1G1X | RR0019 - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   STRUCTURE OF RIBOSOMAL PROTEINS S15, S6, S18, AND 16S RIBOSOMAL RNA

Authors :   S. C. Agalarov, G. S. Prasad, P. M. Funke, C. D. Stout, J. R. Williamson

Date :   13 Oct 00 (Deposition) - 30 Oct 00 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.60

Chains :   Asym. Unit : A,B,C,D,E,F,G,H,I,J
Biol. Unit 1: A,B,C,D,E  (1x)
Biol. Unit 2: F,G,H,I,J  (1x)

Keywords :   Ribosomal Proteins S15, S6, S18, S30 Ribosomal Subunit, Rna, Ribosome (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. C. Agalarov, G. Sridhar Prasad, P. M. Funke, C. D. Stout, J. R. Williamson
Structure Of The S15, S6, S18-Rrna Complex: Assembly Of The 30S Ribosome Central Domain.
Science V. 288 107 2000
PubMed-ID: 10753109 | Reference-DOI: 10.1126/SCIENCE.288.5463.107
(for further references see the PDB file header)

Molecule 1 - 16S RIBOSOMAL RNA
	Chains	:	D, I
	Engineered	:	YES
	Fragment	:	RESIDUES 582-675
	Synthetic	:	YES

Molecule 2 - 16S RIBOSOMAL RNA
	Chains	:	E, J
	Engineered	:	YES
	Fragment	:	RESIDUES 716-759
	Synthetic	:	YES

Molecule 3 - 30S RIBOSOMAL PROTEIN S6
	Chains	:	A, F
	Organism Scientific	:	THERMUS THERMOPHILUS
	Organism Taxid	:	274

Molecule 4 - 30S RIBOSOMAL PROTEIN S15
	Chains	:	B, G
	Organism Scientific	:	THERMUS THERMOPHILUS
	Organism Taxid	:	274

Molecule 5 - 30S RIBOSOMAL PROTEIN S18
	Chains	:	C, H
	Organism Scientific	:	THERMUS THERMOPHILUS
	Organism Taxid	:	274

		1	2	3	4	5	6	7	8	9	10
Asymmetric Unit	:	A	B	C	D	E	F	G	H	I	J
Biological Unit 1 (1x)	:	A	B	C	D	E
Biological Unit 2 (1x)	:						F	G	H	I	J

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 1G1X)

(no "Site" information available for 1G1X)

(no "SS Bond" information available for 1G1X)

(no "Cis Peptide Bond" information available for 1G1X)

(no "SAP(SNP)/Variant" information available for 1G1X)

Asymmetric Unit (3, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RIBOSOMAL_S18	PS00057	Ribosomal protein S18 signature.	RS18_THET8	32-55	2	C:32-53 H:32-53
2	RIBOSOMAL_S15	PS00362	Ribosomal protein S15 signature.	RS15_THET8	39-69	2	B:38-68 G:38-68
3	RIBOSOMAL_S6	PS01048	Ribosomal protein S6 signature.	RS6_THET8	44-53	2	A:44-53 F:44-53

Biological Unit 1 (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RIBOSOMAL_S18	PS00057	Ribosomal protein S18 signature.	RS18_THET8	32-55	1	C:32-53 -
2	RIBOSOMAL_S15	PS00362	Ribosomal protein S15 signature.	RS15_THET8	39-69	1	B:38-68 -
3	RIBOSOMAL_S6	PS01048	Ribosomal protein S6 signature.	RS6_THET8	44-53	1	A:44-53 -

Biological Unit 2 (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RIBOSOMAL_S18	PS00057	Ribosomal protein S18 signature.	RS18_THET8	32-55	1	- H:32-53
2	RIBOSOMAL_S15	PS00362	Ribosomal protein S15 signature.	RS15_THET8	39-69	1	- G:38-68
3	RIBOSOMAL_S6	PS01048	Ribosomal protein S6 signature.	RS6_THET8	44-53	1	- F:44-53

(no "Exon" information available for 1G1X)

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:98
 aligned with RS6_THET8 | Q5SLP8 from UniProtKB/Swiss-Prot  Length:101

    Alignment length:98
                                    10        20        30        40        50        60        70        80        90        
            RS6_THET8     1 MRRYEVNIVLNPNLDQSQLALEKEIIQRALENYGARVEKVEELGLRRLAYPIAKDPQGYFLWYQVEMPEDRVNDLARELRIRDNVRRVMVVKSQEPFL  98
               SCOP domains d1g1xa_ A: Ribosomal protein S6                                                                    SCOP domains
               CATH domains 1g1xA00 A:1-98  [code=3.30.70.60, no name defined]                                                 CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee..eee....hhhhhhhhhhhhhhhhhhh..eeee....eee...........eeee..eeeehhhhhhhhhhhhhh...eeee..ee...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) -------------------------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) -------------------------------------------RIBOSOMAL_--------------------------------------------- PROSITE (3)
                 Transcript -------------------------------------------------------------------------------------------------- Transcript
                 1g1x A   1 MRRYEVNIVLNPNLDQSQLALEKEIIQRALENYGARVEKVEELGLRRLAYPIAKDPQGYFLWYQVEMPEDRVNDLARELRIRDNVRRVMVVKSQEPFL  98
                                    10        20        30        40        50        60        70        80        90

Chain B from PDB  Type:PROTEIN  Length:88
 aligned with RS15_THET8 | Q5SJ76 from UniProtKB/Swiss-Prot  Length:89

    Alignment length:88
                                    11        21        31        41        51        61        71        81        
           RS15_THET8     2 PITKEEKQKVIQEFARFPGDTGSTEVQVALLTLRINRLSEHLKVHKKDHHSHRGLLMMVGQRRRLLRYLQREDPERYRALIEKLGIRG  89
               SCOP domains d1g1xb_ B: Ribosomal protein S15                                                         SCOP domains
               CATH domains 1g1xB00 B:1-88  [code=1.10.287.10, no name defined]                                      CATH domains
               Pfam domains ---------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) -------------------------------------RIBOSOMAL_S15  PDB: B:38-68    -------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------- Transcript
                 1g1x B   1 PITKEEKQKVIQEFARFPGDTGSTEVQVALLTLRINRLSEHLKVHKKDHHSHRGLLMMVGQRRRLLRYLQREDPERYREIVEKLGLRG  88
                                    10        20        30        40        50        60        70        80

Chain C from PDB  Type:PROTEIN  Length:46
 aligned with RS18_THET8 | Q5SLQ0 from UniProtKB/Swiss-Prot  Length:88

    Alignment length:53
                                    39        49        59        69        79   
           RS18_THET8    30 DLRDYRNVEVLKRFLSETGKILPRRRTGLSAKEQRILAKTIKRARILGLLPFT  82
               SCOP domains d1g1xc_ C: Ribo     soma  l protein S18               SCOP domains
               CATH domains 1g1xC00 C:30-82      30s   Ribosomal Protein S18      CATH domains
               Pfam domains ----------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhh.-----....--.....hhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------- SAPs(SNPs)
                    PROSITE --RIBOSOMAL_S18           --------------------------- PROSITE
                 Transcript ----------------------------------------------------- Transcript
                 1g1x C  30 DLRDYRNVEVLKRFL-----ILPR--TGLSGKEQRILAKTIKRARILGLLPFT  82
                                    39    |    -|  |  | 59        69        79   
                                         44    50 53 56

Chain D from PDB  Type:RNA  Length:40
                                                                        
                 1g1x D 582 AAGGCGGCCGAAAGGCUAGACGGUGGGAGAGGGUGGUGGA 675
                                   591  ||   655       665       675
                                      594|                          
                                       649

Chain E from PDB  Type:RNA  Length:44
                                                                            
                 1g1x E 716 ACGCCGAUGGCGAAGGCAGCCACCUGGUCCACCCGUGACGCUUU 759
                                   725       735       745       755

Chain F from PDB  Type:PROTEIN  Length:98
 aligned with RS6_THET8 | Q5SLP8 from UniProtKB/Swiss-Prot  Length:101

    Alignment length:98
                                    10        20        30        40        50        60        70        80        90        
            RS6_THET8     1 MRRYEVNIVLNPNLDQSQLALEKEIIQRALENYGARVEKVEELGLRRLAYPIAKDPQGYFLWYQVEMPEDRVNDLARELRIRDNVRRVMVVKSQEPFL  98
               SCOP domains d1g1xf_ F: Ribosomal protein S6                                                                    SCOP domains
               CATH domains 1g1xF00 F:1-98  [code=3.30.70.60, no name defined]                                                 CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeee....hhhhhhhhhhhhhhhhhhh..eeeeee.................eeeeeeeeehhhhhhhhhhhhhhh..eeeeeeee...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) -------------------------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) -------------------------------------------RIBOSOMAL_--------------------------------------------- PROSITE (3)
                 Transcript -------------------------------------------------------------------------------------------------- Transcript
                 1g1x F   1 MRRYEVNIVLNPNLDQSQLALEKEIIQRALENYGARVEKVEELGLRRLAYPIAKDPQGYFLWYQVEMPEDRVNDLARELRIRDNVRRVMVVKSQEPFL  98
                                    10        20        30        40        50        60        70        80        90

Chain G from PDB  Type:PROTEIN  Length:88
 aligned with RS15_THET8 | Q5SJ76 from UniProtKB/Swiss-Prot  Length:89

    Alignment length:88
                                    11        21        31        41        51        61        71        81        
           RS15_THET8     2 PITKEEKQKVIQEFARFPGDTGSTEVQVALLTLRINRLSEHLKVHKKDHHSHRGLLMMVGQRRRLLRYLQREDPERYRALIEKLGIRG  89
               SCOP domains d1g1xg_ G: Ribosomal protein S15                                                         SCOP domains
               CATH domains 1g1xG00 G:1-88  [code=1.10.287.10, no name defined]                                      CATH domains
               Pfam domains ---------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) -------------------------------------RIBOSOMAL_S15  PDB: G:38-68    -------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------- Transcript
                 1g1x G   1 PITKEEKQKVIQEFARFPGDTGSTEVQVALLTLRINRLSEHLKVHKKDHHSHRGLLMMVGQRRRLLRYLQREDPERYREIVEKLGLRG  88
                                    10        20        30        40        50        60        70        80

Chain H from PDB  Type:PROTEIN  Length:48
 aligned with RS18_THET8 | Q5SLQ0 from UniProtKB/Swiss-Prot  Length:88

    Alignment length:53
                                    39        49        59        69        79   
           RS18_THET8    30 DLRDYRNVEVLKRFLSETGKILPRRRTGLSAKEQRILAKTIKRARILGLLPFT  82
               SCOP domains d1g1xh_ H: Ribos   omal   protein S18                 SCOP domains
               CATH domains 1g1xH00 H:30-82    30s R  ibosomal Protein S18        CATH domains
               Pfam domains ----------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhh...---.....--.....hhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------- SAPs(SNPs)
                    PROSITE --RIBOSOMAL_S18           --------------------------- PROSITE
                 Transcript ----------------------------------------------------- Transcript
                 1g1x H  30 DLRDYRNVEVLKRFLS---KILPR--TGLSGKEQRILAKTIKRARILGLLPFT  82
                                    39     |  49   |  | 59        69        79   
                                          45  49  53 56

Chain I from PDB  Type:RNA  Length:41
                                                                         
                 1g1x I 582 AAGGCGGCCGAAAGGCUAGACGGUGGGAGAGGGUGGUGGAA 676
                                   591  ||   655       665       675 
                                      594|                           
                                       649

Chain J from PDB  Type:RNA  Length:44
                                                                            
                 1g1x J 716 ACGCCGAUGGCGAAGGCAGCCACCUGGUCCACCCGUGACGCUUU 759
                                   725       735       745       755

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Alpha-Beta Plaits (1688)

Homologous Superfamily: [code=3.30.70.60, no name defined] (93)

[unclassified] (2)

1a	1g1xA00	A:1-98
1b	1g1xF00	F:1-98

Class: Few Secondary Structures (1120)

Architecture: Irregular (1120)

Topology: 30s Ribosomal Protein S18 (102)

Homologous Superfamily: 30s Ribosomal Protein S18 (102)

[unclassified] (1)

2a	1g1xH00	H:30-82
2b	1g1xC00	C:30-82

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Helix Hairpins (718)

Homologous Superfamily: [code=1.10.287.10, no name defined] (116)

[unclassified] (2)

3a	1g1xB00	B:1-88
3b	1g1xG00	G:1-88

(no "Pfam Domain" information available for 1G1X)

Asymmetric Unit(hide GO term definitions)

Chain A,F (RS6_THET8 | Q5SLP8)

molecular function
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0019843	rRNA binding	Interacting selectively and non-covalently with ribosomal RNA.
	GO:0003735	structural constituent of ribosome	The action of a molecule that contributes to the structural integrity of the ribosome.
biological process
	GO:0006412	translation	The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome.
cellular component
	GO:0030529	intracellular ribonucleoprotein complex	An intracellular macromolecular complex containing both protein and RNA molecules.
	GO:0005840	ribosome	An intracellular organelle, about 200 A in diameter, consisting of RNA and protein. It is the site of protein biosynthesis resulting from translation of messenger RNA (mRNA). It consists of two subunits, one large and one small, each containing only protein and RNA. Both the ribosome and its subunits are characterized by their sedimentation coefficients, expressed in Svedberg units (symbol: S). Hence, the prokaryotic ribosome (70S) comprises a large (50S) subunit and a small (30S) subunit, while the eukaryotic ribosome (80S) comprises a large (60S) subunit and a small (40S) subunit. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site). Ribosomes from prokaryotes, eukaryotes, mitochondria, and chloroplasts have characteristically distinct ribosomal proteins.

Chain B,G (RS15_THET8 | Q5SJ76)

molecular function
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0019843	rRNA binding	Interacting selectively and non-covalently with ribosomal RNA.
	GO:0003735	structural constituent of ribosome	The action of a molecule that contributes to the structural integrity of the ribosome.
biological process
	GO:0006412	translation	The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome.
cellular component
	GO:0005622	intracellular	The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
	GO:0030529	intracellular ribonucleoprotein complex	An intracellular macromolecular complex containing both protein and RNA molecules.
	GO:0005840	ribosome	An intracellular organelle, about 200 A in diameter, consisting of RNA and protein. It is the site of protein biosynthesis resulting from translation of messenger RNA (mRNA). It consists of two subunits, one large and one small, each containing only protein and RNA. Both the ribosome and its subunits are characterized by their sedimentation coefficients, expressed in Svedberg units (symbol: S). Hence, the prokaryotic ribosome (70S) comprises a large (50S) subunit and a small (30S) subunit, while the eukaryotic ribosome (80S) comprises a large (60S) subunit and a small (40S) subunit. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site). Ribosomes from prokaryotes, eukaryotes, mitochondria, and chloroplasts have characteristically distinct ribosomal proteins.

Chain C,H (RS18_THET8 | Q5SLQ0)

molecular function
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0019843	rRNA binding	Interacting selectively and non-covalently with ribosomal RNA.
	GO:0003735	structural constituent of ribosome	The action of a molecule that contributes to the structural integrity of the ribosome.
biological process
	GO:0006412	translation	The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome.
cellular component
	GO:0005622	intracellular	The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
	GO:0030529	intracellular ribonucleoprotein complex	An intracellular macromolecular complex containing both protein and RNA molecules.
	GO:0005840	ribosome	An intracellular organelle, about 200 A in diameter, consisting of RNA and protein. It is the site of protein biosynthesis resulting from translation of messenger RNA (mRNA). It consists of two subunits, one large and one small, each containing only protein and RNA. Both the ribosome and its subunits are characterized by their sedimentation coefficients, expressed in Svedberg units (symbol: S). Hence, the prokaryotic ribosome (70S) comprises a large (50S) subunit and a small (30S) subunit, while the eukaryotic ribosome (80S) comprises a large (60S) subunit and a small (40S) subunit. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site). Ribosomes from prokaryotes, eukaryotes, mitochondria, and chloroplasts have characteristically distinct ribosomal proteins.

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(no "Related Entries Specified in the PDB File" available for 1G1X)

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