUCGGGAGCCCUAGCACAGGUGCUGCAUGGCCGUCGUCAGCUCGUGCCGUGAGGUGUU
GGGUUAAGUCCCGCAACGAGCGCAACCCCCGCCGUUAGUUGCCAGCGGUUCGGCCGGGCA
CUCUAACGGGACUGCCCGCGAAAGCGGGAGGAAGGAGGGGACGACGUCUGGUCAGCAUGG
CCCUUACGGCCUGGGCGACACACGUGCUACAAUGCCCACUACAAAGCGAUGCCACCCGGC
AACGGGGAGCUAAUCGCAAAAAGGUGGGCCCAGUUCGGAUUGGGGUCUGCAACCCGACCC
CAUGAAGCCGGAAUCGCUAGUAAUCGCGGAUCAGCCAUGCCGCGGUGAAUACGUUCCCGG
GCCUUGUACACACCGCCCGUCACGCCAUGGGAGCGGGCUCUACCCGAAGUCGCCGGGUAA
CCUACGGGAAGCAGGCGCCGAGGGUAGGGCCCGUGACUGGGGCGAAGUCGUAACAAGGUA
GCUGUACCGGAAGGUGCGGCUGGAUCACCUCCUUUCU

Sequence of entity 2 (AB), FASTA

>4V4A_2 30S ribosomal protein S2 (chains AB)
VKELLEAGVHFGHERKRWNPKFARYIYAERNGIHIIDLQKTMEELERTFRFIEDLAMRGG
TILFVGTKKQAQDIVRMEAERAGMPYVNQRWLGGMLTNFKTISQRVHRLEELEALFASPE
IEERPKKEQVRLKHELERLQKYLSGFRLLKRLPDAIFVVDPTKEAIAVREARKLFIPVIA
LADTDSDPDLVDYIIPGNDDAIRSIQLILSRAVDLIIQARGGVVEPSPSYALVQ

Sequence of entity 3 (AC), FASTA

>4V4A_3 30S ribosomal protein S3 (chains AC)
GNKIHPIGFRLGITRDWESRWYAGKKQYRHLLLEDQRIRGLLEKELYSAGLARVDIERAA
DNVAVTVHVAKPGVVIGRGGERIRVLREELAKLTGKNVALNVQEVQNPNLSAPLVAQRVA
EQIERRFAVRRAIKQAVQRVMESGAKGAKVIVSGRIGGAEQARTEWAAQGRVPLHTLRAN
IDYGFALARTTYGVLGVKAYIFLGEV

Sequence of entity 4 (AD), FASTA

>4V4A_4 30S ribosomal protein S4 (chains AD)
GRYIGPVCRLCRREGVKLYLKGERCYSPKCAMERRPYPPGQHGQKRARRPSDYAVRLREK
QKLRRIYGISERQFRNLFEEASKKKGVTGSVFLGLLESRLDNVVYRLGFAVSRRQARQLV
RHGHITVNGRRVDLPSYRVRPGDEIAVAEKSRNLELIRQNLEAMKGRKVGPWLSLDVEGM
KGKFLRLPDREDLALPVNEQLVIEFYSR

Sequence of entity 5 (AE), FASTA

>4V4A_5 30S ribosomal protein S5 (chains AE)
DFEEKMILIRRTARMQAGGRRFRFGALVVVGDRQGRVGLGFGKAPEVPLAVQKAGYYARR
NMVEVPLQNGTIPHEIEVEFGASKIVLKPAAPGTGVIAGAVPRAILELAGVTDILTKELG
SRNPINIAYATMEALRQLRTKADVERLRKG

Sequence of entity 6 (AF), FASTA

>4V4A_6 30S ribosomal protein S6 (chains AF)
MRRYEVNIVLNPNLDQSQLALEKEIIQRALENYGARVEKVEELGLRRLAYPIAKDPQGYF
LWYQVEMPEDRVNDLARELRIRDNVRRVMVVKSQEPFLANA

Sequence of entity 7 (AG), FASTA

>4V4A_7 30S ribosomal protein S7 (chains AG)
ARRRRAEVRQLQPDLVYGDVLVTAFINKIMRDGKKNLAARIFYDACKIIQEKTGQEPLKV
FKQAVENVKPRMEVRSRRVGGANYQVPMEVSPRRQQSLALRWLVQAANQRPERRAAVRIA
HELMDAAEGKGGAVKKKEDVERMAEANRAYAHYRW

Sequence of entity 8 (AH), FASTA

>4V4A_8 30S ribosomal protein S8 (chains AH)
MLTDPIADMLTRIRNATRVYKESTDVPASRFKEEILRILAREGFIKGYERVDVDGKPYLR
VYLKYGPRRQGPDPRPEQVIHHIRRISKPGRRVYVGVKEIPRVRRGLGIAILSTSKGVLT
DREARKLGVGGELICEVW

Sequence of entity 9 (AI), FASTA

>4V4A_9 30S ribosomal protein S9 (chains AI)
EQYYGTGRRKEAVARVFLRPGNGKVTVNGQDFNEYFQGLVRAVAALEPLRAVDALGRFDA
YITVRGGGKSGQIDAIKLGIARALVQYNPDYRAKLKPLGFLTRDARVVERKKYGKHKARR
APQYSKR

Sequence of entity 10 (AJ), FASTA

>4V4A_10 30S ribosomal protein S10 (chains AJ)
KIRIKLRGFDHKTLDASAQKIVEAARRSGAQVSGPIPLPTRVRRFTVIRGPFKHKDSREH
FELRTHNRLVDIINPNRKTIEQLMTLDLPTGVEIEIKT

Sequence of entity 11 (AK), FASTA

>4V4A_11 30S ribosomal protein S11 (chains AK)
KRQVASGRAYIHASYNNTIVTITDPDGNPITWSSGGVIGYKGSRKGTPYAAQLAALDAAK
KAMAYGMQSVDVIVRGTGAGREQAIRALQASGLQVKSIVDDTPVPHNGCRPKKKFRKAS

Sequence of entity 12 (AL), FASTA

>4V4A_12 30S ribosomal protein S12 (chains AL)
PTINQLVRKGREKVRKKSKVPALKGAPFRRGVCTVVRTVTPKKPNSALRKVAKVRLTSGY
EVTAYIPGEGHNLQEHSVVLIRGGRVKDLPGVRYHIVRGVYDAAGVKDRKKSRSKYGTKK
PKEA

Primary citation

X-ray crystal structures of the WT and a hyper-accurate ribosome from Escherichia coli. Vila-Sanjurjo, A., Ridgeway, W.K., Seymaner, V. et al. Proc Natl Acad Sci U S A (2003) 100:8682-8687. DOI 10.1073/pnas.1133380100 · PubMed

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