2HBA - JenaLib

Title :   CRYSTAL STRUCTURE OF N-TERMINAL DOMAIN OF RIBOSOMAL PROTEIN L9 (NTL9) K12M

Authors :   J. -H. Cho, E. Y. Kim, H. Schindelin, D. P. Raleigh

Date :   14 Jun 06 (Deposition) - 29 May 07 (Release) - 24 Sep 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.25

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

Keywords :   L9, Ribosomal Protein, Ntl9, K12M, Rna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. H. Cho, W. Meng, S. Sato, E. Y. Kim, H. Schindelin, D. P. Raleigh
Energetically Significant Networks Of Coupled Interactions Within An Unfolded Protein.
Proc. Natl. Acad. Sci. Usa V. 111 12079 2014
PubMed-ID: 25099351 | Reference-DOI: 10.1073/PNAS.1402054111

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 19)

Asymmetric Unit (3, 19)

No.	Name	Count	Type	Full Name
1	CL	10	Ligand/Ion	CHLORIDE ION
2	IMD	1	Ligand/Ion	IMIDAZOLE
3	ZN	8	Ligand/Ion	ZINC ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	IMD	-1	Ligand/Ion	IMIDAZOLE
3	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	IMD	1	Ligand/Ion	IMIDAZOLE
3	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 3 (1, 2)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	IMD	2	Ligand/Ion	IMIDAZOLE
3	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 4 (1, 2)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	IMD	2	Ligand/Ion	IMIDAZOLE
3	ZN	-1	Ligand/Ion	ZINC ION

Sites (19, 19)

Asymmetric Unit (19, 19)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	MET A:1 , ASP A:23 , CL A:203 , HOH A:210 , HOH B:306	BINDING SITE FOR RESIDUE ZN A 101
02	AC2	SOFTWARE	ASP A:8 , LYS A:10 , CL A:204 , CL A:205 , HOH A:234 , HOH B:304	BINDING SITE FOR RESIDUE ZN A 102
03	AC3	SOFTWARE	HOH A:220 , MET B:1 , ASP B:23 , CL B:210	BINDING SITE FOR RESIDUE ZN B 103
04	AC4	SOFTWARE	ASP B:8 , CL B:206 , HOH B:309 , HOH B:322	BINDING SITE FOR RESIDUE ZN B 104
05	AC5	SOFTWARE	GLU B:17 , CL B:201 , CL B:202 , HOH B:303	BINDING SITE FOR RESIDUE ZN B 105
06	AC6	SOFTWARE	CL A:208 , HOH A:217 , HOH A:233 , HOH B:305	BINDING SITE FOR RESIDUE ZN A 106
07	AC7	SOFTWARE	CL B:207 , CL B:209 , IMD B:301 , HOH B:308	BINDING SITE FOR RESIDUE ZN B 107
08	AC8	SOFTWARE	HOH B:317 , HOH B:334	BINDING SITE FOR RESIDUE ZN B 108
09	AC9	SOFTWARE	GLU B:17 , LYS B:19 , ZN B:105 , CL B:202	BINDING SITE FOR RESIDUE CL B 201
10	BC1	SOFTWARE	GLY B:13 , LYS B:14 , GLU B:17 , ZN B:105 , CL B:201	BINDING SITE FOR RESIDUE CL B 202
11	BC2	SOFTWARE	MET A:1 , ASP A:23 , ZN A:101 , HOH A:241 , LYS B:10 , HOH B:306	BINDING SITE FOR RESIDUE CL A 203
12	BC3	SOFTWARE	ASP A:8 , LYS A:10 , ZN A:102 , CL A:205 , LYS B:14 , ASN B:20	BINDING SITE FOR RESIDUE CL A 204
13	BC4	SOFTWARE	ASP A:8 , ZN A:102 , CL A:204 , HOH A:209 , HOH A:234	BINDING SITE FOR RESIDUE CL A 205
14	BC5	SOFTWARE	ASN A:20 , ASP B:8 , ZN B:104	BINDING SITE FOR RESIDUE CL B 206
15	BC6	SOFTWARE	ALA B:22 , TYR B:25 , ZN B:107 , CL B:209 , IMD B:301	BINDING SITE FOR RESIDUE CL B 207
16	BC7	SOFTWARE	ALA A:22 , TYR A:25 , ZN A:106	BINDING SITE FOR RESIDUE CL A 208
17	BC8	SOFTWARE	ZN B:107 , CL B:207 , IMD B:301	BINDING SITE FOR RESIDUE CL B 209
18	BC9	SOFTWARE	ASP A:8 , MET B:1 , ASP B:23 , ZN B:103	BINDING SITE FOR RESIDUE CL B 210
19	CC1	SOFTWARE	ASP A:8 , ASP B:23 , ZN B:107 , CL B:207 , CL B:209	BINDING SITE FOR RESIDUE IMD B 301

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RIBOSOMAL_L9	PS00651	Ribosomal protein L9 signature.	RL9_GEOSE	13-40	2	A:13-40 B:13-40

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RIBOSOMAL_L9	PS00651	Ribosomal protein L9 signature.	RL9_GEOSE	13-40	1	A:13-40 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RIBOSOMAL_L9	PS00651	Ribosomal protein L9 signature.	RL9_GEOSE	13-40	1	- B:13-40

Biological Unit 3 (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RIBOSOMAL_L9	PS00651	Ribosomal protein L9 signature.	RL9_GEOSE	13-40	4	A:13-40 B:13-40

Biological Unit 4 (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RIBOSOMAL_L9	PS00651	Ribosomal protein L9 signature.	RL9_GEOSE	13-40	4	A:13-40 B:13-40

Exons (0, 0)

Sequences/Alignments

Asymmetric Unit

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

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Chain A from PDB  Type:PROTEIN  Length:52
 aligned with RL9_GEOSE | P02417 from UniProtKB/Swiss-Prot  Length:149

    Alignment length:52
                                    10        20        30        40        50  
             RL9_GEOSE    1 MKVIFLKDVKGKGKKGEIKNVADGYANNFLFKQGLAIEATPANLKALEAQKQ 52
               SCOP domains d2hbaa1 A:1-52 Ribosomal protein L9 N-domain         SCOP domains
               CATH domains 2hbaA00 A:1-52 Ribosomal Protein L9, domain 1        CATH domains
               Pfam domains ---------------------------------------------------- Pfam domains
         Sec.struct. author .eeee............eee.hhhhhhhh......eee.hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------RIBOSOMAL_L9  PDB: A:13-40  ------------ PROSITE
                 Transcript ---------------------------------------------------- Transcript
                  2hba A  1 MKVIFLKDVKGMGKKGEIKNVADGYANNFLFKQGLAIEATPANLKALEAQKQ 52
                                    10        20        30        40        50

Chain B from PDB  Type:PROTEIN  Length:52
 aligned with RL9_GEOSE | P02417 from UniProtKB/Swiss-Prot  Length:149

    Alignment length:52
                                    10        20        30        40        50  
             RL9_GEOSE    1 MKVIFLKDVKGKGKKGEIKNVADGYANNFLFKQGLAIEATPANLKALEAQKQ 52
               SCOP domains d2hbab1 B:1-52 Ribosomal protein L9 N-domain         SCOP domains
               CATH domains 2hbaB00 B:1-52 Ribosomal Protein L9, domain 1        CATH domains
               Pfam domains ---------------------------------------------------- Pfam domains
         Sec.struct. author .eeee............eee.hhhhhhhh......eee.hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------RIBOSOMAL_L9  PDB: B:13-40  ------------ PROSITE
                 Transcript ---------------------------------------------------- Transcript
                  2hba B  1 MKVIFLKDVKGMGKKGEIKNVADGYANNFLFKQGLAIEATPANLKALEAQKQ 52
                                    10        20        30        40        50

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Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (1, 2)

Pfam Domains (0, 0)

Gene Ontology (7, 7)

Asymmetric Unit(hide GO term definitions)

Chain A,B (RL9_GEOSE | P02417)

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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