5V8I image
Deposition Date 2017-03-22
Release Date 2018-03-28
Last Version Date 2025-03-19
Entry Detail
PDB ID:
5V8I
Keywords:
RIBOSOME
Title:
Thermus thermophilus 70S ribosome lacking ribosomal protein uS17
Biological Source:
Source Organism:
Escherichia coli (strain K12) (Taxon ID: 83333)
Thermus thermophilus HB27 (Taxon ID: 262724)
Host Organism:
Escherichia coli
Method Details:
Experimental Method:
X-RAY DIFFRACTION
Resolution:
3.25 Å
R-Value Free:
0.27
R-Value Work:
0.22
R-Value Observed:
0.22
Space Group:
P 21 21 21
5V8I validation report
Macromolecular Entities
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L27
Gene (Uniprot):rpmA
Chain IDs:V (auth: 10), VB (auth: 20)
Chain Length:85
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
UniProt ID:Q72HR3 Pfam ID:PF01016
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L28
Gene (Uniprot):rpmB
Chain IDs:W (auth: 11), WB (auth: 21)
Chain Length:98
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
UniProt ID:Q72G84 Pfam ID:PF00830
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L29
Gene (Uniprot):rpmC
Chain IDs:X (auth: 12), XB (auth: 22)
Chain Length:72
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
UniProt ID:Q72I12 Pfam ID:PF00831
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L30
Gene (Uniprot):rpmD
Chain IDs:Y (auth: 13), YB (auth: 23)
Chain Length:60
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
UniProt ID:Q72I22 Pfam ID:PF00327
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L31
Gene (Uniprot):rpmE
Chain IDs:Z (auth: 14), ZB (auth: 24)
Chain Length:71
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
UniProt ID:Q72JR0 Pfam ID:PF01197
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L32
Gene (Uniprot):rpmF
Chain IDs:AA (auth: 15), AC (auth: 25)
Chain Length:60
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
UniProt ID:P62652 Pfam ID:PF01783
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L33
Gene (Uniprot):rpmG
Chain IDs:BA (auth: 16), BC (auth: 26)
Chain Length:54
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
UniProt ID:Q72GW3 Pfam ID:PF00471
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L34
Gene (Uniprot):rpmH
Chain IDs:CA (auth: 17), CC (auth: 27)
Chain Length:49
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB27/ATCC BAA-163 / DSM 7039)
UniProt ID:P80340 Pfam ID:PF00468
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L35
Gene (Uniprot):rpmI
Chain IDs:DA (auth: 18), DC (auth: 28)
Chain Length:65
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
UniProt ID:Q72L77 Pfam ID:PF01632
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L36
Gene (Uniprot):rpmJ
Chain IDs:EA (auth: 19), EC (auth: 29)
Chain Length:37
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
UniProt ID:Q72I28 Pfam ID:PF00444
Polymer Type:polyribonucleotide
Molecule:23S Ribosomal RNA
Chain IDs:A (auth: 1A), AB (auth: 2A)
Chain Length:1522
Number of Molecules:2
Biological Source:Thermus thermophilus HB27
Polymer Type:polyribonucleotide
Molecule:5S Ribosomal RNA
Chain IDs:B (auth: 1B), BB (auth: 2B)
Chain Length:256
Number of Molecules:2
Biological Source:Thermus thermophilus HB27
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L2
Gene (Uniprot):rplB
Chain IDs:C (auth: 1D), CB (auth: 2D)
Chain Length:276
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
UniProt ID:Q72I07 Pfam ID:PF00181, PF03947
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L3
Gene (Uniprot):rplC
Chain IDs:D (auth: 1E), DB (auth: 2E)
Chain Length:162
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
UniProt ID:Q72I04 Pfam ID:PF00297
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L4
Chain IDs:E (auth: 1F), EB (auth: 2F)
Chain Length:101
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
UniProt ID:Q72I05 Pfam ID:PF00573
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L5
Gene (Uniprot):rplE
Chain IDs:F (auth: 1G), FB (auth: 2G)
Chain Length:182
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
UniProt ID:Q72I16 Pfam ID:PF00281, PF00673
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L6
Gene (Uniprot):rplF
Chain IDs:G (auth: 1H), GB (auth: 2H)
Chain Length:180
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
UniProt ID:Q72I19 Pfam ID:PF00347
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L9
Gene (Uniprot):rplI
Chain IDs:H (auth: 1I), HB (auth: 2I)
Chain Length:148
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
UniProt ID:Q72GV5 Pfam ID:PF01281, PF03948
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L13
Gene (Uniprot):rplM
Chain IDs:I (auth: 1N), IB (auth: 2N)
Chain Length:140
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
UniProt ID:Q72IN1 Pfam ID:PF00572
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L14
Gene (Uniprot):rplN
Chain IDs:J (auth: 1O), JB (auth: 2O)
Chain Length:122
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
UniProt ID:Q72I14 Pfam ID:PF00238
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L15
Gene (Uniprot):rplO
Chain IDs:K (auth: 1P), KB (auth: 2P)
Chain Length:88
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
UniProt ID:Q72I23 Pfam ID:PF00828
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L16
Gene (Uniprot):rplP
Chain IDs:L (auth: 1Q), LB (auth: 2Q)
Chain Length:141
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
UniProt ID:Q72I11 Pfam ID:PF00252
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L17
Gene (Uniprot):rplQ
Chain IDs:M (auth: 1R), MB (auth: 2R)
Chain Length:118
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
UniProt ID:Q72I33 Pfam ID:PF01196
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L18
Gene (Uniprot):rplR
Chain IDs:N (auth: 1S), NB (auth: 2S)
Chain Length:112
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
UniProt ID:Q72I20 Pfam ID:PF00861
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L19
Gene (Uniprot):rplS
Chain IDs:O (auth: 1T), OB (auth: 2T)
Chain Length:146
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
UniProt ID:Q72JU9 Pfam ID:PF01245
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L20
Gene (Uniprot):rplT
Chain IDs:P (auth: 1U), PB (auth: 2U)
Chain Length:118
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
UniProt ID:Q72L76 Pfam ID:PF00453
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L21
Gene (Uniprot):rplU
Chain IDs:Q (auth: 1V), QB (auth: 2V)
Chain Length:101
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
UniProt ID:Q72HR2 Pfam ID:PF00829
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L22
Gene (Uniprot):rplV
Chain IDs:R (auth: 1W), RB (auth: 2W)
Chain Length:113
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
UniProt ID:Q72I09 Pfam ID:PF00237
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L23
Gene (Uniprot):rplW
Chain IDs:S (auth: 1X), SB (auth: 2X)
Chain Length:96
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
UniProt ID:Q72I06 Pfam ID:PF00276
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L24
Gene (Uniprot):rplX
Chain IDs:T (auth: 1Y), TB (auth: 2Y)
Chain Length:110
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
UniProt ID:Q72I15 Pfam ID:PF00467, PF17136
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L25
Gene (Uniprot):rplY
Chain IDs:U (auth: 1Z), UB (auth: 2Z)
Chain Length:206
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
UniProt ID:Q72IA7 Pfam ID:PF01386, PF14693
Polymer Type:polyribonucleotide
Molecule:16S Ribosomal RNA
Chain IDs:FA (auth: 1a), FC (auth: 2a)
Chain Length:1522
Number of Molecules:2
Biological Source:Thermus thermophilus HB27
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S2
Gene (Uniprot):rpsB
Chain IDs:GA (auth: 1b), GC (auth: 2b)
Chain Length:256
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
UniProt ID:P62662 Pfam ID:PF00318
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S3
Gene (Uniprot):rpsC
Chain IDs:HA (auth: 1c), HC (auth: 2c)
Chain Length:239
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
UniProt ID:P62663 Pfam ID:PF07650, PF00189
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S4
Gene (Uniprot):rpsD
Chain IDs:IA (auth: 1d), IC (auth: 2d)
Chain Length:276
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
UniProt ID:P62664 Pfam ID:PF00163, PF01479
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S5
Gene (Uniprot):rpsE
Chain IDs:JA (auth: 1e), JC (auth: 2e)
Chain Length:162
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
UniProt ID:P62665 Pfam ID:PF00333, PF03719
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S6
Gene (Uniprot):rpsF
Chain IDs:KA (auth: 1f), KC (auth: 2f)
Chain Length:101
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
UniProt ID:P62666 Pfam ID:PF01250
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S7
Gene (Uniprot):rpsG
Chain IDs:LA (auth: 1g), LC (auth: 2g)
Chain Length:182
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
UniProt ID:P62667 Pfam ID:PF00177
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S8
Gene (Uniprot):rpsH
Chain IDs:MA (auth: 1h), MC (auth: 2h)
Chain Length:180
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
UniProt ID:P62668 Pfam ID:PF00410
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S9
Gene (Uniprot):rpsI
Chain IDs:NA (auth: 1i), NC (auth: 2i)
Chain Length:148
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
UniProt ID:P62669 Pfam ID:PF00380
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S10
Gene (Uniprot):rpsJ
Chain IDs:OA (auth: 1j), OC (auth: 2j)
Chain Length:105
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
UniProt ID:P62653 Pfam ID:PF00338
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S11
Gene (Uniprot):rpsK
Chain IDs:PA (auth: 1k), PC (auth: 2k)
Chain Length:129
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
UniProt ID:P62654 Pfam ID:PF00411
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S12
Gene (Uniprot):rpsL
Chain IDs:QA (auth: 1l), QC (auth: 2l)
Chain Length:135
Number of Molecules:2
Biological Source:Thermus parvatiensis (strain HB27 / ATCC BAA-163 / DSM 7039)
UniProt ID:H7GHW0 Pfam ID:PF00164
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S13
Gene (Uniprot):rpsM
Chain IDs:RA (auth: 1m), RC (auth: 2m)
Chain Length:126
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
UniProt ID:P62655 Pfam ID:PF00416
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S14 type Z
Gene (Uniprot):rpsZ
Chain IDs:SA (auth: 1n), SC (auth: 2n)
Chain Length:140
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
UniProt ID:P62656 Pfam ID:PF00253
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S15
Gene (Uniprot):rpsO
Chain IDs:TA (auth: 1o), TC (auth: 2o)
Chain Length:122
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
UniProt ID:P62657 Pfam ID:PF00312
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S16
Gene (Uniprot):rpsP
Chain IDs:UA (auth: 1p), UC (auth: 2p)
Chain Length:88
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
UniProt ID:P62238 Pfam ID:PF00886
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S18
Gene (Uniprot):rpsR
Chain IDs:VA (auth: 1r), VC (auth: 2r)
Chain Length:118
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
UniProt ID:P62659 Pfam ID:PF01084
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S19
Gene (Uniprot):rpsS
Chain IDs:WA (auth: 1s), WC (auth: 2s)
Chain Length:112
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
UniProt ID:P62660 Pfam ID:PF00203
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S20
Gene (Uniprot):rpsT
Chain IDs:XA (auth: 1t), XC (auth: 2t)
Chain Length:146
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
UniProt ID:P62661 Pfam ID:PF01649
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein Thx
Gene (Uniprot):rpsU
Chain IDs:YA (auth: 1u), YC (auth: 2u)
Chain Length:118
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
UniProt ID:P62613 Pfam ID:PF17070
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosome-associated inhibitor A
Gene (Uniprot):raiA
Chain IDs:ZA (auth: 1y), ZC (auth: 2y)
Chain Length:110
Number of Molecules:2
Biological Source:Escherichia coli (strain K12)
UniProt ID:P0AD49 Pfam ID:PF02482
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
0TD QA ASP modified residue
2MA A A modified residue
2MG FA G modified residue
4OC FA C modified residue
5MC A C modified residue
5MU A U modified residue
G7M FA G modified residue
M2G FA G modified residue
MA6 FA A modified residue
OMC A C modified residue
OMG A G modified residue
OMU A U modified residue
PSU A U modified residue
UR3 FA U modified residue
Ligand Molecules
ARG
MG
MPD
SF4
ZN
Primary Citation
Structural robustness of the ribosome inferred from X-ray crystal structures of the 30S ribosomal subunit and the 70S ribosome lacking ribosomal protein uS17
To be published ? ? ? (?)
Primary Citation of related structures
5V8I