1DD4 - JenaLib

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Title :   CRYSTAL STRUCTURE OF RIBOSOMAL PROTEIN L12 FROM THERMOTOGA MARITIM

Authors :   M. C. Wahl, G. P. Bourenkov, H. D. Bartunik, R. Huber

Date :   08 Nov 99 (Deposition) - 13 Nov 00 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D  (1x)
Biol. Unit 2: A,B,C,D  (2x)

Keywords :   Dimer Formation, Flexibility, Hinge Region, Four-Helix- Bundle, Five-Helix- Bundle, Alpha-Beta Structure, Helical Hairpin, Domains, Ribosome (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. C. Wahl, G. P. Bourenkov, H. D. Bartunik, R. Huber
Flexibility, Conformational Diversity And Two Dimerization Modes In Complexes Of Ribosomal Protein L12.
Embo J. V. 19 174 2000
PubMed-ID: 10637222 | Reference-DOI: 10.1093/EMBOJ/19.2.174
(for further references see the PDB file header)

Molecule 1 - 50S RIBOSOMAL PROTEIN L7/L12
	Chains	:	A, B
	Organism Scientific	:	THERMOTOGA MARITIMA
	Organism Taxid	:	2336

Molecule 2 - 50S RIBOSOMAL PROTEIN L7/L12
	Chains	:	C, D
	Organism Scientific	:	THERMOTOGA MARITIMA
	Organism Taxid	:	2336

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A	B	C	D
Biological Unit 2 (2x)	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 2)

No.	Name	Count	Type	Full Name
1	TBR	2	Ligand/Ion	HEXATANTALUM DODECABROMIDE

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	TBR	2	Ligand/Ion	HEXATANTALUM DODECABROMIDE

Biological Unit 2 (1, 4)

No.	Name	Count	Type	Full Name
1	TBR	4	Ligand/Ion	HEXATANTALUM DODECABROMIDE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LYS A:12 , LEU A:13 , ALA A:51 , GLU A:55 , LYS B:103 , GLU B:110	BINDING SITE FOR RESIDUE TBR A 401
2	AC2	SOFTWARE	LYS A:103 , GLU A:110 , GLU B:11 , LYS B:12 , LEU B:13	BINDING SITE FOR RESIDUE TBR A 402

(no "SS Bond" information available for 1DD4)

(no "Cis Peptide Bond" information available for 1DD4)

(no "SAP(SNP)/Variant" information available for 1DD4)

(no "PROSITE Motif" information available for 1DD4)

(no "Exon" information available for 1DD4)

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:128
 aligned with RL7_THEMA | P29396 from UniProtKB/Swiss-Prot  Length:128

    Alignment length:128
                                    10        20        30        40        50        60        70        80        90       100       110       120        
            RL7_THEMA     1 MTIDEIIEAIEKLTVSELAELVKKLEDKFGVTAAAPVAVAAAPVAGAAAGAAQEEKTEFDVVLKSFGQNKIQVIKVVREITGLGLKEAKDLVEKAGSPDAVIKSGVSKEEAEEIKKKLEEAGAEVELK 128
               SCOP domains d1dd4a1 A:1-57                                           d1dd4a2 A:58-128 Ribosomal protein L7/12, C-terminal domain             SCOP domains
               CATH domains ---------------------------------------------------------1dd4A02 A:58-128  [code=3.30.1390.10, no name defined]                  CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeee...hhhhhhhhhhhhhh.hhhhhhhhhh.......eeeeeehhhhhhhhhhhhhh...eeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1dd4 A   1 MTIDEIIEAIEKLTVSELAELVKKLEDKFGVTAAAPVAVAAAPVAGAAAGAAQEEKTEFDVVLKSFGQNKIQVIKVVREITGLGLKEAKDLVEKAGSPDAVIKSGVSKEEAEEIKKKLEEAGAEVELK 128
                                    10        20        30        40        50        60        70        80        90       100       110       120

Chain B from PDB  Type:PROTEIN  Length:128
 aligned with RL7_THEMA | P29396 from UniProtKB/Swiss-Prot  Length:128

    Alignment length:128
                                    10        20        30        40        50        60        70        80        90       100       110       120        
            RL7_THEMA     1 MTIDEIIEAIEKLTVSELAELVKKLEDKFGVTAAAPVAVAAAPVAGAAAGAAQEEKTEFDVVLKSFGQNKIQVIKVVREITGLGLKEAKDLVEKAGSPDAVIKSGVSKEEAEEIKKKLEEAGAEVELK 128
               SCOP domains d1dd4b1 B:1-57                                           d1dd4b2 B:58-128 Ribosomal protein L7/12, C-terminal domain             SCOP domains
               CATH domains ---------------------------------------------------------1dd4B02 B:58-128  [code=3.30.1390.10, no name defined]                  CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeee...hhhhhhhhhhhhhh.hhhhhhhhhh.......eeeeee..hhhhhhhhhhhhh..eeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1dd4 B   1 MTIDEIIEAIEKLTVSELAELVKKLEDKFGVTAAAPVAVAAAPVAGAAAGAAQEEKTEFDVVLKSFGQNKIQVIKVVREITGLGLKEAKDLVEKAGSPDAVIKSGVSKEEAEEIKKKLEEAGAEVELK 128
                                    10        20        30        40        50        60        70        80        90       100       110       120

Chain C from PDB  Type:PROTEIN  Length:35
 aligned with RL7_THEMA | P29396 from UniProtKB/Swiss-Prot  Length:128

    Alignment length:35
                                    10        20        30     
            RL7_THEMA     1 MTIDEIIEAIEKLTVSELAELVKKLEDKFGVTAAA  35
               SCOP domains d1dd4c_ C:                          SCOP domains
               CATH domains ----------------------------------- CATH domains
               Pfam domains ----------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhh..hhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------- PROSITE
                 Transcript ----------------------------------- Transcript
                 1dd4 C   1 MTIDEIIEAIEKLTVSELAELVKKLEDKFGVTAAA  35
                                    10        20        30

Chain D from PDB  Type:PROTEIN  Length:40
 aligned with RL7_THEMA | P29396 from UniProtKB/Swiss-Prot  Length:128

    Alignment length:40
                                    10        20        30        40
            RL7_THEMA     1 MTIDEIIEAIEKLTVSELAELVKKLEDKFGVTAAAPVAVA  40
               SCOP domains d1dd4d_ D:                               SCOP domains
               CATH domains 1dd4D01 D:1-30                ---------- CATH domains
               Pfam domains ---------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhh.hhhhhhhhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------- PROSITE
                 Transcript ---------------------------------------- Transcript
                 1dd4 D   1 MTIDEIIEAIEKLTVSELAELVKKLEDKFGVTAAAPVAVA  40
                                    10        20        30        40

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	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 '\|'

(no "Pfam Domain" information available for 1DD4)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (RL7_THEMA | P29396)

molecular function
	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:0022625	cytosolic large ribosomal subunit	The large subunit of a ribosome located in the cytosol.
	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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	RL7_THEMA \| P29396	:	1dd3 1l1u 1zav 1zaw 1zax

1dd3	1DD3 CONTAINS THE SAME MOLECULE IN SPACE GROUP C2221

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