2FH5 - JenaLib

Asym.Unit - manually (Jmol Viewer)

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Title :   THE STRUCTURE OF THE MAMMALIAN SRP RECEPTOR

Authors :   O. Schlenker, K. Wild, I. Sinning

Date :   23 Dec 05 (Deposition) - 31 Jan 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.45

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

Keywords :   Endomembrane Targeting, Gtpase, Gap, Longin Domain, Sedl, Signal Recognition Particle Receptor, X-Ray Structure, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   O. Schlenker, A. Hendricks, I. Sinning, K. Wild
The Structure Of The Mammalian Signal Recognition Particle (Srp) Receptor As Prototype For The Interaction Of Small Gtpases With Longin Domains.
J. Biol. Chem. V. 281 8898 2006
PubMed-ID: 16439358 | Reference-DOI: 10.1074/JBC.M512415200
(for further references see the PDB file header)

Molecule 1 - SIGNAL RECOGNITION PARTICLE RECEPTOR ALPHA SUBUNIT
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET16B
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 1-129
	Gene	:	SRPR
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	SR-ALPHA, DOCKING PROTEIN ALPHA, DP-ALPHA

Molecule 2 - SIGNAL RECOGNITION PARTICLE RECEPTOR BETA SUBUNIT
	Chains	:	B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET16B
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 63-269
	Gene	:	SRPRB
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Synonym	:	SR-BETA

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 2)

No.	Name	Count	Type	Full Name
1	GTP	1	Ligand/Ion	GUANOSINE-5'-TRIPHOSPHATE
2	MG	1	Ligand/Ion	MAGNESIUM ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	GTP	1	Ligand/Ion	GUANOSINE-5'-TRIPHOSPHATE
2	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 2 (1, 4)

No.	Name	Count	Type	Full Name
1	GTP	4	Ligand/Ion	GUANOSINE-5'-TRIPHOSPHATE
2	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 3 (1, 2)

No.	Name	Count	Type	Full Name
1	GTP	2	Ligand/Ion	GUANOSINE-5'-TRIPHOSPHATE
2	MG	-1	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	THR B:76 , SER B:93 , GTP B:301 , HOH B:357 , HOH B:358	BINDING SITE FOR RESIDUE MG B 270
2	AC2	SOFTWARE	CYS B:71 , ASP B:72 , SER B:73 , GLY B:74 , LYS B:75 , THR B:76 , LEU B:77 , THR B:90 , THR B:92 , SER B:93 , GLY B:118 , ASN B:178 , LYS B:179 , ASP B:181 , ILE B:182 , SER B:245 , ALA B:246 , LYS B:247 , MG B:270 , HOH B:302 , HOH B:303 , HOH B:317 , HOH B:357 , HOH B:358	BINDING SITE FOR RESIDUE GTP B 301

Asymmetric Unit

No.	Residues
1	A:17	-	A:25

(no "Cis Peptide Bond" information available for 2FH5)

(no "SAP(SNP)/Variant" information available for 2FH5)

(no "PROSITE Motif" information available for 2FH5)

Asymmetric Unit (4, 4)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.2b	ENST00000332118	2b	ENSE00002174793	chr11:126138854-126138583	272	SRPRA_HUMAN	1-39	39	1	A:1-39	39
1.3	ENST00000332118	3	ENSE00001465013	chr11:126137981-126137898	84	SRPRA_HUMAN	40-67	28	1	A:40-67 (gaps)	28
1.4b	ENST00000332118	4b	ENSE00001299168	chr11:126137607-126137444	164	SRPRA_HUMAN	68-122	55	1	A:68-122	55
1.4d	ENST00000332118	4d	ENSE00001506987	chr11:126137230-126137070	161	SRPRA_HUMAN	122-176	55	1	A:122-129	8
1.5	ENST00000332118	5	ENSE00001465010	chr11:126136817-126136658	160	SRPRA_HUMAN	176-229	54	0	-	-
1.6	ENST00000332118	6	ENSE00001465009	chr11:126136524-126136371	154	SRPRA_HUMAN	229-280	52	0	-	-
1.7b	ENST00000332118	7b	ENSE00001465008	chr11:126136173-126136082	92	SRPRA_HUMAN	281-311	31	0	-	-
1.8	ENST00000332118	8	ENSE00001465007	chr11:126135976-126135858	119	SRPRA_HUMAN	311-351	41	0	-	-
1.9	ENST00000332118	9	ENSE00001465006	chr11:126135718-126135632	87	SRPRA_HUMAN	351-380	30	0	-	-
1.10b	ENST00000332118	10b	ENSE00001465005	chr11:126135335-126135163	173	SRPRA_HUMAN	380-437	58	0	-	-
1.11c	ENST00000332118	11c	ENSE00001465004	chr11:126135067-126134854	214	SRPRA_HUMAN	438-509	72	0	-	-
1.12b	ENST00000332118	12b	ENSE00001465002	chr11:126134434-126134271	164	SRPRA_HUMAN	509-563	55	0	-	-
1.13a	ENST00000332118	13a	ENSE00001465001	chr11:126134184-126134086	99	SRPRA_HUMAN	564-596	33	0	-	-
1.13d	ENST00000332118	13d	ENSE00001465000	chr11:126133939-126132833	1107	SRPRA_HUMAN	597-638	42	0	-	-

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:124
 aligned with SRPRA_HUMAN | P08240 from UniProtKB/Swiss-Prot  Length:638

    Alignment length:131
                              1                                                                                                                                
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128 
          SRPRA_HUMAN     - --MLDFFTIFSKGGLVLWCFQGVSDSCTGPVNALIRSVLLQERGGNNSFTHEALTLKYKLDNQFELVFVVGFQKILTLTYVDKLIDDVHRLFRDKYRTEIQQQSALSLLNGTFDFQNDFLRLLREAEESSK 129
               SCOP domains --d2fh5a1 A:1-129 Signal recognition parti       cle receptor alpha subunit, N-terminal domain                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeee....eeeee........hhhhhhhhhhhhhh-------.....eeeeeee....eeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhh....hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) --Exon 1.2b  PDB: A:1-39 UniProt: 1-39   Exon 1.3  PDB: A:40-67 (gapsExon 1.4b  PDB: A:68-122 UniProt: 68-122               ------- Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------------------------------------------------------------------------------------1.4d     Transcript 1 (2)
                 2fh5 A  0A HSMVDFFTIFSKGGLVLWCFQGVSDSCTGPVNALIRSVLLQE-------THEALTLKYKLDNQFELVFVVGFQKILTLTYVDKLIDDVHRLFRDKYRTEIQQQSALSLLNGTFDFQNDFLRLLREAEESSK 129
                            ||       8        18        28        38 |      48        58        68        78        88        98       108       118       128 
                            ||                                      40      48                                                                                 
                           0A|                                                                                                                                 
                            0B

Chain B from PDB  Type:PROTEIN  Length:188
 aligned with SRPRB_MOUSE | P47758 from UniProtKB/Swiss-Prot  Length:269

    Alignment length:207
                                    72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       
          SRPRB_MOUSE    63 RAVLFVGLCDSGKTLLFVRLLTGQYRDTQTSITDSSAIYKVNNNRGNSLTLIDLPGHESLRFQLLDRFKSSARAVVFVVDSAAFQREVKDVAEFLYQVLIDSMALKNSPSLLIACNKQDIAMAKSAKLIQQQLEKELNTLRVTRSAAPSTLDSSSTAPAQLGKKGKEFEFSQLPLKVEFLECSAKGGRGDTGSADIQDLEKWLAKIA 269
               SCOP domains d2fh5b1 B:63-269 Signal recognition particle receptor beta-subunit                                                                                                                                              SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.....hhhhhhhhhhhh...........eeeeee.......eeeeee...hhhhhhhhhhhhh..eeeeeeeee..hhhhhhhhhhhhhhhhhhhhhh.....eeeeeee........hhhhhhhhhhhhhhhhhhhh.------------...........hhhhh...eeeee....-------...hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2fh5 B  63 RAVLFVGLCDSGKTLLFVRLLTGQYRDTQTSITDSSAIYKVNNNRGNSLTLIDLPGHESLRFQLLDRFKSSARAVVFVVDSAAFQREVKDVAEFLYQVLIDSMALKNSPSLLIACNKQDIAMAKSAKLIQQQLEKELNTLRVTRS------------PAQLGKKGKEFEFSQLPLKVEFLECSAK-------SADIQDLEKWLAKIA 269
                                    72        82        92       102       112       122       132       142       152       162       172       182       192       202    |    -       222       232       242    |    -  |    262       
                                                                                                                                                                          207          220                        247     255

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 '\|'

(no "CATH Domain" information available for 2FH5)

(no "Pfam Domain" information available for 2FH5)

Asymmetric Unit(hide GO term definitions)

Chain A (SRPRA_HUMAN | P08240)

molecular function
	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: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.
	GO:0005047	signal recognition particle binding	Interacting selectively and non-covalently with the signal recognition particle.
biological process
	GO:0036498	IRE1-mediated unfolded protein response	A series of molecular signals mediated by the endoplasmic reticulum stress sensor IRE1 (Inositol-requiring transmembrane kinase/endonuclease). Begins with activation of IRE1 in response to endoplasmic reticulum (ER) stress, and ends with regulation of a downstream cellular process, e.g. transcription. One target of activated IRE1 is the transcription factor HAC1 in yeast, or XBP1 in mammals; IRE1 cleaves an intron of a mRNA coding for HAC1/XBP1 to generate an activated HAC1/XBP1 transcription factor, which controls the up regulation of UPR-related genes. At least in mammals, IRE1 can also signal through additional intracellular pathways including JNK and NF-kappaB.
	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:0006886	intracellular protein transport	The directed movement of proteins in a cell, including the movement of proteins between specific compartments or structures within a cell, such as organelles of a eukaryotic cell.
	GO:0006810	transport	The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
	GO:0005783	endoplasmic reticulum	The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
	GO:0005789	endoplasmic reticulum membrane	The lipid bilayer surrounding the endoplasmic reticulum.
	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:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	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.

Chain B (SRPRB_MOUSE | P47758)

molecular function
	GO:0005525	GTP binding	Interacting selectively and non-covalently with GTP, guanosine triphosphate.
	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:0007264	small GTPase mediated signal transduction	Any series of molecular signals in which a small monomeric GTPase relays one or more of the signals.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005881	cytoplasmic microtubule	Any microtubule in the cytoplasm of a cell.
	GO:0005783	endoplasmic reticulum	The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
	GO:0005789	endoplasmic reticulum membrane	The lipid bilayer surrounding the endoplasmic reticulum.
	GO:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	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:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

Asymmetric 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
		GTP	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MG	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2fh5)

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]
		Biological Unit 3	[ Jena3D ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Asym. Unit - sites PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 1 - sites PNG format \| Biol. Unit 2 PNG format \| Biol. Unit 3 PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	2fh5
		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
	SRPRA_HUMAN \| P08240
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt
	SRPRB_MOUSE \| P47758
		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

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
	SRPRA_HUMAN \| P08240
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)
	SRPRB_MOUSE \| P47758
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	SRPRA_HUMAN \| P08240	:	2go5 5l3q
	SRPRB_MOUSE \| P47758	:	2go5

(no "Related Entries Specified in the PDB File" available for 2FH5)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 2)

Sites (2, 2)

SS Bonds (1, 1)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (4, 4)

Sequences/Alignments

Classification and Annotation

SCOP Domains (2, 2)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (19, 25)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File