4DR6

Crystal structure of the Thermus thermophilus (HB8) 30S ribosomal subunit with codon, near-cognate transfer RNA anticodon stem-loop mismatched at the first codon position and streptomycin bound


ChainDomainClassArchitectureTopologyHomology
C3.30.300.20 Alpha Beta 2-Layer Sandwich GMP Synthetase Chain A, domain 3
C3.30.1140.32 Alpha Beta 2-Layer Sandwich Ribosomal protein S3 C-terminal domain Ribosomal protein S3, C-terminal domain
D1.10.1050.10 Mainly Alpha Orthogonal Bundle Ribosomal Protein S4 Delta 41 Chain A, domain 1
D1.10.1050.10 Mainly Alpha Orthogonal Bundle Ribosomal Protein S4 Delta 41 Chain A, domain 1
D3.10.290.10 Alpha Beta Roll Structural Genomics Hypothetical 15.5 Kd Protein In mrcA-pckA Intergenic Region Chain A
E3.30.160.20 Alpha Beta 2-Layer Sandwich Double Stranded RNA Binding Domain
E3.30.230.10 Alpha Beta 2-Layer Sandwich Ribosomal Protein S5 domain 2
F3.30.70.60 Alpha Beta 2-Layer Sandwich Alpha-Beta Plaits Ribosomal protein S6/Translation elongation factor EF1B
G1.10.455.10 Mainly Alpha Orthogonal Bundle Ribosomal Protein S7 Ribosomal protein S7/S5
H3.30.1370.30 Alpha Beta 2-Layer Sandwich Ribosomal Protein S8 Chain: A, domain 1
H3.30.1490.10 Alpha Beta 2-Layer Sandwich Dna Ligase domain 1
I3.30.230.10 Alpha Beta 2-Layer Sandwich Ribosomal Protein S5 domain 2
J3.30.70.600 Alpha Beta 2-Layer Sandwich Alpha-Beta Plaits Ribosomal protein S10
K3.30.420.80 Alpha Beta 2-Layer Sandwich Nucleotidyltransferase domain 5
L2.40.50.140 Mainly Beta Beta Barrel OB fold (Dihydrolipoamide Acetyltransferase, E2P) Nucleic acid-binding proteins
N4.10.830.10 Few Secondary Structures Irregular 30s Ribosomal Protein S14 Chain N
O1.10.287.10 Mainly Alpha Orthogonal Bundle Helix Hairpins S15/NS1, RNA-binding
P3.30.1320.10 Alpha Beta 2-Layer Sandwich S16 Ribosomal Protein Chain: A
Q2.40.50.140 Mainly Beta Beta Barrel OB fold (Dihydrolipoamide Acetyltransferase, E2P) Nucleic acid-binding proteins
R4.10.640.10 Few Secondary Structures Irregular 30s Ribosomal Protein S18 Ribosomal protein S18
S3.30.860.10 Alpha Beta 2-Layer Sandwich 30s Ribosomal Protein S19 Chain A
M1.10.8.50 Mainly Alpha Orthogonal Bundle Helicase, Ruva Protein domain 3
M4.10.910.10 Few Secondary Structures Irregular 30s ribosomal protein s13 domain 2
B3.40.50.10490 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold Glucose-6-phosphate isomerase like protein
B3.40.50.10490 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold Glucose-6-phosphate isomerase like protein
B1.10.287.610 Mainly Alpha Orthogonal Bundle Helix Hairpins Helix hairpin bin
T1.20.58.110 Mainly Alpha Up-down Bundle Methane Monooxygenase Hydroxylase Chain G, domain 1

Protein Family Annotation Pfam Database Homepage

ChainsAccessionIdentifierDescriptionCommentsSource
CPF07650KH domain (KH_2)KH domain- Domain
CPF00189Ribosomal protein S3, C-terminal domain (Ribosomal_S3_C)Ribosomal protein S3, C-terminal domainThis family contains a central domain Pfam:PF00013, hence the amino and carboxyl terminal domains are stored separately. This is a minimal carboxyl-terminal domain. Some are much longer.Domain
DPF00163Ribosomal protein S4/S9 N-terminal domain (Ribosomal_S4)Ribosomal protein S4/S9 N-terminal domain- Family
DPF01479S4 domain (S4)S4 domainThe S4 domain is a small domain consisting of 60-65 amino acid residues that was detected in the bacterial ribosomal protein S4, eukaryotic ribosomal S9, two families of pseudouridine synthases, a novel family of predicted RNA methylases, a yeast pro ...The S4 domain is a small domain consisting of 60-65 amino acid residues that was detected in the bacterial ribosomal protein S4, eukaryotic ribosomal S9, two families of pseudouridine synthases, a novel family of predicted RNA methylases, a yeast protein containing a pseudouridine synthetase and a deaminase domain, bacterial tyrosyl-tRNA synthetases, and a number of uncharacterized, small proteins that may be involved in translation regulation [1]. The S4 domain probably mediates binding to RNA.
Domain
EPF03719Ribosomal protein S5, C-terminal domain (Ribosomal_S5_C)Ribosomal protein S5, C-terminal domain- Domain
EPF00333Ribosomal protein S5, N-terminal domain (Ribosomal_S5)Ribosomal protein S5, N-terminal domain- Domain
FPF01250Ribosomal protein S6 (Ribosomal_S6)Ribosomal protein S6- Domain
GPF00177Ribosomal protein S7p/S5e (Ribosomal_S7)Ribosomal protein S7p/S5eThis family contains ribosomal protein S7 from prokaryotes and S5 from eukaryotes.Domain
HPF00410Ribosomal protein S8 (Ribosomal_S8)Ribosomal protein S8- Domain
IPF00380Ribosomal protein S9/S16 (Ribosomal_S9)Ribosomal protein S9/S16- Family
JPF00338Ribosomal protein S10p/S20e (Ribosomal_S10)Ribosomal protein S10p/S20e- Family
KPF00411Ribosomal protein S11 (Ribosomal_S11)Ribosomal protein S11- Family
LPF00164Ribosomal protein S12/S23 (Ribosom_S12_S23)Ribosomal protein S12/S23- Family
NPF00253Ribosomal protein S14p/S29e (Ribosomal_S14)Ribosomal protein S14p/S29e- Family
OPF00312Ribosomal protein S15 (Ribosomal_S15)Ribosomal protein S15- Domain
PPF00886Ribosomal protein S16 (Ribosomal_S16)Ribosomal protein S16- Family
QPF00366Ribosomal protein S17 (Ribosomal_S17)Ribosomal protein S17- Domain
RPF01084Ribosomal protein S18 (Ribosomal_S18)Ribosomal protein S18- Family
SPF00203Ribosomal protein S19 (Ribosomal_S19)Ribosomal protein S19- Domain
MPF00416Ribosomal protein S13/S18 (Ribosomal_S13)Ribosomal protein S13/S18- Family
BPF00318Ribosomal protein S2 (Ribosomal_S2)Ribosomal protein S2- Family
TPF01649Ribosomal protein S20 (Ribosomal_S20p)Ribosomal protein S20- Family
UPF1707030S ribosomal protein Thx (Thx)30S ribosomal protein Thx- Family

Gene Product Annotation Gene Product Annotation

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
A16S rRNAnone none none
C30S ribosomal protein S3
D30S ribosomal protein S4
E30S ribosomal protein S5
F30S ribosomal protein S6
G30S ribosomal protein S7
H30S ribosomal protein S8
I30S ribosomal protein S9
J30S ribosomal protein S10
K30S ribosomal protein S11
L30S ribosomal protein S12
N30S ribosomal protein S14
O30S ribosomal protein S15
P30S ribosomal protein S16
Q30S ribosomal protein S17
R30S ribosomal protein S18
S30S ribosomal protein S19
W5'-R(P*UP*UP*GP*AP*GP*GP*(PSU)P*GP*G)-3'none none none
a5'-R(P*CP*UP*UP*GP*AP*GP*GP*(PSU)P*GP*GP*U)-3'none none none
b5'-R(*UP*UP*U)-3'none none none
M30S ribosomal protein S13
B30S ribosomal protein S2
T30S ribosomal protein S20
U30S ribosomal protein THX
V5'-R(*UP*UP*UP*U)-3'none none none