3T5I - JenaLib

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Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Title :   STRUCTURE OF FULLY MODIFIED FARNESYLATED RHEB PEPTIDE IN COMPLEX WITH PDE6D

Authors :   S. A. Ismail, Y. -X. Chen, A. Wittinghofer

Date :   27 Jul 11 (Deposition) - 02 Nov 11 (Release) - 30 Nov 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

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

Keywords :   Immunoglobulin-Like Beta Sandwitch Fold, Rheb, Farnesyl, Prenyl, Signaling Protein, Lipid Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. A. Ismail, Y. X. Chen, A. Rusinova, A. Chandra, M. Bierbaum, L. Gremer, G. Triola, H. Waldmann, P. I. Bastiaens, A. Wittinghofer
Arl2-Gtp And Arl3-Gtp Regulate A Gdi-Like Transport System For Farnesylated Cargo.
Nat. Chem. Biol. V. 7 942 2011
PubMed-ID: 22002721 | Reference-DOI: 10.1038/NCHEMBIO.686

Molecule 1 - RETINAL ROD RHODOPSIN-SENSITIVE CGMP 3',5'-CYCLIC PHOSPHODIESTERASE SUBUNIT DELTA
	Chains	:	B, A, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	FULL LENGTH PDE DELTA
	Gene	:	PDE6D, PDED
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	GMP-PDE DELTA, PROTEIN P17

Molecule 2 - C-TERMINAL FARNESYLATED RHEB PEPTIDE CSQQGKSS(CMT)
	Chains	:	Q, R
	Engineered	:	YES
	Fragment	:	C-TERMINAL FARNESYLATED RHEB PEPTIDE
	Other Details	:	PEPTIDE SYNTHESIS , THE SEQUENCE IS THE CTERMINAL SEQUENCE OF RHEB
	Synthetic	:	YES

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 6)

No.	Name	Count	Type	Full Name
1	CMT	2	Mod. Amino Acid	O-METHYLCYSTEINE
2	FAR	4	Ligand/Ion	FARNESYL

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	CMT	1	Mod. Amino Acid	O-METHYLCYSTEINE
2	FAR	1	Ligand/Ion	FARNESYL

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	CMT	-1	Mod. Amino Acid	O-METHYLCYSTEINE
2	FAR	1	Ligand/Ion	FARNESYL

Biological Unit 3 (1, 1)

No.	Name	Count	Type	Full Name
1	CMT	-1	Mod. Amino Acid	O-METHYLCYSTEINE
2	FAR	1	Ligand/Ion	FARNESYL

Biological Unit 4 (2, 2)

No.	Name	Count	Type	Full Name
1	CMT	1	Mod. Amino Acid	O-METHYLCYSTEINE
2	FAR	1	Ligand/Ion	FARNESYL

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLN B:78 , ILE B:129 , PHE B:133 , LEU B:147	BINDING SITE FOR RESIDUE FAR B 3010
2	AC2	SOFTWARE	LEU A:38 , LEU A:63 , GLN A:78 , ILE A:129 , THR A:131 , PHE A:133 , SER A:143 , LEU A:147 , SER R:13 , CMT R:14	BINDING SITE FOR RESIDUE FAR A 2010
3	AC3	SOFTWARE	MET C:20 , GLN C:78 , TRP C:90 , HOH C:271	BINDING SITE FOR RESIDUE FAR C 4010
4	AC4	SOFTWARE	MET D:20 , VAL D:59 , GLN D:78 , ILE D:129 , THR D:131 , PHE D:133 , SER D:143 , CMT Q:14	BINDING SITE FOR RESIDUE FAR Q 5010

(no "SS Bond" information available for 3T5I)

(no "Cis Peptide Bond" information available for 3T5I)

(no "SAP(SNP)/Variant" information available for 3T5I)

(no "PROSITE Motif" information available for 3T5I)

Asymmetric Unit (5, 20)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.3a	ENST00000287600	3a	ENSE00001829481	chr2:232646019-232645775	245	PDE6D_HUMAN	1-17	17	4	A:2-17 B:4-17 C:2-17 D:2-17	16 14 16 16
1.5b	ENST00000287600	5b	ENSE00001029423	chr2:232603898-232603810	89	PDE6D_HUMAN	17-47	31	4	A:17-47 B:17-47 C:17-47 D:17-47	31 31 31 31
1.6a	ENST00000287600	6a	ENSE00001029425	chr2:232602848-232602723	126	PDE6D_HUMAN	47-89	43	4	A:47-89 B:47-89 C:47-89 D:47-89	43 43 43 43
1.7	ENST00000287600	7	ENSE00001029421	chr2:232602002-232601897	106	PDE6D_HUMAN	89-124	36	4	A:89-124 B:89-124 (gaps) C:89-124 D:89-124	36 36 36 36
1.9b	ENST00000287600	9b	ENSE00001872609	chr2:232597743-232597135	609	PDE6D_HUMAN	124-150	27	4	A:124-150 B:124-150 C:124-150 D:124-150	27 27 27 27

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:149
 aligned with PDE6D_HUMAN | O43924 from UniProtKB/Swiss-Prot  Length:150

    Alignment length:149
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141         
          PDE6D_HUMAN     2 SAKDERAREILRGFKLNWMNLRDAETGKILWQGTEDLSVPGVEHEARVPKKILKCKAVSRELNFSSTEQMEKFRLEQKVYFKGQCLEEWFFEFGFVIPNSTNTWQSLIEAAPESQMMPASVLTGNVIIETKFFDDDLLVSTSRVRLFYV 150
               SCOP domains d3t5ia_ A: GMP-PDE delta                                                                                                                              SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhheeeeeeeeee.....eeeee.........eeeeeee.hhhhh..eeeeeeeee...eeeeeeeeeeee..eeeeeeeeeeeee...eeeeeee........ee.hhhhhh..eeeeeeeee..eeeeeeeeeeeee Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.3a       -----------------------------Exon 1.6a  PDB: A:47-89 UniProt: 47-89     ----------------------------------Exon 1.9b  PDB: A:124-150   Transcript 1 (1)
           Transcript 1 (2) ---------------Exon 1.5b  PDB: A:17-47        -----------------------------------------Exon 1.7  PDB: A:89-124             -------------------------- Transcript 1 (2)
                 3t5i A   2 SAKDERAREILRGFKLNWMNLRDAETGKILWQGTEDLSVPGVEHEARVPKKILKCKAVSRELNFSSTEQMEKFRLEQKVYFKGQCLEEWFFEFGFVIPNSTNTWQSLIEAAPESQMMPASVLTGNVIIETKFFDDDLLVSTSRVRLFYV 150
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141

Chain B from PDB  Type:PROTEIN  Length:142
 aligned with PDE6D_HUMAN | O43924 from UniProtKB/Swiss-Prot  Length:150

    Alignment length:147
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       
          PDE6D_HUMAN     4 KDERAREILRGFKLNWMNLRDAETGKILWQGTEDLSVPGVEHEARVPKKILKCKAVSRELNFSSTEQMEKFRLEQKVYFKGQCLEEWFFEFGFVIPNSTNTWQSLIEAAPESQMMPASVLTGNVIIETKFFDDDLLVSTSRVRLFYV 150
               SCOP domains d3t5ib_ B: GMP-PDE delta                                                                                                                            SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhheeeeeeeeee.....eeeee.........eeeeeee.hhhhh.eeeeeeeeee...eeeeeeeeeeee..eeeeeeeeeeeee...eeeeeeeeee..-----.hhhhhh..eeeeeeeee..eeeeeeeeeeeee Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.3a     -----------------------------Exon 1.6a  PDB: B:47-89 UniProt: 47-89     ----------------------------------Exon 1.9b  PDB: B:124-150   Transcript 1 (1)
           Transcript 1 (2) -------------Exon 1.5b  PDB: B:17-47        -----------------------------------------Exon 1.7  PDB: B:89-124 (gaps)      -------------------------- Transcript 1 (2)
                 3t5i B   4 KDERAREILRGFKLNWMNLRDAETGKILWQGTEDLSVPGVEHEARVPKKILKCKAVSRELNFSSTEQMEKFRLEQKVYFKGQCLEEWFFEFGFVIPNSTNTWQSLIEAA-----MPASVLTGNVIIETKFFDDDLLVSTSRVRLFYV 150
                                    13        23        33        43        53        63        73        83        93       103        |-    |  123       133       143       
                                                                                                                                      112   118

Chain C from PDB  Type:PROTEIN  Length:149
 aligned with PDE6D_HUMAN | O43924 from UniProtKB/Swiss-Prot  Length:150

    Alignment length:149
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141         
          PDE6D_HUMAN     2 SAKDERAREILRGFKLNWMNLRDAETGKILWQGTEDLSVPGVEHEARVPKKILKCKAVSRELNFSSTEQMEKFRLEQKVYFKGQCLEEWFFEFGFVIPNSTNTWQSLIEAAPESQMMPASVLTGNVIIETKFFDDDLLVSTSRVRLFYV 150
               SCOP domains d3t5ic_ C: GMP-PDE delta                                                                                                                              SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhheeeeeeeeee.....eeeee..........eeeeee.hhhhh.eeeeeeeeee...eeeeeeeeeeee..eeeeeeeeeeeee...eeeeeeeeee........hhhhhh..eeeeeeeee..eeeeeeeeeeeee Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.3a       -----------------------------Exon 1.6a  PDB: C:47-89 UniProt: 47-89     ----------------------------------Exon 1.9b  PDB: C:124-150   Transcript 1 (1)
           Transcript 1 (2) ---------------Exon 1.5b  PDB: C:17-47        -----------------------------------------Exon 1.7  PDB: C:89-124             -------------------------- Transcript 1 (2)
                 3t5i C   2 SAKDERAREILRGFKLNWMNLRDAETGKILWQGTEDLSVPGVEHEARVPKKILKCKAVSRELNFSSTEQMEKFRLEQKVYFKGQCLEEWFFEFGFVIPNSTNTWQSLIEAAPESQMMPASVLTGNVIIETKFFDDDLLVSTSRVRLFYV 150
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141

Chain D from PDB  Type:PROTEIN  Length:149
 aligned with PDE6D_HUMAN | O43924 from UniProtKB/Swiss-Prot  Length:150

    Alignment length:149
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141         
          PDE6D_HUMAN     2 SAKDERAREILRGFKLNWMNLRDAETGKILWQGTEDLSVPGVEHEARVPKKILKCKAVSRELNFSSTEQMEKFRLEQKVYFKGQCLEEWFFEFGFVIPNSTNTWQSLIEAAPESQMMPASVLTGNVIIETKFFDDDLLVSTSRVRLFYV 150
               SCOP domains d3t5id_ D: GMP-PDE delta                                                                                                                              SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhheeeeeeeeee.....eeeee.........eeeeeee.hhhhh..eeeeeeeee...eeeeeeeeeeee..eeeeeeeeeeeee...eeeeeee........ee.hhhhhh..eeeeeeeee..eeeeeeeeeeeee Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.3a       -----------------------------Exon 1.6a  PDB: D:47-89 UniProt: 47-89     ----------------------------------Exon 1.9b  PDB: D:124-150   Transcript 1 (1)
           Transcript 1 (2) ---------------Exon 1.5b  PDB: D:17-47        -----------------------------------------Exon 1.7  PDB: D:89-124             -------------------------- Transcript 1 (2)
                 3t5i D   2 SAKDERAREILRGFKLNWMNLRDAETGKILWQGTEDLSVPGVEHEARVPKKILKCKAVSRELNFSSTEQMEKFRLEQKVYFKGQCLEEWFFEFGFVIPNSTNTWQSLIEAAPESQMMPASVLTGNVIIETKFFDDDLLVSTSRVRLFYV 150
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141

Chain Q from PDB  Type:PROTEIN  Length:3
                                   
               SCOP domains --- SCOP domains
               CATH domains --- CATH domains
               Pfam domains --- Pfam domains
         Sec.struct. author ... Sec.struct. author
                 SAPs(SNPs) --- SAPs(SNPs)
                    PROSITE --- PROSITE
                 Transcript --- Transcript
                 3t5i Q  12 SSc  14
                              |
                             14-CMT

Chain R from PDB  Type:PROTEIN  Length:3
                                   
               SCOP domains --- SCOP domains
               CATH domains --- CATH domains
               Pfam domains --- Pfam domains
         Sec.struct. author ... Sec.struct. author
                 SAPs(SNPs) --- SAPs(SNPs)
                    PROSITE --- PROSITE
                 Transcript --- Transcript
                 3t5i R  12 SSc  14
                              |
                              |
                             14-CMT

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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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: Immunoglobulin-like beta-sandwich (7299)

Superfamily: E set domains (509)

Family: RhoGDI-like (34)

Protein domain: GMP-PDE delta (10)

Human (Homo sapiens) [TaxId: 9606] (10)

1a	d3t5ia_	A:
1b	d3t5ib_	B:
1c	d3t5ic_	C:
1d	d3t5id_	D:

(no "CATH Domain" information available for 3T5I)

(no "Pfam Domain" information available for 3T5I)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (PDE6D_HUMAN | O43924)

molecular function
	GO:0004114	3',5'-cyclic-nucleotide phosphodiesterase activity	Catalysis of the reaction: nucleoside 3',5'-cyclic phosphate + H2O = nucleoside 5'-phosphate.
	GO:0005095	GTPase inhibitor activity	Stops, prevents or reduces the activity of any enzyme that catalyzes the hydrolysis of GTP to GDP and orthophosphate.
	GO:0017137	Rab GTPase binding	Interacting selectively and non-covalently with Rab protein, any member of the Rab subfamily of the Ras superfamily of monomeric GTPases.
	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:0034260	negative regulation of GTPase activity	Any process that stops or reduces the rate of GTP hydrolysis by a GTPase.
	GO:0050896	response to stimulus	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 stimulus. The process begins with detection of the stimulus and ends with a change in state or activity or the cell or organism.
	GO:0007601	visual perception	The series of events required for an organism to receive a visual stimulus, convert it to a molecular signal, and recognize and characterize the signal. Visual stimuli are detected in the form of photons and are processed to form an image.
cellular component
	GO:0042995	cell projection	A prolongation or process extending from a cell, e.g. a flagellum or axon.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0031410	cytoplasmic vesicle	A vesicle found in the cytoplasm of a cell.
	GO:0030659	cytoplasmic vesicle membrane	The lipid bilayer surrounding a cytoplasmic vesicle.
	GO:0005856	cytoskeleton	Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles.
	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:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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Description

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Ligands, Modified Residues, Ions (2, 6)

Sites (4, 4)

SS Bonds (0, 0)

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Exons (5, 20)

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