2V3C - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE SRP54-SRP19-7S.S SRP RNA COMPLEX OF M. JANNASCHII

Authors :   T. Hainzl, S. Huang, A. E. Sauer-Eriksson

Date :   15 Jun 07 (Deposition) - 04 Sep 07 (Release) - 24 Mar 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

Chains :   Asym. Unit : A,B,C,D,M,N
Biol. Unit 1: A,C,M  (1x)
Biol. Unit 2: B,D,N  (1x)

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

Reference :   T. Hainzl, S. Huang, A. E. Sauer-Eriksson
Interaction Of Signal-Recognition Particle 54 Gtpase Domain And Signal-Recognition Particle Rna In The Free Signal-Recognition Particle.
Proc. Natl. Acad. Sci. Usa V. 104 14911 2007
PubMed-ID: 17846429 | Reference-DOI: 10.1073/PNAS.0702467104

Molecule 1 - SIGNAL RECOGNITION PARTICLE 19 KDA PROTEIN
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Scientific	:	METHANOCALDOCOCCUS JANNASCHII
	Organism Taxid	:	2190
	Synonym	:	SRP19

Molecule 2 - SIGNAL RECOGNITION 54 KDA PROTEIN
	Chains	:	C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	RESIDUES 3-427
	Organism Scientific	:	METHANOCALDOCOCCUS JANNASCHII
	Organism Taxid	:	2190
	Synonym	:	SRP54

Molecule 3 - 7S RNA
	Chains	:	M, N
	Organism Scientific	:	METHANOCALDOCOCCUS JANNASCHII
	Organism Taxid	:	2190
	Synthetic	:	YES

		1	2	3	4	5	6
Asymmetric Unit	:	A	B	C	D	M	N
Biological Unit 1 (1x)	:	A		C		M
Biological Unit 2 (1x)	:		B		D		N

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 2V3C)

(no "Site" information available for 2V3C)

(no "SS Bond" information available for 2V3C)

(no "Cis Peptide Bond" information available for 2V3C)

(no "SAP(SNP)/Variant" information available for 2V3C)

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_METJA	268-281	2	C:268-281 D:268-281

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SRP54	PS00300	SRP54-type proteins GTP-binding domain signature.	SRP54_METJA	268-281	1	C:268-281 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SRP54	PS00300	SRP54-type proteins GTP-binding domain signature.	SRP54_METJA	268-281	1	- D:268-281

(no "Exon" information available for 2V3C)

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: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 d2v3ca_ A: SRP19                                                                        SCOP domains
               CATH domains 2v3cA00 A:1-87 SRP19                                                                    CATH domains
               Pfam domains --------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eehhhhh.....................hhhhhhhhhhhh....eee....hhhhh.....eee.....hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------- Transcript
                 2v3c A   1 MIIWPSYIDKKKSRREGRKVPEELAIEKPSLKDIEKALKKLGLEPKIYRDKRYPRQHWEICGCVEVDYKGNKLQLLKEICKIIKGKN  87
                                    10        20        30        40        50        60        70        80

Chain B 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 d2v3cb_ B: SRP19                                                                        SCOP domains
               CATH domains 2v3cB00 B:1-87 SRP19                                                                    CATH domains
               Pfam domains --------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eehhhhh.....................hhhhhhhhh.......eee....hhhhh.....eee.....hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------- Transcript
                 2v3c B   1 MIIWPSYIDKKKSRREGRKVPEELAIEKPSLKDIEKALKKLGLEPKIYRDKRYPRQHWEICGCVEVDYKGNKLQLLKEICKIIKGKN  87
                                    10        20        30        40        50        60        70        80

Chain C from PDB  Type:PROTEIN  Length:404
 aligned with SRP54_METJA | Q57565 from UniProtKB/Swiss-Prot  Length:451

    Alignment length:427
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       
          SRP54_METJA     2 LDKLGENLNKALNKLKAAAFVDKKLIKEVIKDIQRALIQADVNVKLVLKMSKEIERRALEEKTPKGLSKKEHIIKIVYEELVKLLGEEAKKLELNPKKQNVILLVGIQGSGKTTTAAKLARYIQKRGLKPALIAADTYRPAAYEQLKQLAEKIHVPIYGDETRTKSPVDIVKEGMEKFKKADVLIIDTAGRHKEEKGLLEEMKQIKEITNPDEIILVIDGTIGQQAGIQAKAFKEAVGEIGSIIVTKLDGSAKGGGALSAVAETKAPIKFIGIGEGIDDLEPFDPKKFISRLLGMGDLESLLEKAEDMVDEKTEESIDAIMRGKFTLNELMTQLEAIENMGSMKKILSMIPGFGGAMPKELSHLTEAKIKKYKVIISSMTKEERENPKIIKASRIRRIARGSGTTENDVREVLRYYETTKNAIDKLR 428
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh..........hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhh...............eeee.......hhhhhhhhhhhhhhhh.eeee.......hhhhhhhhhhhhh...ee...........hhhhhhhh.....eeeee......hhhhhhhhhhhh.......eeeeeee.hhhhhhhhhhhhhhh.....eeeeee.......hhhhhhhhhhh...eeee............hhhhhhhhhh......................hhhhhh...hhhhhhhhhh......-----------------------.hhhhhhhhhhhhh..hhhhhh.....hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------SRP54         --------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2v3c C   2 MDKLGENLNKALNKLKAAAFVDKKLIKEVIKDIQRALIQADVNVKLVLKMSKEIERRALEEKTPKGLSKKEHIIKIVYEELVKLLGEEAKKLELNPKKQNVILLVGIQGSGKTTTAAKLARYIQKRGLKPALIAADTYRPAAYEQLKQLAEKIHVPIYGDETRTKSPVDIVKEGMEKFKKADVLIIDTAGRHKEEKGLLEEMKQIKEITNPDEIILVIDGTIGQQAGIQAKAFKEAVGEIGSIIVTKLDGSAKGGGALSAVAETKAPIKFIGIGEGIDDLEPFDPKKFISRLLGMGDLESLLEKAEDMVDEKTEESIDAIMRGKFTLNELMTQLEAIENM-----------------------LTEAKIKKYKVIISSMTKEERENPKIIKASRIRRIARGSGTTENDVREVLRYYETTKNAIDKLH 428
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341         -         -   |   371       381       391       401       411       421       
                                                                                                                                                                                                                                                                                                                                                                             341                     365

Chain D from PDB  Type:PROTEIN  Length:402
 aligned with SRP54_METJA | Q57565 from UniProtKB/Swiss-Prot  Length:451

    Alignment length:427
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       
          SRP54_METJA     2 LDKLGENLNKALNKLKAAAFVDKKLIKEVIKDIQRALIQADVNVKLVLKMSKEIERRALEEKTPKGLSKKEHIIKIVYEELVKLLGEEAKKLELNPKKQNVILLVGIQGSGKTTTAAKLARYIQKRGLKPALIAADTYRPAAYEQLKQLAEKIHVPIYGDETRTKSPVDIVKEGMEKFKKADVLIIDTAGRHKEEKGLLEEMKQIKEITNPDEIILVIDGTIGQQAGIQAKAFKEAVGEIGSIIVTKLDGSAKGGGALSAVAETKAPIKFIGIGEGIDDLEPFDPKKFISRLLGMGDLESLLEKAEDMVDEKTEESIDAIMRGKFTLNELMTQLEAIENMGSMKKILSMIPGFGGAMPKELSHLTEAKIKKYKVIISSMTKEERENPKIIKASRIRRIARGSGTTENDVREVLRYYETTKNAIDKLR 428
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhh..hhhhh........hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh...........hhhhhhhhhhhhhh.................ee.ee......hhhhh..hhhhhhhhh...ee.............hhhhh.............hhhhhhhhhhh.........ee...............hhhhhh........eeehhhhh..hhhhhhhhhh.......eee.....hhhhhhh...hhhhh..eeee.................hhhhhh.................hhhhhh.......hhhhhhhhh.....-------------------------.hhhhhhhhhhhhh..hhhhhhh....hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------SRP54         --------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2v3c D   2 MDKLGENLNKALNKLKAAAFVDKKLIKEVIKDIQRALIQADVNVKLVLKMSKEIERRALEEKTPKGLSKKEHIIKIVYEELVKLLGEEAKKLELNPKKQNVILLVGIQGSGKTTTAAKLARYIQKRGLKPALIAADTYRPAAYEQLKQLAEKIHVPIYGDETRTKSPVDIVKEGMEKFKKADVLIIDTAGRHKEEKGLLEEMKQIKEITNPDEIILVIDGTIGQQAGIQAKAFKEAVGEIGSIIVTKLDGSAKGGGALSAVAETKAPIKFIGIGEGIDDLEPFDPKKFISRLLGMGDLESLLEKAEDMVDEKTEESIDAIMRGKFTLNELMTQLEAIE-------------------------LTEAKIKKYKVIISSMTKEERENPKIIKASRIRRIARGSGTTENDVREVLRYYETTKNAIDKLH 428
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       | -         -         -   |   371       381       391       401       411       421       
                                                                                                                                                                                                                                                                                                                                                                           339                       365

Chain M from PDB  Type:RNA  Length:96
                                                                                                                                
                 2v3c M 142 GGCGGUGGGGGAGCAUCUCCUGUAGGGGAGAUGUAACCCCCUUUACCUGCCGAACCCCGCCAGGCCCGGAAGGGAGCAACGGUAGGCAGGACGUCG 237
                                   151       161       171       181       191       201       211       221       231

Chain N from PDB  Type:RNA  Length:96
                                                                                                                                
                 2v3c N 142 GGCGGUGGGGGAGCAUCUCCUGUAGGGGAGAUGUAACCCCCUUUACCUGCCGAACCCCGCCAGGCCCGGAAGGGAGCAACGGUAGGCAGGACGUCG 237
                                   151       161       171       181       191       201       211       221       231

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 Unit

Classes(

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Folds(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

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Organisms( (-)

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Class: Alpha and beta proteins (a+b) (23004)

Fold: SRP19 (11)

Superfamily: SRP19 (11)

Family: SRP19 (9)

Protein domain: SRP19 (9)

Methanococcus jannaschii [TaxId: 2190] (3)

1a	d2v3ca_	A:
1b	d2v3cb_	B:

Asymmetric Unit

Classes(

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Architectures( (-)

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Topologies( (-)

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Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Phenylalanyl-tRNA Synthetase; Chain B, domain 1 (22)

Homologous Superfamily: SRP19 (8)

Methanocaldococcus jannaschii. Organism_taxid: 2190. (1)

1a	2v3cA00	A:1-87
1b	2v3cB00	B:1-87

(no "Pfam Domain" information available for 2V3C)

Asymmetric Unit(hide GO term definitions)

Chain A,B (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: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.

Chain C,D (SRP54_METJA | Q57565)

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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	2v3c
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	SRP19_METJA \| Q58440
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	SRP54_METJA \| Q57565
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UniProtKB/Swiss-Prot
	SRP19_METJA \| Q58440	:	1l9a 1lng 3ndb 4xco
	SRP54_METJA \| Q57565	:	3ndb 4xco

1l9a	CRYSTAL STRUCTURE OF SRP19 IN COMPLEX WITH THE S DOMAIN OFSIGNAL RECOGNITION PARTICLE RNA
1lng	CRYSTAL STRUCTURE OF THE SRP19-7S.S SRP RNA COMPLEX OF M.JANNASCHII

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