1E8O | PR0041 - JenaLib

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Title :   CORE OF THE ALU DOMAIN OF THE MAMMALIAN SRP

Authors :   O. Weichenrieder, K. Wild, K. Strub, S. Cusack

Date :   28 Sep 00 (Deposition) - 08 Nov 00 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.20

Chains :   Asym./Biol. Unit : A,B,C,D,E

Keywords :   Alu Ribonucleoprotein Particle, Protein Recognition Of An Rna U-Turn, Translational Control, Alu Rnp Assembly And Transport, Alu Retroposition (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   O. Weichenrieder, K. Wild, K. Strub, S. Cusack
Structure And Assembly Of The Alu Domain Of The Mammalian Signal Recognition Particle
Nature V. 408 167 2000
PubMed-ID: 11089964 | Reference-DOI: 10.1038/35041507

Molecule 1 - SIGNAL RECOGNITION PARTICLE 9 KDA PROTEIN
	Cellular Location	:	CYTOPLASM, NUCLEUS?
	Chains	:	A, C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Plasmid	:	PEH9
	Synonym	:	SRP9

Molecule 2 - SIGNAL RECOGNITION PARTICLE 14 KDA PROTEIN
	Cellular Location	:	CYTOPLASM, NUCLEUS?
	Chains	:	B, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	TRUNCATED AFTER K107
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Plasmid	:	PEH9
	Synonym	:	SRP14

Molecule 3 - 7SL RNA
	Cellular Location	:	CYTOPLASM, NUCLEUS
	Chains	:	E
	Fragment	:	ALU RNA 5' DOMAIN
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Other Details	:	G1-U47 OF 7SL RNA PLUS A 5'GG AND A 3'C
	Other Details - Source	:	THE RNA WAS PRODUCED BY IN VITRO TRANSCRIPTION WITH T7 RNA POLYMERASE USING RIBOZYME TECHNOLOGY.
	Plasmid	:	PSA50H
	Synthetic	:	YES

		1	2	3	4	5
Asymmetric/Biological Unit	:	A	B	C	D	E

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 4)

No.	Name	Count	Type	Full Name
1	GDP	1	Mod. Nucleotide	GUANOSINE-5'-DIPHOSPHATE
2	SO4	3	Ligand/Ion	SULFATE ION

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLN B:8 , ARG B:15 , U E:135	BINDING SITE FOR RESIDUE SO4 E1149
2	AC2	SOFTWARE	ARG B:59	BINDING SITE FOR RESIDUE SO4 B1002
3	AC3	SOFTWARE	PRO A:2 , LYS A:52	BINDING SITE FOR RESIDUE SO4 A1076

(no "SS Bond" information available for 1E8O)

(no "Cis Peptide Bond" information available for 1E8O)

Asymmetric/Biological Unit (1, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_028058	S	68	I	SRP14_HUMAN	Polymorphism	1802600	B/D	S	68	I

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(no "PROSITE Motif" information available for 1E8O)

Asymmetric/Biological Unit (8, 16)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000267884	1	ENSE00001099640	chr15:40331389-40331294	96	SRP14_HUMAN	1-8	8	2	B:2-8 D:2-8	7 7
1.2	ENST00000267884	2	ENSE00000942420	chr15:40331149-40331077	73	SRP14_HUMAN	9-33	25	2	B:9-33 D:9-33	25 25
1.3	ENST00000267884	3	ENSE00000942421	chr15:40330595-40330483	113	SRP14_HUMAN	33-70	38	2	B:33-70 (gaps) D:33-70 (gaps)	38 38
1.4	ENST00000267884	4	ENSE00000942422	chr15:40329219-40329187	33	SRP14_HUMAN	71-81	11	2	B:71-81 D:71-81	11 11
1.5	ENST00000267884	5	ENSE00001099638	chr15:40328701-40327891	811	SRP14_HUMAN	82-136	55	2	B:82-95 D:82-95	14 14

2.1a	ENST00000304786	1a	ENSE00001442734	chr1:225965531-225965714	184	SRP09_HUMAN	1-24	24	2	A:2-24 C:5-24	23 20
2.2	ENST00000304786	2	ENSE00000961765	chr1:225971002-225971070	69	SRP09_HUMAN	25-47	23	2	A:25-47 C:25-47	23 23
2.5b	ENST00000304786	5b	ENSE00001838300	chr1:225976942-225978168	1227	SRP09_HUMAN	48-86	39	2	A:48-75 C:48-75	28 28

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:74
 aligned with SRP09_HUMAN | P49458 from UniProtKB/Swiss-Prot  Length:86

    Alignment length:74
                                    11        21        31        41        51        61        71    
          SRP09_HUMAN     2 PQYQTWEEFSRAAEKLYLADPMKARVVLKYRHSDGNLCVKVTDDLVCLVYKTDQAQDVKKIEKFHSQLMRLMVA  75
               SCOP domains d1e8oa_ A: Signal recognition particle 9KDa protein, SRP9                  SCOP domains
               CATH domains 1e8oA00 A:2-75                                                             CATH domains
               Pfam domains -------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhh.....eeee........eeeeee....eeeeee...hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------- PROSITE
               Transcript 2 Exon 2.1a  PDB: A:2-24 Exon 2.2  PDB: A:25-47 Exon 2.5b  PDB: A:48-75      Transcript 2
                 1e8o A   2 PQYQTWEEFSRAAEKLYLADPMKARVVLKYRHSDGNLCVKVTDDLVCLVYKTDQAQDVKKIEKFHSQLMRLMVA  75
                                    11        21        31        41        51        61        71

Chain B from PDB  Type:PROTEIN  Length:75
 aligned with SRP14_HUMAN | P37108 from UniProtKB/Swiss-Prot  Length:136

    Alignment length:94
                                    11        21        31        41        51        61        71        81        91    
          SRP14_HUMAN     2 VLLESEQFLTELTRLFQKCRTSGSVYITLKKYDGRTKPIPKKGTVEGFEPADNKCLLRATDGKKKISTVVSSKEVNKFQMAYSNLLRANMDGLK  95
               SCOP domains d1e8ob_ B: Signal recognition par                   ticle 14KDa protein, SRP14                 SCOP domains
               CATH domains 1e8oB00 B:2-95 Signal recognition                    particle alu RNA binding heterodimer, srp CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhh.....eeeeeee.-------------------.eeeeeee....eeeeeee..hhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------I--------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) 1.1    Exon 1.2  PDB: B:9-33    -------------------------------------Exon 1.4   Exon 1.5       Transcript 1 (1)
           Transcript 1 (2) -------------------------------Exon 1.3  PDB: B:33-70 (gaps)         ------------------------- Transcript 1 (2)
                 1e8o B   2 VLLESEQFLTELTRLFQKCRTSGSVYITLKKYD-------------------NKCLLRATDGKKKISTVVSSKEVNKFQMAYSNLLRANMDGLK  95
                                    11        21        31  |      -         -  |     61        71        81        91    
                                                           34                  54

Chain C from PDB  Type:PROTEIN  Length:71
 aligned with SRP09_HUMAN | P49458 from UniProtKB/Swiss-Prot  Length:86

    Alignment length:71
                                    14        24        34        44        54        64        74 
          SRP09_HUMAN     5 QTWEEFSRAAEKLYLADPMKARVVLKYRHSDGNLCVKVTDDLVCLVYKTDQAQDVKKIEKFHSQLMRLMVA  75
               SCOP domains d1e8oc_ C: Signal recognition particle 9KDa protein, SRP9               SCOP domains
               CATH domains 1e8oC00 C:5-75                                                          CATH domains
               Pfam domains ----------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhh....eeee........eeeeee.....eeeee.hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------- PROSITE
               Transcript 2 Exon 2.1a           Exon 2.2  PDB: C:25-47 Exon 2.5b  PDB: C:48-75      Transcript 2
                 1e8o C   5 QTWEEFSRAAEKLYLADPMKARVVLKYRHSDGNLCVKVTDDLVCLVYKTDQAQDVKKIEKFHSQLMRLMVA  75
                                    14        24        34        44        54        64        74

Chain D from PDB  Type:PROTEIN  Length:76
 aligned with SRP14_HUMAN | P37108 from UniProtKB/Swiss-Prot  Length:136

    Alignment length:94
                                    11        21        31        41        51        61        71        81        91    
          SRP14_HUMAN     2 VLLESEQFLTELTRLFQKCRTSGSVYITLKKYDGRTKPIPKKGTVEGFEPADNKCLLRATDGKKKISTVVSSKEVNKFQMAYSNLLRANMDGLK  95
               SCOP domains d1e8od_ D: Signal recognition part                  icle 14KDa protein, SRP14                  SCOP domains
               CATH domains 1e8oD00 D:2-95 Signal recognition                   particle alu RNA binding heterodimer, srp9 CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhh.......eeeeeee..------------------.eeeeeee....eeeeeee..hhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------I--------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) 1.1    Exon 1.2  PDB: D:9-33    -------------------------------------Exon 1.4   Exon 1.5       Transcript 1 (1)
           Transcript 1 (2) -------------------------------Exon 1.3  PDB: D:33-70 (gaps)         ------------------------- Transcript 1 (2)
                 1e8o D   2 VLLESEQFLTELTRLFQKCRTSGSVYITLKKYDG------------------NKCLLRATDGKKKISTVVSSKEVNKFQMAYSNLLRANMDGLK  95
                                    11        21        31   |     -         -  |     61        71        81        91    
                                                            35                 54

Chain E from PDB  Type:RNA  Length:50
                                                                                  
                 1e8o E  99 gGGCCGGGCGCGGUGGCGCGCGCCUGUAGUCCCAGCUACUCGGGAGGCUC 148
                            |      108       118       128       138       148
                           99-GDP

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/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Signal recognition particle alu RNA binding heterodimer, srp9/1 (3)

Homologous Superfamily: Signal recognition particle alu RNA binding heterodimer, srp9/1 (3)

Human (Homo sapiens) (1)

1a	1e8oD00	D:2-95
1b	1e8oB00	B:2-95
1c	1e8oA00	A:2-75
1d	1e8oC00	C:5-75

(no "Pfam Domain" information available for 1E8O)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,C (SRP09_HUMAN | P49458)

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.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0005047	signal recognition particle binding	Interacting selectively and non-covalently with the signal recognition particle.
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:0006616	SRP-dependent cotranslational protein targeting to membrane, translocation	The process during cotranslational membrane targeting wherein proteins move across a membrane. SRP and its receptor initiate the transfer of the nascent chain across the endoplasmic reticulum (ER) membrane; they then dissociate from the chain, which is transferred to a set of transmembrane proteins, collectively called the translocon. Once the nascent chain translocon complex is assembled, the elongating chain passes directly from the large ribosomal subunit into the centers of the translocon, a protein-lined channel within the membrane. The growing chain is never exposed to the cytosol and does not fold until it reaches the ER lumen.
	GO:0045900	negative regulation of translational elongation	Any process that stops, prevents, or reduces the frequency, rate or extent of translational elongation.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	GO:0070062	extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
	GO:0048500	signal recognition particle	A complex of protein and RNA which facilitates translocation of proteins across membranes.
	GO:0005785	signal recognition particle receptor complex	A transmembrane heterodimeric protein located in the membrane of the rough endoplasmic reticulum. Both subunits contain GTPase domains with which signal recognition particle interacts. In the presence of GTP and SRP receptor, SRP is released from the ribosome-nascent chain complex.
	GO:0005786	signal recognition particle, endoplasmic reticulum targeting	A ribonucleoprotein particle of 325 kDa composed of a 7S (300 nucleotide) RNA molecule and a complex of six different polypeptides. This binds both to the N-terminal signal peptide for proteins destined for the endoplasmic reticulum as they emerge from the large ribosomal subunit and also to the ribosome. This binding arrests further translation thereby preventing the proteins from being released into the cytosol. The SRP-ribosome complex then diffuses to the endoplasmic reticulum where it is bound to the signal recognition particle receptor, which allows resumption of protein synthesis and facilitates the passage of the growing polypeptide chain through the translocon. Through a process involving GTP hydrolysis, the SRP-SRP receptor complex dissociates and SRP returns to the cytosol. Of the six polypeptides of SRP the 54 kDa subunit (SRP54) is the central player. It contains an N-terminal GTPase domain and a C-terminal domain that binds directly to the signal peptide and the SRP RNA. Examples of this component are found in Mus musculus, Saccharomyces cerevisiae and Arabidopsis thaliana.

Chain B,D (SRP14_HUMAN | P37108)

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.
	GO:0030942	endoplasmic reticulum signal peptide binding	Interacting selectively and non-covalently with an endoplasmic reticulum signal peptide, a specific peptide sequence that acts as a signal to localize the protein within the endoplasmic reticulum.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
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:0006613	cotranslational protein targeting to membrane	The targeting of proteins to a membrane that occurs during translation. The transport of most secretory proteins, particularly those with more than 100 amino acids, into the endoplasmic reticulum lumen occurs in this manner, as does the import of some proteins into mitochondria.
	GO:0045047	protein targeting to ER	The process of directing proteins towards the endoplasmic reticulum (ER) using signals contained within the protein. One common mechanism uses a 16- to 30-residue signal sequence, typically located at the N-terminus of the protein and containing positively charged amino acids followed by a continuous stretch of hydrophobic residues, which directs the ribosome to the ER membrane and initiates transport of the growing polypeptide across the ER membrane.
	GO:0042493	response to drug	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	GO:0070062	extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
	GO:0048500	signal recognition particle	A complex of protein and RNA which facilitates translocation of proteins across membranes.
	GO:0005786	signal recognition particle, endoplasmic reticulum targeting	A ribonucleoprotein particle of 325 kDa composed of a 7S (300 nucleotide) RNA molecule and a complex of six different polypeptides. This binds both to the N-terminal signal peptide for proteins destined for the endoplasmic reticulum as they emerge from the large ribosomal subunit and also to the ribosome. This binding arrests further translation thereby preventing the proteins from being released into the cytosol. The SRP-ribosome complex then diffuses to the endoplasmic reticulum where it is bound to the signal recognition particle receptor, which allows resumption of protein synthesis and facilitates the passage of the growing polypeptide chain through the translocon. Through a process involving GTP hydrolysis, the SRP-SRP receptor complex dissociates and SRP returns to the cytosol. Of the six polypeptides of SRP the 54 kDa subunit (SRP54) is the central player. It contains an N-terminal GTPase domain and a C-terminal domain that binds directly to the signal peptide and the SRP RNA. Examples of this component are found in Mus musculus, Saccharomyces cerevisiae and Arabidopsis thaliana.

Asymmetric/Biological Unit
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	1e8o
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	SRP14_HUMAN \| P37108
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	SRP09_HUMAN \| P49458	:	1e8s 1ry1 4uyj 4uyk 5aox
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Description

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Ligands, Modified Residues, Ions (2, 4)

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Exons (8, 16)

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