1L9A | PR0067 - JenaLib

Title :   CRYSTAL STRUCTURE OF SRP19 IN COMPLEX WITH THE S DOMAIN OF SIGNAL RECOGNITION PARTICLE RNA

Authors :   C. Oubridge, A. Kuglstatter, L. Jovine, K. Nagai

Date :   22 Mar 02 (Deposition) - 28 Jun 02 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.90

Chains :   Asym./Biol. Unit : A,B

Keywords :   Protein-Rna Complex, Ribonucleoprotein, Srp, Signal Recognition Particle, Tetraloop, Signaling Protein/Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. Oubridge, A. Kuglstatter, L. Jovine, K. Nagai
Crystal Structure Of Srp19 In Complex With The S Domain Of Srp Rna And Its Implication For The Assembly Of The Signal Recognition Particle.
Mol. Cell V. 9 1251 2002
PubMed-ID: 12086622 | Reference-DOI: 10.1016/S1097-2765(02)00530-0
(for further references see the PDB file header)

Compounds

Molecule 1 - SIGNAL RECOGNITION PARTICLE RNA S DOMAIN
	Chains	:	B
	Engineered	:	YES
	Mutation	:	YES
	Other Details	:	MUTANT (C112G, G113A, G238U, G239C) 7SL RNA (NUCLEOTIDES 112-239)
	Other Details - Source	:	THIS SEQUENCE IS 7SL RNA FROM HOMO SAPIENS. 128 NT RNA FRAGMENT WAS IN VITRO TRANSCRIBED UNDER CONTROL OF A T7 PROMOTER WITH T7 RNA POLYMERASE. IT WAS COTRANSCRIBED WITH 2 CIS-ACTING HAMMERHEAD RIBOZYMES TO CLEAVE HOMOGENEOUS RNA FROM THE FULL LENGTH TRANSCRIPT.
	Synonym	:	SRP RNA, 7S RNA, 7SL RNA
	Synthetic	:	YES

Molecule 2 - SIGNAL RECOGNITION PARTICLE 19 KDA PROTEIN
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PRET3A
	Expression System Strain	:	C41 (DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	SRP19
	Mutation	:	YES
	Organism Scientific	:	METHANOCALDOCOCCUS JANNASCHII
	Organism Taxid	:	2190
	Synonym	:	SRP19

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 26)

Sites (24, 24)

Asymmetric Unit (24, 24)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	A B:205	BINDING SITE FOR RESIDUE MG B 101
02	AC2	SOFTWARE	U B:218	BINDING SITE FOR RESIDUE MG B 102
03	AC3	SOFTWARE	G B:193	BINDING SITE FOR RESIDUE MG B 103
04	AC4	SOFTWARE	G B:187	BINDING SITE FOR RESIDUE MG B 104
05	AC5	SOFTWARE	A B:215	BINDING SITE FOR RESIDUE MG B 105
06	AC6	SOFTWARE	C B:219	BINDING SITE FOR RESIDUE MG B 106
07	AC7	SOFTWARE	GLU A:22 , HOH B:18 , HOH B:19	BINDING SITE FOR RESIDUE MG A 107
08	AC8	SOFTWARE	G B:209 , G B:210	BINDING SITE FOR RESIDUE MG B 108
09	AC9	SOFTWARE	G B:164 , G B:165	BINDING SITE FOR RESIDUE MG B 110
10	BC1	SOFTWARE	HOH B:20 , U B:226 , G B:227	BINDING SITE FOR RESIDUE MG B 111
11	BC2	SOFTWARE	A B:215	BINDING SITE FOR RESIDUE MG B 240
12	BC3	SOFTWARE	HOH B:16 , G B:152	BINDING SITE FOR RESIDUE MG B 241
13	BC4	SOFTWARE	HOH B:11 , HOH B:12 , HOH B:13 , HOH B:14 , C B:170 , A B:172	BINDING SITE FOR RESIDUE MG B 242
14	BC5	SOFTWARE	HOH B:12 , HOH B:14 , U B:171 , A B:172	BINDING SITE FOR RESIDUE MG B 243
15	BC6	SOFTWARE	G B:227 , A B:228	BINDING SITE FOR RESIDUE MG B 244
16	BC7	SOFTWARE	G B:164	BINDING SITE FOR RESIDUE MG B 245
17	BC8	SOFTWARE	U B:166 , U B:167	BINDING SITE FOR RESIDUE MG B 246
18	BC9	SOFTWARE	G B:237 , U B:238	BINDING SITE FOR RESIDUE MG B 247
19	CC1	SOFTWARE	C B:225 , U B:226	BINDING SITE FOR RESIDUE MG B 248
20	CC2	SOFTWARE	A B:208 , G B:209	BINDING SITE FOR RESIDUE MG B 249
21	CC3	SOFTWARE	G B:206 , C B:207	BINDING SITE FOR RESIDUE MG B 250
22	CC4	SOFTWARE	HOH B:5	BINDING SITE FOR RESIDUE MG B 251
23	CC5	SOFTWARE	ASP A:33	BINDING SITE FOR RESIDUE MG A 124
24	CC6	SOFTWARE	TYR A:68 , CYS A:74 , LEU A:75	BINDING SITE FOR RESIDUE MMC A 88

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Asymmetric/Biological 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:87
 aligned with SRP19_METJA | Q58440 from UniProtKB/Swiss-Prot  Length:87

    Alignment length:87
                                    10        20        30        40        50        60        70        80       
          SRP19_METJA     1 MIIWPSYIDKKKSRREGRKVPEELAIEKPSLKDIEKALKKLGLEPKIYRDKRYPRQHWEICGCVEVDYKGNKLQLLKEICKIIKGKN  87
               SCOP domains d1l9aa_ A: SRP19                                                                        SCOP domains
               CATH domains 1l9aA00 A:1-87 SRP19                                                                    CATH domains
               Pfam domains SRP19-1l9aA01 A:1-87                                                                    Pfam domains
         Sec.struct. author eeehhhhhh....................hhhhhhhhhhhh....eee....hhhhhhh...eeee....hhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------- Transcript
                 1l9a A   1 MIIWPSYIDKKKSRREGRKVPEELAIEKPSLKDIEKALKKLGLEPKIYRDKRYPRQHWEIAGRVEVDYKGNKLCLLKEIAKIIKGKN  87
                                    10        20        30        40        50        60        70        80

Chain B from PDB  Type:RNA  Length:126
                                                                                                                                                              
                 1l9a B 112 GACACUAAGUUCGGCAUCAAUAUGGUGACCUCCCGGGAGCGGGGGACCACCAGGUUGCCUAGAGGGGUGAACCGGCCCAGGUCGGAAACGGAGCAGGUCAAAACUCCCGUGCUGAUCAGUAGUGUc 239
                                   121       131       141       151       161       171||     183       193       203       213       223       233     |
                                                                                      172|                                                             239-CCC
                                                                                       175

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 '\|'

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (1, 1)

Pfam Domains (1, 1)

Gene Ontology (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (SRP19_METJA | Q58440)

molecular function
	GO:0008312	7S RNA binding	Interacting selectively and non-covalently with 7S RNA, the RNA component of the signal recognition particle (SRP).
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
biological process
	GO:0006614	SRP-dependent cotranslational protein targeting to membrane	The targeting of proteins to a membrane that occurs during translation and is dependent upon two key components, the signal-recognition particle (SRP) and the SRP receptor. SRP is a cytosolic particle that transiently binds to the endoplasmic reticulum (ER) signal sequence in a nascent protein, to the large ribosomal unit, and to the SRP receptor in the ER membrane.
	GO:0006612	protein targeting to membrane	The process of directing proteins towards a membrane, usually using signals contained within the protein.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0048500	signal recognition particle	A complex of protein and RNA which facilitates translocation of proteins across membranes.

Visualization

Interactive Views

Asymmetric/Biological Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		CCC	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MG	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MMC	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]
		AC6	[ RasMol ]	+environment [ RasMol ]
		AC7	[ RasMol ]	+environment [ RasMol ]
		AC8	[ RasMol ]	+environment [ RasMol ]
		AC9	[ RasMol ]	+environment [ RasMol ]
		BC1	[ RasMol ]	+environment [ RasMol ]
		BC2	[ RasMol ]	+environment [ RasMol ]
		BC3	[ RasMol ]	+environment [ RasMol ]
		BC4	[ RasMol ]	+environment [ RasMol ]
		BC5	[ RasMol ]	+environment [ RasMol ]
		BC6	[ RasMol ]	+environment [ RasMol ]
		BC7	[ RasMol ]	+environment [ RasMol ]
		BC8	[ RasMol ]	+environment [ RasMol ]
		BC9	[ RasMol ]	+environment [ RasMol ]
		CC1	[ RasMol ]	+environment [ RasMol ]
		CC2	[ RasMol ]	+environment [ RasMol ]
		CC3	[ RasMol ]	+environment [ RasMol ]
		CC4	[ RasMol ]	+environment [ RasMol ]
		CC5	[ RasMol ]	+environment [ RasMol ]
		CC6	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1l9a)

Still Images

Databases and Analysis Tools

Databases

Access by PDB/NDB ID
	1l9a
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	SRP19_METJA \| Q58440
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	(no 'Enzyme Classificator' available)
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Analysis Tools

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	SRP19_METJA \| Q58440
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

Description