3DM5 - JenaLib

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Biological Unit 5 (Jmol Viewer)

Title :   STRUCTURES OF SRP54 AND SRP19, THE TWO PROTEINS ASSEMBLING THE RIBONUCLEIC CORE OF THE SIGNAL RECOGNITION PARTICLE FROM THE ARCHAEON PYROCOCCUS FURIOSUS.

Authors :   P. F. Egea, J. Napetschnig, P. Walter, R. M. Stroud

Date :   30 Jun 08 (Deposition) - 04 Nov 08 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.51

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

Keywords :   Protein-Rna, Signal Recognition Particle, Srp-Gtpase, Protein Targeting, Cytoplasm, Gtp-Binding, Nucleotide- Binding, Ribonucleoprotein, Rna-Binding, Rna Binding Protein, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   P. F. Egea, J. Napetschnig, P. Walter, R. M. Stroud
Structures Of Srp54 And Srp19, The Two Proteins That Organize The Ribonucleic Core Of The Signal Recognition Particle From Pyrococcus Furiosus.
Plos One V. 3 E3528 2008
PubMed-ID: 18953414 | Reference-DOI: 10.1371/JOURNAL.PONE.0003528
(for further references see the PDB file header)

Molecule 1 - SIGNAL RECOGNITION 54 KDA PROTEIN
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET 28B
	Expression System Strain	:	BL21(DE3) ROSETTA2
	Expression System Vector Type	:	PLASMID
	Gene	:	SRP54, PF1731
	Organism Scientific	:	PYROCOCCUS FURIOSUS
	Organism Taxid	:	2261
	Strain	:	DSM3638
	Synonym	:	SRP54

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 15)

No.	Name	Count	Type	Full Name
1	ACT	2	Ligand/Ion	ACETATE ION
2	GDP	2	Ligand/Ion	GUANOSINE-5'-DIPHOSPHATE
3	SO4	11	Ligand/Ion	SULFATE ION

Biological Unit 1 (3, 30)

No.	Name	Count	Type	Full Name
1	ACT	4	Ligand/Ion	ACETATE ION
2	GDP	4	Ligand/Ion	GUANOSINE-5'-DIPHOSPHATE
3	SO4	22	Ligand/Ion	SULFATE ION

Biological Unit 2 (3, 16)

No.	Name	Count	Type	Full Name
1	ACT	2	Ligand/Ion	ACETATE ION
2	GDP	2	Ligand/Ion	GUANOSINE-5'-DIPHOSPHATE
3	SO4	12	Ligand/Ion	SULFATE ION

Biological Unit 3 (3, 14)

No.	Name	Count	Type	Full Name
1	ACT	2	Ligand/Ion	ACETATE ION
2	GDP	2	Ligand/Ion	GUANOSINE-5'-DIPHOSPHATE
3	SO4	10	Ligand/Ion	SULFATE ION

Biological Unit 4 (3, 8)

No.	Name	Count	Type	Full Name
1	ACT	1	Ligand/Ion	ACETATE ION
2	GDP	1	Ligand/Ion	GUANOSINE-5'-DIPHOSPHATE
3	SO4	6	Ligand/Ion	SULFATE ION

Biological Unit 5 (3, 7)

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

Asymmetric Unit (12, 12)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	LYS A:126 , ARG A:127 , ASP A:380	BINDING SITE FOR RESIDUE SO4 A 444
02	AC2	SOFTWARE	LYS B:126 , ARG B:127 , ASP B:380	BINDING SITE FOR RESIDUE SO4 B 444
03	AC3	SOFTWARE	ARG A:288 , ARG A:292	BINDING SITE FOR RESIDUE SO4 A 445
04	AC4	SOFTWARE	ARG A:148 , HIS B:145	BINDING SITE FOR RESIDUE SO4 B 445
05	AC5	SOFTWARE	HIS A:145 , ARG B:148	BINDING SITE FOR RESIDUE SO4 A 446
06	AC6	SOFTWARE	ARG A:33 , GLN B:227 , ASN B:230	BINDING SITE FOR RESIDUE SO4 A 447
07	AC7	SOFTWARE	ASP A:197 , LYS A:198	BINDING SITE FOR RESIDUE SO4 A 448
08	AC8	SOFTWARE	LYS B:72 , LYS B:311	BINDING SITE FOR RESIDUE SO4 B 446
09	AC9	SOFTWARE	GLN A:227 , ASN A:230 , ARG B:33	BINDING SITE FOR RESIDUE SO4 B 447
10	BC1	SOFTWARE	SER B:70 , LYS B:71	BINDING SITE FOR RESIDUE SO4 B 448
11	BC2	SOFTWARE	GLY A:110 , SER A:111 , GLY A:112 , LYS A:113 , THR A:114 , THR A:115 , LYS A:119 , ARG A:140 , GLN A:146 , LYS A:248 , ASP A:250 , GLY A:273 , THR A:274 , GLY A:275 , GLU A:276 , GLU B:276	BINDING SITE FOR RESIDUE GDP A 501
12	BC3	SOFTWARE	GLU A:276 , GLY B:110 , SER B:111 , GLY B:112 , LYS B:113 , THR B:114 , THR B:115 , LYS B:119 , ARG B:140 , GLN B:146 , LYS B:248 , ASP B:250 , GLY B:273 , THR B:274 , GLY B:275 , GLU B:276	BINDING SITE FOR RESIDUE GDP B 501

(no "SS Bond" information available for 3DM5)

Asymmetric Unit

No.	Residues
1	Gly A:344	-	Pro A:345
2	Gly B:344	-	Pro B:345

(no "SAP(SNP)/Variant" information available for 3DM5)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SRP54	PS00300	SRP54-type proteins GTP-binding domain signature.	SRP54_PYRFU	268-281	2	A:268-281 B:268-281

Biological Unit 1 (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SRP54	PS00300	SRP54-type proteins GTP-binding domain signature.	SRP54_PYRFU	268-281	4	A:268-281 B:268-281

Biological Unit 2 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SRP54	PS00300	SRP54-type proteins GTP-binding domain signature.	SRP54_PYRFU	268-281	2	A:268-281 -

Biological Unit 3 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SRP54	PS00300	SRP54-type proteins GTP-binding domain signature.	SRP54_PYRFU	268-281	2	- B:268-281

Biological Unit 4 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SRP54	PS00300	SRP54-type proteins GTP-binding domain signature.	SRP54_PYRFU	268-281	1	A:268-281 -

Biological Unit 5 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SRP54	PS00300	SRP54-type proteins GTP-binding domain signature.	SRP54_PYRFU	268-281	1	- B:268-281

(no "Exon" information available for 3DM5)

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:416
 aligned with SRP54_PYRFU | Q8U070 from UniProtKB/Swiss-Prot  Length:443

    Alignment length:435
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430     
          SRP54_PYRFU     1 MVLDNLGKALANTLKKIARASSVDEALIKELVRDIQRALIQADVNVRLVLQLTREIQRRALEEKPPAGISKKEHIIKIVYEELTKFLGTEAKPIEIKEKPTILLMVGIQGSGKTTTVAKLARYFQKRGYKVGVVCSDTWRPGAYHQLRQLLDRYHIEVFGNPQEKDAIKLAKEGVDYFKSKGVDIIIVDTAGRHKEDKALIEEMKQISNVIHPHEVILVIDGTIGQQAYNQALAFKEATPIGSIIVTKLDGSAKGGGALSAVAATGAPIKFIGTGEKIDDIEPFDPPRFVSRLLGLGDIQGLLEKFKELEKEVEIKEEDIERFLRGKFTLKDMYAQLEAMRKMGPLKQILRMIPGLGYSLPDDVISIGEERLKKFKVIMDSMTEEELLNPEIINYSRIKRIARGSGTSTKDVKELLDQYRQMKKLFKSMNKRQLS 435
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh.............eeeeee.....hhhhhhhhhhhhhhh....eeeee.....hhhhhhhhhhhhhhh.eee......hhhhhhhhhhhhhhhh...eeeee.......hhhhhhhhhhhhhhhh..eeeeeee.hhhhhhhhhhhhhhhh...eeeeee......hhhhhhhhhhh....eeeee.......eee.hhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh...-------------------...hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------SRP54         ---------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3dm5 A   1 MVLDNLGKALANTLKKIARASSVDEALIKELVRDIQRALIQADVNVRLVLQLTREIQRRALEEKPPAGISKKEHIIKIVYEELTKFLGTEAKPIEIKEKPTILLMVGIQGSGKTTTVAKLARYFQKRGYKVGVVCSDTWRPGAYHQLRQLLDRYHIEVFGNPQEKDAIKLAKEGVDYFKSKGVDIIIVDTAGRHKEDKALIEEMKQISNVIHPHEVILVIDGTIGQQAYNQALAFKEATPIGSIIVTKLDGSAKGGGALSAVAATGAPIKFIGTGEKIDDIEPFDPPRFVSRLLGLGDIQGLLEKFKELEKEVEIKEEDIERFLRGKFTLKDMYAQLEAMRKMGP-------------------ISIGEERLKKFKVIMDSMTEEELLNPEIINYSRIKRIARGSGTSTKDVKELLDQYRQMKKLFKSMNKRQLS 435
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340    |    -         -    |  370       380       390       400       410       420       430     
                                                                                                                                                                                                                                                                                                                                                                                  345                 365

Chain B from PDB  Type:PROTEIN  Length:413
 aligned with SRP54_PYRFU | Q8U070 from UniProtKB/Swiss-Prot  Length:443

    Alignment length:434
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430    
          SRP54_PYRFU     1 MVLDNLGKALANTLKKIARASSVDEALIKELVRDIQRALIQADVNVRLVLQLTREIQRRALEEKPPAGISKKEHIIKIVYEELTKFLGTEAKPIEIKEKPTILLMVGIQGSGKTTTVAKLARYFQKRGYKVGVVCSDTWRPGAYHQLRQLLDRYHIEVFGNPQEKDAIKLAKEGVDYFKSKGVDIIIVDTAGRHKEDKALIEEMKQISNVIHPHEVILVIDGTIGQQAYNQALAFKEATPIGSIIVTKLDGSAKGGGALSAVAATGAPIKFIGTGEKIDDIEPFDPPRFVSRLLGLGDIQGLLEKFKELEKEVEIKEEDIERFLRGKFTLKDMYAQLEAMRKMGPLKQILRMIPGLGYSLPDDVISIGEERLKKFKVIMDSMTEEELLNPEIINYSRIKRIARGSGTSTKDVKELLDQYRQMKKLFKSMNKRQL 434
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhh.............eeeeeee....hhhhhhhhhhhhhhh....eeeeee.....hhhhhhhhhhhhhh.eeee.....hhhhhhhhhhhhhhhh...eeeeee......hhhhhh-hhhhhhhhh..eeeeeee.hhhhhhhhhhhhhhhh...eeeeee......hhhhhhhhhhh....eeeee.......eee.hhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh....--------------------...hhhhhhhhhhhh..hhhhhhhhhhh.hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------SRP54         --------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3dm5 B   1 MVLDNLGKALANTLKKIARASSVDEALIKELVRDIQRALIQADVNVRLVLQLTREIQRRALEEKPPAGISKKEHIIKIVYEELTKFLGTEAKPIEIKEKPTILLMVGIQGSGKTTTVAKLARYFQKRGYKVGVVCSDTWRPGAYHQLRQLLDRYHIEVFGNPQEKDAIKLAKEGVDYFKSKGVDIIIVDTAGRHKEDKALIE-MKQISNVIHPHEVILVIDGTIGQQAYNQALAFKEATPIGSIIVTKLDGSAKGGGALSAVAATGAPIKFIGTGEKIDDIEPFDPPRFVSRLLGLGDIQGLLEKFKELEKEVEIKEEDIERFLRGKFTLKDMYAQLEAMRKMGP--------------------SIGEERLKKFKVIMDSMTEEELLNPEIINYSRIKRIARGSGTSTKDVKELLDQYRQMKKLFKSMNKRQL 434
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200 | |   210       220       230       240       250       260       270       280       290       300       310       320       330       340    |    -         -     | 370       380       390       400       410       420       430    
                                                                                                                                                                                                                                   202 |                                                                                                                                          345                  366                                                                    
                                                                                                                                                                                                                                     204

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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 "SCOP Domain" information available for 3DM5)

(no "CATH Domain" information available for 3DM5)

(no "Pfam Domain" information available for 3DM5)

Asymmetric Unit(hide GO term definitions)

Chain A,B (SRP54_PYRFU | Q8U070)

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:0005525	GTP binding	Interacting selectively and non-covalently with GTP, guanosine triphosphate.
	GO:0003924	GTPase activity	Catalysis of the reaction: GTP + H2O = GDP + phosphate.
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
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:0030529	intracellular ribonucleoprotein complex	An intracellular macromolecular complex containing both protein and RNA molecules.
	GO:0048500	signal recognition particle	A complex of protein and RNA which facilitates translocation of proteins across membranes.

Asymmetric Unit
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	Cis Peptide Bonds
		Gly A:344 - Pro A:345	[ RasMol ]
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3dlu	STRUCTURE OF THE PROTEIN SRP19 FROM PYROCOCCUS FURIOSUS. MONOCLINIC CRYSTAL FORM
3dlv	STRUCTURE OF THE PROTEIN SRP19 FROM PYROCOCCUS FURIOSUS. ORTHORHOMBIC CRYSTAL FORM

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Ligands, Modified Residues, Ions (3, 15)

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