4V84: Complex containing domain 3 of CrPV IGR IRES RNA

Name: PDB 4V84: Crystal structure of a complex containing domain 3 of CrPV IGR IRES RNA bound to the 70S ribosome.
Published: 2014-07-09
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

Crystal structure of a complex containing domain 3 of CrPV IGR IRES RNA bound to the 70S ribosome. Determined by X-ray diffraction at 3.4 Å resolution. Released 9 Jul 2014.

Method: X-ray diffraction
Resolution: 3.4 Å
Organisms: Thermus thermophilus HB27, Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039), Thermus thermophilus
Chains: 106
Atoms: 282,142
Mol. weight: 4282.69 kDa
Ligands: ZN, MG
Released: 9 Jul 2014

Explore 4V84 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4V84 contains 410 α-helices and 642 β-strands across 98 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.

Chains AB and CB: 12 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	10-13	4
β-strand	32-34	3	9
α-helix	36-38	3
β-strand	41-42	2	9
α-helix	44-63	20
β-strand	69-71	3	10
α-helix	77-82	6
α-helix	105-112	8
α-helix	116-120	5
α-helix	132-149	18
β-strand	162-164	3	10
α-helix	171-179	9
β-strand	184-188	5	10
α-helix	194-196	3
β-strand	199-202	4	10
α-helix	208-223	16
α-helix	230-233	4
α-helix	236-239	4

Chains AC and CC: 9 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	7-10	4
β-strand	20	1	16
α-helix	29-45	17
α-helix	48-50	3
β-strand	52-55	4	17
β-strand	57	1	16
β-strand	59	1	18
β-strand	63	1	19
β-strand	64	1	18
β-strand	68	1	17
β-strand	69	1	20
β-strand	70	1	17
α-helix	73-75	3
α-helix	84-94	11
β-strand	98	1	19
β-strand	104	1	20
α-helix	109-111	3
α-helix	113-125	13
α-helix	132-144	13
β-strand	148-154	7	21
β-strand	165-170	6	21
α-helix	182	1
β-strand	183-184	2	21
β-strand	187	1	21
β-strand	191	1	22
β-strand	194	1	22
β-strand	197-203	7	21

Chain AD: 10 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	12-15	4
α-helix	24-27	4
α-helix	53-66	14
α-helix	72-84	13
α-helix	89-99	11
β-strand	100	1	31
α-helix	101-107	7
α-helix	114-122	9
β-strand	126	1	32
β-strand	128	1	33
β-strand	131	1	33
β-strand	139	1	31
α-helix	140-141	2
β-strand	148	1	32
α-helix	156-162	7
β-strand	174-177	4	34
β-strand	182-185	4	34
α-helix	200-206	7

Chain AE: 4 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	7-14	8	51
β-strand	17-20	4	52
β-strand	23-26	4	52
β-strand	28-35	8	51
β-strand	40-41	2	51
β-strand	44-48	5	51
α-helix	51-64	14
β-strand	67-68	2	51
β-strand	80-84	5	53
β-strand	87-93	7	53
β-strand	100-101	2	53
α-helix	104-111	8
β-strand	118-124	7	53
α-helix	128-139	12
α-helix	145-152	8

Chains AF and CF: 2 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	3-10	8	63
α-helix	16-32	17
β-strand	37	1	63
β-strand	47	1	64
β-strand	57	1	64
β-strand	59-66	8	63
α-helix	71-79	9
β-strand	85	1	63
β-strand	89	1	63
β-strand	92	1	63
β-strand	98-99	2	65

Chains AG and CG: 8 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	21-30	10
α-helix	36-53	18
α-helix	58-66	9
β-strand	73-79	7	72
β-strand	84-90	7	72
α-helix	91-92	2
α-helix	93-110	18
α-helix	116-129	14
α-helix	136-147	12
α-helix	149-152	4

Chain AH: 4 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	5-19	15
β-strand	23-24	2	83
α-helix	30-41	12
β-strand	45-49	5	83
β-strand	52-53	2	84
β-strand	56-57	2	84
β-strand	60-63	4	83
β-strand	83-85	3	85
β-strand	88	1	86
β-strand	91	1	86
β-strand	95	1	87
α-helix	97-99	3
β-strand	109-111	3	85
β-strand	114	1	88
β-strand	117	1	88
β-strand	120	1	85
α-helix	121-127	7
β-strand	131	1	87
β-strand	135-137	3	85

Chains AI and CI: 6 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	4-8	5	97
β-strand	15-19	5	97
β-strand	21	1	98
β-strand	28	1	97
α-helix	33-36	4
α-helix	43-46	4
α-helix	48-52	5
α-helix	56-58	3
β-strand	59	1	98
β-strand	62-65	4	97
α-helix	70-87	18
α-helix	111-113	3

61 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
ribosomal RNA 16S	AA, CA	RNA	1506	Thermus thermophilus HB27
30S ribosomal protein S2	AB, CB	protein	234	Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)	P62662 (AlphaFold model)
30S ribosomal protein S3	AC, CC	protein	206	Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)	P62663 (AlphaFold model)
30S ribosomal protein S4	AD, CD	protein	208	Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)	P62664 (AlphaFold model)
30S ribosomal protein S5	AE, CE	protein	151	Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)	P62665 (AlphaFold model)
30S ribosomal protein S6	AF, CF	protein	101	Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)	P62666
30S ribosomal protein S7	AG, CG	protein	155	Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)	P62667
30S ribosomal protein S8	AH, CH	protein	138	Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)	P62668
30S ribosomal protein S9	AI, CI	protein	127	Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)	P62669
30S ribosomal protein S10	AJ, CJ	protein	98	Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)	P62653
30S ribosomal protein S11	AK, CK	protein	119	Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)	P62654
30S ribosomal protein S12	AL, CL	protein	124	Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)	P61941

41 more molecules are not listed.

Sequence of entity 1 (AA, CA), FASTA

>4V84_1 ribosomal RNA 16S (chains AA, CA)
UGGAGAGUUUGAUCCUGGCUCAGGGUGAACGCUGGCGGCGUGCCUAAGACAUGCAAGUCG
UGCGGGCCGCGGGGUUUUACUCCGUGGUCAGCGGCGGACGGGUGAGUAACGCGUGGGUGA
CCUACCCGGAAGAGGGGGACAACCCGGGGAAACUCGGGCUAAUCCCCCAUGUGGACCCGC
CCCUUGGGGUGUGUCCAAAGGGCUUUGCCCGCUUCCGGAUGGGCCCGCGUCCCAUCAGCU
AGUUGGUGGGGUAAUGGCCCACCAAGGCGACGACGGGUAGCCGGUCUGAGAGGAUGGCCG
GCCACAGGGGCACUGAGACACGGGCCCCACUCCUACGGGAGGCAGCAGUUAGGAAUCUUC
CGCAAUGGGCGCAAGCCUGACGGAGCGACGCCGCUUGGAGGAAGAAGCCCUUCGGGGUGU
AAACUCCUGAACCCGGGACGAAACCCCCGAGGAGGGGACUGACGGUACCGGGGUAAUAGC
GCCGGCCAACUCCGUGCCAGCAGCCGCGGUAAUACGGAGGGCGCGAGCGUUACCCGGAUU
CACUGGGCGUAAAGGGCGUGUAGGCGGCCUGGGGCGUCCCAUGUGAAAGACCACGGCUCA
ACCGUGGGGGAGCGUGGGAUACGCUCAGGCUAGACGGUGGGAGAGGGUGGUGGAAUUCCC
GGAGUAGCGGUGAAAUGCGCAGAUACCGGGAGGAACGCCGAUGGCGAAGGCAGCCACCUG
GUCCACCCGUGACGCUGAGGCGCGAAAGCGUGGGGAGCAAACCGGAUUAGAUACCCGGGU
AGUCCACGCCCUAAACGAUGCGCGCUAGGUCUCUGGGUCUCCUGGGGGCCGAAGCUAACG
CGUUAAGCGCGCCGCCUGGGGAGUACGGCCGCAAGGCUGAAACUCAAAGGAAUUGACGGG
GGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGAAGCAACGCGAAGAACCUUACCAG
GCCUUGACAUGCUAGGGAACCCGGGUGAAAGCCUGGGGUGCCCCGCGAGGGGAGCCCUAG
CACAGGUGCUGCAUGGCCGUCGUCAGCUCGUGCCGUGAGGUGUUGGGUUAAGUCCCGCAA
CGAGCGCAACCCCCGCCGUUAGUUGCCAGCGGUUCGGCCGGGCACUCUAACGGGACUGCC
CGCGAAAGCGGGAGGAAGGAGGGGACGACGUCUGGUCAGCAUGGCCCUUACGGCCUGGGC
GACACACGUGCUACAAUGCCCACUACAAAGCGAUGCCACCCGGCAACGGGGAGCUAAUCG
CAAAAAGGUGGGCCCAGUUCGGAUUGGGGUCUGCAACCCGACCCCAUGAAGCCGGAAUCG
CUAGUAAUCGCGGAUCAGCCAUGCCGCGGUGAAUACGUUCCCGGGCCUUGUACACACCGC
CCGUCACGCCAUGGGAGCGGGCUCUACCCGAAGUCGCCGGGAGCCUACGGGCAGGCGCCG
AGGGUAGGGCCCGUGACUGGGGCGAAGUCGUAACAAGGUAGCUGUACCGGAAGGUGCGGC
UGGAUC

Sequence of entity 2 (AB, CB), FASTA

>4V84_2 30S ribosomal protein S2 (chains AB, CB)
VKELLEAGVHFGHERKRWNPKFARYIYAERNGIHIIDLQKTMEELERTFRFIEDLAMRGG
TILFVGTKKQAQDIVRMEAERAGMPYVNQRWLGGMLTNFKTISQRVHRLEELEALFASPE
IEERPKKEQVRLKHELERLQKYLSGFRLLKRLPDAIFVVDPTKEAIAVREARKLFIPVIA
LADTDSDPDLVDYIIPGNDDAIRSIQLILSRAVDLIIQARGGVVEPSPSYALVQ

Sequence of entity 3 (AC, CC), FASTA

>4V84_3 30S ribosomal protein S3 (chains AC, CC)
GNKIHPIGFRLGITRDWESRWYAGKKQYRHLLLEDQRIRGLLEKELYSAGLARVDIERAA
DNVAVTVHVAKPGVVIGRGGERIRVLREELAKLTGKNVALNVQEVQNPNLSAPLVAQRVA
EQIERRFAVRRAIKQAVQRVMESGAKGAKVIVSGRIGGAEQARTEWAAQGRVPLHTLRAN
IDYGFALARTTYGVLGVKAYIFLGEV

Sequence of entity 4 (AD, CD), FASTA

>4V84_4 30S ribosomal protein S4 (chains AD, CD)
GRYIGPVCRLCRREGVKLYLKGERCYSPKCAMERRPYPPGQHGQKRARRPSDYAVRLREK
QKLRRIYGISERQFRNLFEEASKKKGVTGSVFLGLLESRLDNVVYRLGFAVSRRQARQLV
RHGHITVNGRRVDLPSYRVRPGDEIAVAEKSRNLELIRQNLEAMKGRKVGPWLSLDVEGM
KGKFLRLPDREDLALPVNEQLVIEFYSR

Sequence of entity 5 (AE, CE), FASTA

>4V84_5 30S ribosomal protein S5 (chains AE, CE)
DFEEKMILIRRTARMQAGGRRFRFGALVVVGDRQGRVGLGFGKAPEVPLAVQKAGYYARR
NMVEVPLQNGTIPHEIEVEFGASKIVLKPAAPGTGVIAGAVPRAILELAGVTDILTKELG
SRNPINIAYATMEALRQLRTKADVERLRKGE

Sequence of entity 6 (AF, CF), FASTA

>4V84_6 30S ribosomal protein S6 (chains AF, CF)
MRRYEVNIVLNPNLDQSQLALEKEIIQRALENYGARVEKVEELGLRRLAYPIAKDPQGYF
LWYQVEMPEDRVNDLARELRIRDNVRRVMVVKSQEPFLANA

Sequence of entity 7 (AG, CG), FASTA

>4V84_7 30S ribosomal protein S7 (chains AG, CG)
ARRRRAEVRQLQPDLVYGDVLVTAFINKIMRDGKKNLAARIFYDACKIIQEKTGQEPLKV
FKQAVENVKPRMEVRSRRVGGANYQVPMEVSPRRQQSLALRWLVQAANQRPERRAAVRIA
HELMDAAEGKGGAVKKKEDVERMAEANRAYAHYRW

Sequence of entity 8 (AH, CH), FASTA

>4V84_8 30S ribosomal protein S8 (chains AH, CH)
MLTDPIADMLTRIRNATRVYKESTDVPASRFKEEILRILAREGFIKGYERVDVDGKPYLR
VYLKYGPRRQGPDPRPEQVIHHIRRISKPGRRVYVGVKEIPRVRRGLGIAILSTSKGVLT
DREARKLGVGGELICEVW

Sequence of entity 9 (AI, CI), FASTA

>4V84_9 30S ribosomal protein S9 (chains AI, CI)
EQYYGTGRRKEAVARVFLRPGNGKVTVNGQDFNEYFQGLVRAVAALEPLRAVDALGRFDA
YITVRGGGKSGQIDAIKLGIARALVQYNPDYRAKLKPLGFLTRDARVVERKKYGKHKARR
APQYSKR

Sequence of entity 10 (AJ, CJ), FASTA

>4V84_10 30S ribosomal protein S10 (chains AJ, CJ)
KIRIKLRGFDHKTLDASAQKIVEAARRSGAQVSGPIPLPTRVRRFTVIRGPFKHKDSREH
FELRTHNRLVDIINPNRKTIEQLMTLDLPTGVEIEIKT

Sequence of entity 11 (AK, CK), FASTA

>4V84_11 30S ribosomal protein S11 (chains AK, CK)
KRQVASGRAYIHASYNNTIVTITDPDGNPITWSSGGVIGYKGSRKGTPYAAQLAALDAAK
KAMAYGMQSVDVIVRGTGAGREQAIRALQASGLQVKSIVDDTPVPHNGCRPKKKFRKAS

Sequence of entity 12 (AL, CL), FASTA

>4V84_12 30S ribosomal protein S12 (chains AL, CL)
PTINQLVRKGREKVRKKSKVPALKGAPFRRGVCTVVRTVTPKKPNSALRKVAKVRLTSGY
EVTAYIPGEGHNLQEHSVVLIRGGRVKDLPGVRYHIVRGVYDAAGVKDRKKSRSKYGTKK
PKEA

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	4
MG	Magnesium ion	Mg	1194

Primary citation

Crystal structures of complexes containing domains from two viral internal ribosome entry site (IRES) RNAs bound to the 70S ribosome. Zhu, J., Korostelev, A., Costantino, D.A. et al. Proc Natl Acad Sci U S A (2011) 108:1839-1844. DOI 10.1073/pnas.1018582108 · PubMed

Other PDB entries of the same protein (UniProt P62662 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5J4D 3.1 Å, E. coli release factor 1 bound to the 70S ribosome in response to a pseudouridylated…
6N1D 3.2 Å, X-ray Crystal complex showing Spontaneous Ribosomal Translocation of mRNA and tRNAs into…
4V63 3.21 Å, Structural basis for translation termination on the 70S ribosome.
5V8I 3.25 Å, Thermus thermophilus 70S ribosome lacking ribosomal protein uS17
4V9N 3.4 Å, Crystal structure of the 70S ribosome bound with the Q253P mutant of release factor RF2.
4V9Q 3.4 Å, Crystal Structure of Blasticidin S Bound to Thermus Thermophilus 70S Ribosome.
6B4V 3.4 Å, Antibiotic blasticidin S and E. coli release factor 1 bound to the 70S ribosome
6BOH 3.4 Å, Antibiotic blasticidin S and E. coli release factor 1 (containing deletion 302-304)…
4V83 3.5 Å, Crystal structure of a complex containing domain 3 from the PSIV IGR IRES RNA bound to…
4V9K 3.5 Å, 70S ribosome translocation intermediate GDPNP-I containing elongation factor EFG/GDPNP,…
4V9L 3.5 Å, 70S Ribosome translocation intermediate FA-3.6A containing elongation factor EFG/FUSIDIC…
6BOK 3.55 Å, E. coli release factor 1 (containing deletion 302-304) bound to the 70S ribosome

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