A structural basis for streptomycin resistance

Demirci, H., Murphy IV, F., Murphy, E., Gregory, S.T., Dahlberg, A.E., Jogl, G.

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Crystal structure of the Thermus thermophilus 30S ribosomal subunit with a 16S rRNA mutation, U20G

Annotation data related to this entry.

4DV0

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Domain Annotation: CATH Classification (version 3.5.0)

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Domain	Class	Architecture	Topology	Homology
4dv0B02	Mainly Alpha	Orthogonal Bundle	Helix Hairpins	Helix hairpin bin
4dv0C01	Alpha Beta	2-Layer Sandwich	GMP Synthetase; Chain A, domain 3
4dv0C02	Alpha Beta	2-Layer Sandwich	Ribosomal protein S3 C-terminal domain
4dv0D01	Mainly Alpha	Orthogonal Bundle	Ribosomal Protein S4 Delta 41; Chain A, domain 1	Ribosomal Protein S4 Delta 41; Chain A, domain 1
4dv0D02	Alpha Beta	Roll	Structural Genomics Hypothetical 15.5 Kd Protein In mrcA- pckA Intergenic Region; Chain A	Structural Genomics Hypothetical 15.5 Kd Protein In Mrca- pcka Intergenic Region; Chain
4dv0E01	Alpha Beta	2-Layer Sandwich	Double Stranded RNA Binding Domain
4dv0E02	Alpha Beta	2-Layer Sandwich	Ribosomal Protein S5; domain 2
4dv0F00	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits
4dv0G00	Mainly Alpha	Orthogonal Bundle	Ribosomal Protein S7	Ribosomal Protein S7;
4dv0H02	Alpha Beta	2-Layer Sandwich	Dna Ligase; domain 1
4dv0I00	Alpha Beta	2-Layer Sandwich	Ribosomal Protein S5; domain 2
4dv0K00	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase; domain 5
4dv0L00	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	Nucleic acid-binding proteins
4dv0M01	Mainly Alpha	Orthogonal Bundle	Helicase, Ruva Protein; domain 3
4dv0M02	Few Secondary Structures	Irregular	30s ribosomal protein s13; domain 2	30s ribosomal protein s13, domain 2
4dv0N00	Few Secondary Structures	Irregular	30s Ribosomal Protein S14; Chain N	30s Ribosomal Protein S14; Chain N
4dv0O00	Mainly Alpha	Orthogonal Bundle	Helix Hairpins
4dv0R00	Few Secondary Structures	Irregular	30s Ribosomal Protein S18	30s Ribosomal Protein S18
4dv0S00	Alpha Beta	2-Layer Sandwich	30s Ribosomal Protein S19; Chain A	30s Ribosomal Protein S19; Chain A
4dv0T00	Mainly Alpha	Up-down Bundle	Methane Monooxygenase Hydroxylase; Chain G, domain 1

Protein Family Annotation: Pfam Classification

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Chain	Pfam Accession	Pfam Family Identifier	Pfam Description	Type	Comment
P	PF00886	Ribosomal_S16	Ribosomal protein S16	Family
M	PF00416	Ribosomal_S13	Ribosomal protein S13/S18	Family
J	PF00338	Ribosomal_S10	Ribosomal protein S10p/S20e	Family
T	PF01649	Ribosomal_S20p	Ribosomal protein S20	Family
C	PF00189	Ribosomal_S3_C	Ribosomal protein S3, C-terminal domain	Domain	This 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. Source: Pfam
O	PF00312	Ribosomal_S15	Ribosomal protein S15	Domain	Source: Pfam
Q	PF00366	Ribosomal_S17	Ribosomal protein S17	Domain	Source: Pfam
G	PF00177	Ribosomal_S7	Ribosomal protein S7p/S5e	Domain	This family contains ribosomal protein S7 from prokaryotes and S5 from eukaryotes. Source: Pfam
S	PF00203	Ribosomal_S19	Ribosomal protein S19	Domain	Source: Pfam
E	PF00333	Ribosomal_S5	Ribosomal protein S5, N-terminal domain	Domain	Source: Pfam
R	PF01084	Ribosomal_S18	Ribosomal protein S18	Family
B	PF00318	Ribosomal_S2	Ribosomal protein S2	Family
F	PF01250	Ribosomal_S6	Ribosomal protein S6	Domain	Source: Pfam
C	PF07650	KH_2	KH domain	Domain	Source: Pfam
L	PF00164	Ribosom_S12_S23	Ribosomal protein S12/S23	Family
D	PF00163	Ribosomal_S4	Ribosomal protein S4/S9 N-terminal domain	Family
I	PF00380	Ribosomal_S9	Ribosomal protein S9/S16	Family
K	PF00411	Ribosomal_S11	Ribosomal protein S11	Family
D	PF01479	S4	S4 domain	Domain	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. Source: Pfam
E	PF03719	Ribosomal_S5_C	Ribosomal protein S5, C-terminal domain	Domain	Source: Pfam
H	PF00410	Ribosomal_S8	Ribosomal protein S8	Domain	Source: Pfam
N	PF00253	Ribosomal_S14	Ribosomal protein S14p/S29e	Family

Gene Product Annotation: GO Terms

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Polymer	Molecular Function	Biological Process	Cellular Component
16S rRNA (4DV0:A)	none	none	none
ribosomal protein S2 (4DV0:B)	RNA binding structural constituent of ribosome rRNA binding	translation	intracellular ribosome small ribosomal subunit ribonucleoprotein complex
ribosomal protein S3 (4DV0:C)	RNA binding mRNA binding structural constituent of ribosome rRNA binding	translation	intracellular ribosome small ribosomal subunit ribonucleoprotein complex
ribosomal protein S4 (4DV0:D)	RNA binding structural constituent of ribosome rRNA binding metal ion binding	translation	intracellular ribosome small ribosomal subunit ribonucleoprotein complex
ribosomal protein S5 (4DV0:E)	RNA binding structural constituent of ribosome rRNA binding	translation	ribosome small ribosomal subunit ribonucleoprotein complex
ribosomal protein S6 (4DV0:F)	RNA binding structural constituent of ribosome rRNA binding	translation	ribosome ribonucleoprotein complex
ribosomal protein S7 (4DV0:G)	tRNA binding RNA binding structural constituent of ribosome rRNA binding	translation	ribosome small ribosomal subunit ribonucleoprotein complex
ribosomal protein S8 (4DV0:H)	RNA binding structural constituent of ribosome rRNA binding	translation	ribosome ribonucleoprotein complex
ribosomal protein S9 (4DV0:I)	tRNA binding RNA binding structural constituent of ribosome rRNA binding	translation	ribosome ribonucleoprotein complex
ribosomal protein S10 (4DV0:J)	tRNA binding RNA binding structural constituent of ribosome rRNA binding	translation	intracellular ribosome ribonucleoprotein complex
ribosomal protein S11 (4DV0:K)	RNA binding structural constituent of ribosome rRNA binding	translation	intracellular ribosome ribonucleoprotein complex
ribosomal protein S12 (4DV0:L)	tRNA binding RNA binding structural constituent of ribosome rRNA binding	translation	intracellular ribosome small ribosomal subunit ribonucleoprotein complex
ribosomal protein S13 (4DV0:M)	tRNA binding nucleic acid binding RNA binding structural constituent of ribosome rRNA binding	translation	intracellular ribosome ribonucleoprotein complex
ribosomal protein S14 (4DV0:N)	RNA binding structural constituent of ribosome zinc ion binding rRNA binding metal ion binding	translation	intracellular ribosome ribonucleoprotein complex
ribosomal protein S15 (4DV0:O)	RNA binding structural constituent of ribosome rRNA binding	translation	intracellular ribosome ribonucleoprotein complex
ribosomal protein S16 (4DV0:P)	structural constituent of ribosome	translation	intracellular ribosome ribonucleoprotein complex
ribosomal protein S17 (4DV0:Q)	RNA binding structural constituent of ribosome rRNA binding	translation	intracellular ribosome ribonucleoprotein complex
ribosomal protein S18 (4DV0:R)	RNA binding structural constituent of ribosome rRNA binding	translation	intracellular ribosome ribonucleoprotein complex
ribosomal protein S19 (4DV0:S)	RNA binding structural constituent of ribosome rRNA binding	translation	ribosome small ribosomal subunit ribonucleoprotein complex
ribosomal protein S20 (4DV0:T)	RNA binding structural constituent of ribosome rRNA binding	translation	intracellular ribosome ribonucleoprotein complex
ribosomal protein THX (4DV0:U)	RNA binding rRNA binding	none	ribosome ribonucleoprotein complex

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