2GHJ - JenaLib

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Title :   CRYSTAL STRUCTURE OF FOLDED AND PARTIALLY UNFOLDED FORMS OF AQUIFEX AEOLICUS RIBOSOMAL PROTEIN L20

Authors :   Y. Timsit, F. Allemand, C. Chiaruttini, M. Springer

Date :   27 Mar 06 (Deposition) - 18 Apr 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.90

Chains :   Asym. Unit : A,B,D,E
Biol. Unit 1: A,D  (1x)
Biol. Unit 2: B,E  (1x)
Biol. Unit 3: A,B,D,E  (1x)
Biol. Unit 4: B,D  (1x)
Biol. Unit 5: A,E  (1x)

Keywords :   Folding Intermediate; Ribosomal Protein Extension, Structural Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. Timsit, F. Allemand, C. Chiaruttini, M. Springer
Coexistence Of Two Protein Folding States In The Crystal Structure Of Ribosomal Protein L20
Embo Rep. V. 7 1013 2006
PubMed-ID: 16977336 | Reference-DOI: 10.1038/SJ.EMBOR.7400803
(for further references see the PDB file header)

Molecule 1 - 50S RIBOSOMAL PROTEIN L20
	Chains	:	A, B, D, E
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	RPLT
	Organism Scientific	:	AQUIFEX AEOLICUS
	Organism Taxid	:	63363
	Other Details	:	DIMER A,D IS FORMED BY FOLDED, DIMER B,E BY UNFOLDED MONOMERS

		1	2	3	4
Asymmetric Unit	:	A	B	D	E
Biological Unit 1 (1x)	:	A		D
Biological Unit 2 (1x)	:		B		E
Biological Unit 3 (1x)	:	A	B	D	E
Biological Unit 4 (1x)	:		B	D
Biological Unit 5 (1x)	:	A			E

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 14)

No.	Name	Count	Type	Full Name
1	MSE	8	Mod. Amino Acid	SELENOMETHIONINE
2	SO4	6	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 8)

No.	Name	Count	Type	Full Name
1	MSE	4	Mod. Amino Acid	SELENOMETHIONINE
2	SO4	4	Ligand/Ion	SULFATE ION

Biological Unit 2 (2, 6)

No.	Name	Count	Type	Full Name
1	MSE	4	Mod. Amino Acid	SELENOMETHIONINE
2	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 3 (2, 14)

No.	Name	Count	Type	Full Name
1	MSE	8	Mod. Amino Acid	SELENOMETHIONINE
2	SO4	6	Ligand/Ion	SULFATE ION

Biological Unit 4 (2, 7)

No.	Name	Count	Type	Full Name
1	MSE	4	Mod. Amino Acid	SELENOMETHIONINE
2	SO4	3	Ligand/Ion	SULFATE ION

Biological Unit 5 (2, 7)

No.	Name	Count	Type	Full Name
1	MSE	4	Mod. Amino Acid	SELENOMETHIONINE
2	SO4	3	Ligand/Ion	SULFATE ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP D:89 , ARG D:90 , LYS D:91	BINDING SITE FOR RESIDUE SO4 D 119
2	AC2	SOFTWARE	TRP A:59 , ARG A:90 , LYS A:91	BINDING SITE FOR RESIDUE SO4 A 119
3	AC3	SOFTWARE	GLU E:54 , ARG E:56 , ARG E:90 , LYS E:91	BINDING SITE FOR RESIDUE SO4 E 119
4	AC4	SOFTWARE	ARG B:56 , LEU B:88 , ASP B:89 , ARG B:90 , LYS B:91	BINDING SITE FOR RESIDUE SO4 B 119
5	AC5	SOFTWARE	ALA A:19 , GLY A:21 , TYR A:22 , ARG A:23 , GLY A:24 , TYR A:30 , TYR E:42 , ARG E:46	BINDING SITE FOR RESIDUE SO4 A 120
6	AC6	SOFTWARE	TYR B:42 , ARG B:46 , LYS D:20 , GLY D:21 , TYR D:22 , ARG D:23 , GLY D:24 , TYR D:30	BINDING SITE FOR RESIDUE SO4 D 120

(no "SS Bond" information available for 2GHJ)

(no "Cis Peptide Bond" information available for 2GHJ)

(no "SAP(SNP)/Variant" information available for 2GHJ)

Asymmetric Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RIBOSOMAL_L20	PS00937	Ribosomal protein L20 signature.	RL20_AQUAE	52-68	4	A:52-68 B:52-68 D:52-68 E:52-68

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RIBOSOMAL_L20	PS00937	Ribosomal protein L20 signature.	RL20_AQUAE	52-68	2	A:52-68 - D:52-68 -

Biological Unit 2 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RIBOSOMAL_L20	PS00937	Ribosomal protein L20 signature.	RL20_AQUAE	52-68	2	- B:52-68 - E:52-68

Biological Unit 3 (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RIBOSOMAL_L20	PS00937	Ribosomal protein L20 signature.	RL20_AQUAE	52-68	4	A:52-68 B:52-68 D:52-68 E:52-68

Biological Unit 4 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RIBOSOMAL_L20	PS00937	Ribosomal protein L20 signature.	RL20_AQUAE	52-68	2	- B:52-68 D:52-68 -

Biological Unit 5 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RIBOSOMAL_L20	PS00937	Ribosomal protein L20 signature.	RL20_AQUAE	52-68	2	A:52-68 - - E:52-68

(no "Exon" information available for 2GHJ)

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:101
 aligned with RL20_AQUAE | O67086 from UniProtKB/Swiss-Prot  Length:118

    Alignment length:101
                                    27        37        47        57        67        77        87        97       107       117 
           RL20_AQUAE    18 LAKGYRGQRSRSYRRAKEAVMRALYYQYRDRKLRKREFRRLWIARINAAVRAYGLNYSTFINGLKKAGIELDRKILADMAVRDPQAFEQVVNKVKEALQVQ 118
               SCOP domains ----------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------2ghjA02 A:50-118 Ribosomal protein L20                                CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------RIBOSOMAL_L20    -------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------- Transcript
                 2ghj A  18 LAKGYRGQRSRSYRRAKEAVmRALYYQYRDRKLRKREFRRLWIARINAAVRAYGLNYSTFINGLKKAGIELDRKILADmAVRDPQAFEQVVNKVKEALQVQ 118
                                    27        37|       47        57        67        77        87        97       107       117 
                                               38-MSE                                                    96-MSE

Chain B from PDB  Type:PROTEIN  Length:92
 aligned with RL20_AQUAE | O67086 from UniProtKB/Swiss-Prot  Length:118

    Alignment length:92
                                    36        46        56        66        76        86        96       106       116  
           RL20_AQUAE    27 SRSYRRAKEAVMRALYYQYRDRKLRKREFRRLWIARINAAVRAYGLNYSTFINGLKKAGIELDRKILADMAVRDPQAFEQVVNKVKEALQVQ 118
               SCOP domains -------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh...hhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------RIBOSOMAL_L20    -------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------- Transcript
                 2ghj B  27 SRSYRRAKEAVmRALYYQYRDRKLRKREFRRLWIARINAAVRAYGLNYSTFINGLKKAGIELDRKILADmAVRDPQAFEQVVNKVKEALQVQ 118
                                    36 |      46        56        66        76        86        96       106       116  
                                      38-MSE                                                    96-MSE

Chain D from PDB  Type:PROTEIN  Length:101
 aligned with RL20_AQUAE | O67086 from UniProtKB/Swiss-Prot  Length:118

    Alignment length:101
                                    27        37        47        57        67        77        87        97       107       117 
           RL20_AQUAE    18 LAKGYRGQRSRSYRRAKEAVMRALYYQYRDRKLRKREFRRLWIARINAAVRAYGLNYSTFINGLKKAGIELDRKILADMAVRDPQAFEQVVNKVKEALQVQ 118
               SCOP domains ----------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------2ghjD02 D:50-118 Ribosomal protein L20                                CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------RIBOSOMAL_L20    -------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------- Transcript
                 2ghj D  18 LAKGYRGQRSRSYRRAKEAVmRALYYQYRDRKLRKREFRRLWIARINAAVRAYGLNYSTFINGLKKAGIELDRKILADmAVRDPQAFEQVVNKVKEALQVQ 118
                                    27        37|       47        57        67        77        87        97       107       117 
                                               38-MSE                                                    96-MSE

Chain E from PDB  Type:PROTEIN  Length:92
 aligned with RL20_AQUAE | O67086 from UniProtKB/Swiss-Prot  Length:118

    Alignment length:92
                                    36        46        56        66        76        86        96       106       116  
           RL20_AQUAE    27 SRSYRRAKEAVMRALYYQYRDRKLRKREFRRLWIARINAAVRAYGLNYSTFINGLKKAGIELDRKILADMAVRDPQAFEQVVNKVKEALQVQ 118
               SCOP domains -------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------2ghjE02 E:53-118 Ribosomal protein L20                             CATH domains
               Pfam domains -------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh...hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------RIBOSOMAL_L20    -------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------- Transcript
                 2ghj E  27 SRSYRRAKEAVmRALYYQYRDRKLRKREFRRLWIARINAAVRAYGLNYSTFINGLKKAGIELDRKILADmAVRDPQAFEQVVNKVKEALQVQ 118
                                    36 |      46        56        66        76        86        96       106       116  
                                      38-MSE                                                    96-MSE

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 '\|'

(no "SCOP Domain" information available for 2GHJ)

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: c-terminal domain of poly(a) binding protein (10)

Homologous Superfamily: Ribosomal protein L20 (2)

Aquifex aeolicus. Organism_taxid: 63363. (1)

1a	2ghjE02	E:53-118
1b	2ghjA02	A:50-118
1c	2ghjD02	D:50-118

(no "Pfam Domain" information available for 2GHJ)

Asymmetric Unit(hide GO term definitions)

Chain A,B,D,E (RL20_AQUAE | O67086)

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:0000027	ribosomal large subunit assembly	The aggregation, arrangement and bonding together of constituent RNAs and proteins to form the large ribosomal subunit.
	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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