3FMA - JenaLib

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Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Biological Unit 5 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE GYF DOMAIN OF SMY2 IN COMPLEX WITH A PROLINE-RICH PEPTIDE FROM BBP/SCSF1

Authors :   M. R. Ash, K. Faelber

Date :   19 Dec 08 (Deposition) - 22 Dec 09 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

Chains :   Asym. Unit : A,B,C,D,E,L,M,N,O,P
Biol. Unit 1: A,L  (1x)
Biol. Unit 2: B,M  (1x)
Biol. Unit 3: C,N  (1x)
Biol. Unit 4: D,O  (1x)
Biol. Unit 5: E,P  (1x)

Keywords :   Gyf Domain, Poly-Proline Binding, Proline-Rich Peptide, Domain Swap, Prs, Ragnya, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. R. Ash, K. Faelber, D. Kosslick, G. Albert, Y. Roske, M. Kofler, M. Schuemann, E. Krause, C. Freund
Smy2-Type Gyf Domain Recognition In Mrna Surveillance Complexes
To Be Published
PubMed: search

Molecule 1 - PROTEIN SMY2
	Chains	:	A, B, C, D, E
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28
	Expression System Strain	:	B834(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	GYF DOMAIN
	Gene	:	SMY2
	Organism Common	:	YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932
	Synonym	:	SUPPRESSOR OF MYO2-66 PROTEIN

Molecule 2 - BRANCHPOINT-BRIDGING PROTEIN
	Chains	:	L, M, N, O, P
	Engineered	:	YES
	Fragment	:	PROLINE-RICH PEPTIDE
	Other Details	:	FMOC SOLID PHASE SYNTHESIS
	Synonym	:	SPLICING FACTOR 1, ZINC FINGER PROTEIN BBP, MUD SYNTHETIC- LETHAL 5 PROTEIN
	Synthetic	:	YES

		1	2	3	4	5	6	7	8	9	10
Asymmetric Unit	:	A	B	C	D	E	L	M	N	O	P
Biological Unit 1 (1x)	:	A					L
Biological Unit 2 (1x)	:		B					M
Biological Unit 3 (1x)	:			C					N
Biological Unit 4 (1x)	:				D					O
Biological Unit 5 (1x)	:					E					P

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 15)

No.	Name	Count	Type	Full Name
1	MSE	15	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 1 (1, 3)

No.	Name	Count	Type	Full Name
1	MSE	3	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 2 (1, 3)

No.	Name	Count	Type	Full Name
1	MSE	3	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 3 (1, 3)

No.	Name	Count	Type	Full Name
1	MSE	3	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 4 (1, 3)

No.	Name	Count	Type	Full Name
1	MSE	3	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 5 (1, 3)

No.	Name	Count	Type	Full Name
1	MSE	3	Mod. Amino Acid	SELENOMETHIONINE

(no "Site" information available for 3FMA)

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

Asymmetric Unit

No.	Residues
1	Gly A:29	-	Pro A:30
2	Gly B:29	-	Pro B:30
3	Gly C:29	-	Pro C:30
4	Gly D:29	-	Pro D:30
5	Gly E:29	-	Pro E:30

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

Asymmetric Unit (1, 5)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GYF	PS50829	GYF domain profile.	SMY2_YEAST	205-261	5	A:15-71 B:15-71 C:15-71 D:15-71 E:15-71

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GYF	PS50829	GYF domain profile.	SMY2_YEAST	205-261	1	A:15-71 - - - -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GYF	PS50829	GYF domain profile.	SMY2_YEAST	205-261	1	- B:15-71 - - -

Biological Unit 3 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GYF	PS50829	GYF domain profile.	SMY2_YEAST	205-261	1	- - C:15-71 - -

Biological Unit 4 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GYF	PS50829	GYF domain profile.	SMY2_YEAST	205-261	1	- - - D:15-71 -

Biological Unit 5 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GYF	PS50829	GYF domain profile.	SMY2_YEAST	205-261	1	- - - - E:15-71

(no "Exon" information available for 3FMA)

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:81
 aligned with SMY2_YEAST | P32909 from UniProtKB/Swiss-Prot  Length:740

    Alignment length:81
                                   212       222       232       242       252       262       272       282 
           SMY2_YEAST   203 SVESSWRYIDTQGQIHGPFTTQMMSQWYIGGYFASTLQISRLGSTPETLGINDIFITLGELMTKLEKYDTDPFTTFDKLHV 283
               SCOP domains --------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee.....eeeeeehhhhhhhhhhh......eeee..............eehhhhhhhhh....hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --GYF  PDB: A:15-71 UniProt: 205-261                       ---------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------- Transcript
                 3fma A  13 SVESSWRYIDTQGQIHGPFTTQmmSQWYIGGYFASTLQISRLGSTPETLGINDIFITLGELmTKLEKYDTDPFTTFDKLHV  93
                                    22        32  ||    42        52        62        72 |      82        92 
                                                 35-MSE                                 74-MSE               
                                                  36-MSE

Chain B from PDB  Type:PROTEIN  Length:84
 aligned with SMY2_YEAST | P32909 from UniProtKB/Swiss-Prot  Length:740

    Alignment length:84
                                   212       222       232       242       252       262       272       282    
           SMY2_YEAST   203 SVESSWRYIDTQGQIHGPFTTQMMSQWYIGGYFASTLQISRLGSTPETLGINDIFITLGELMTKLEKYDTDPFTTFDKLHVQTT 286
               SCOP domains ------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeee.....eeeeeehhhhhhhhhh.......eeee..............eehhhhhhhhhhh..hhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --GYF  PDB: B:15-71 UniProt: 205-261                       ------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------ Transcript
                 3fma B  13 SVESSWRYIDTQGQIHGPFTTQmmSQWYIGGYFASTLQISRLGSTPETLGINDIFITLGELmTKLEKYDTDPFTTFDKLHVQTT  96
                                    22        32  ||    42        52        62        72 |      82        92    
                                                 35-MSE                                 74-MSE                  
                                                  36-MSE

Chain C from PDB  Type:PROTEIN  Length:86
 aligned with SMY2_YEAST | P32909 from UniProtKB/Swiss-Prot  Length:740

    Alignment length:86
                                   210       220       230       240       250       260       270       280      
           SMY2_YEAST   201 PVSVESSWRYIDTQGQIHGPFTTQMMSQWYIGGYFASTLQISRLGSTPETLGINDIFITLGELMTKLEKYDTDPFTTFDKLHVQTT 286
               SCOP domains -------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeee.....eeeeeehhhhhhhhhh.......eeee..............eehhhhhhhhhhh..hhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----GYF  PDB: C:15-71 UniProt: 205-261                       ------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------- Transcript
                 3fma C  11 PVSVESSWRYIDTQGQIHGPFTTQmmSQWYIGGYFASTLQISRLGSTPETLGINDIFITLGELmTKLEKYDTDPFTTFDKLHVQTT  96
                                    20        30    ||  40        50        60        70   |    80        90      
                                                   35-MSE                                 74-MSE                  
                                                    36-MSE

Chain D from PDB  Type:PROTEIN  Length:85
 aligned with SMY2_YEAST | P32909 from UniProtKB/Swiss-Prot  Length:740

    Alignment length:85
                                   211       221       231       241       251       261       271       281     
           SMY2_YEAST   202 VSVESSWRYIDTQGQIHGPFTTQMMSQWYIGGYFASTLQISRLGSTPETLGINDIFITLGELMTKLEKYDTDPFTTFDKLHVQTT 286
               SCOP domains ------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee.....eeeeeehhhhhhhhhh.......eeee..............eehhhhhhhhhhhh.hhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---GYF  PDB: D:15-71 UniProt: 205-261                       ------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------- Transcript
                 3fma D  12 VSVESSWRYIDTQGQIHGPFTTQmmSQWYIGGYFASTLQISRLGSTPETLGINDIFITLGELmTKLEKYDTDPFTTFDKLHVQTT  96
                                    21        31   ||   41        51        61        71  |     81        91     
                                                  35-MSE                                 74-MSE                  
                                                   36-MSE

Chain E from PDB  Type:PROTEIN  Length:85
 aligned with SMY2_YEAST | P32909 from UniProtKB/Swiss-Prot  Length:740

    Alignment length:85
                                   211       221       231       241       251       261       271       281     
           SMY2_YEAST   202 VSVESSWRYIDTQGQIHGPFTTQMMSQWYIGGYFASTLQISRLGSTPETLGINDIFITLGELMTKLEKYDTDPFTTFDKLHVQTT 286
               SCOP domains ------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee.....eeeeeehhhhhhhhhh.......eeee..............eehhhhhhhhhhh..hhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---GYF  PDB: E:15-71 UniProt: 205-261                       ------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------- Transcript
                 3fma E  12 VSVESSWRYIDTQGQIHGPFTTQmmSQWYIGGYFASTLQISRLGSTPETLGINDIFITLGELmTKLEKYDTDPFTTFDKLHVQTT  96
                                    21        31   ||   41        51        61        71  |     81        91     
                                                  35-MSE                                 74-MSE                  
                                                   36-MSE

Chain L from PDB  Type:PROTEIN  Length:7
 aligned with BBP_YEAST | Q12186 from UniProtKB/Swiss-Prot  Length:476

    Alignment length:7
            BBP_YEAST   443 APPPGLS 449
               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
                 3fma L   4 APPPGLS  10

Chain M from PDB  Type:PROTEIN  Length:7
 aligned with BBP_YEAST | Q12186 from UniProtKB/Swiss-Prot  Length:476

    Alignment length:7
            BBP_YEAST   442 IAPPPGL 448
               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
                 3fma M   3 IAPPPGL   9

Chain N from PDB  Type:PROTEIN  Length:6
 aligned with BBP_YEAST | Q12186 from UniProtKB/Swiss-Prot  Length:476

    Alignment length:6
            BBP_YEAST   443 APPPGL 448
               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
                 3fma N   4 APPPGL   9

Chain O from PDB  Type:PROTEIN  Length:7
 aligned with BBP_YEAST | Q12186 from UniProtKB/Swiss-Prot  Length:476

    Alignment length:7
            BBP_YEAST   443 APPPGLS 449
               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
                 3fma O   4 APPPGLS  10

Chain P from PDB  Type:PROTEIN  Length:7
 aligned with BBP_YEAST | Q12186 from UniProtKB/Swiss-Prot  Length:476

    Alignment length:7
            BBP_YEAST   443 APPPGLS 449
               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
                 3fma P   4 APPPGLS  10

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 "SCOP Domain" information available for 3FMA)

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

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

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D,E (SMY2_YEAST | P32909)

molecular function
	GO:0003674	molecular_function	Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions.
biological process
	GO:0006888	ER to Golgi vesicle-mediated transport	The directed movement of substances from the endoplasmic reticulum (ER) to the Golgi, mediated by COP II vesicles. Small COP II coated vesicles form from the ER and then fuse directly with the cis-Golgi. Larger structures are transported along microtubules to the cis-Golgi.
cellular component
	GO:0000932	P-body	A focus in the cytoplasm where mRNAs may become inactivated by decapping or some other mechanism. Protein and RNA localized to these foci are involved in mRNA degradation, nonsense-mediated mRNA decay (NMD), translational repression, and RNA-mediated gene silencing.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005789	endoplasmic reticulum membrane	The lipid bilayer surrounding the endoplasmic reticulum.
	GO:0019898	extrinsic component of membrane	The component of a membrane consisting of gene products and protein complexes that are loosely bound to one of its surfaces, but not integrated into the hydrophobic region.

Chain L,M,N,O,P (BBP_YEAST | Q12186)

molecular function
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0003676	nucleic acid binding	Interacting selectively and non-covalently with any nucleic acid.
	GO:0045131	pre-mRNA branch point binding	Interacting selectively and non-covalently with a pre-mRNA branch point sequence, located upstream of the 3' splice site.
	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:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0008380	RNA splicing	The process of removing sections of the primary RNA transcript to remove sequences not present in the mature form of the RNA and joining the remaining sections to form the mature form of the RNA.
	GO:0006397	mRNA processing	Any process involved in the conversion of a primary mRNA transcript into one or more mature mRNA(s) prior to translation into polypeptide.
	GO:0000398	mRNA splicing, via spliceosome	The joining together of exons from one or more primary transcripts of messenger RNA (mRNA) and the excision of intron sequences, via a spliceosomal mechanism, so that mRNA consisting only of the joined exons is produced.
cellular component
	GO:0000243	commitment complex	A spliceosomal complex that is formed by association of the U1 snRNP with the 5' splice site of an unspliced intron in an RNA transcript.
	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: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.

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	Cis Peptide Bonds
		Gly A:29 - Pro A:30	[ RasMol ]
		Gly B:29 - Pro B:30	[ RasMol ]
		Gly C:29 - Pro C:30	[ RasMol ]
		Gly D:29 - Pro D:30	[ RasMol ]
		Gly E:29 - Pro E:30	[ RasMol ]

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1l2z	CD2BP2-GYF DOMAIN IN COMPLEX WITH PROLINE-RICH CD2 TAIL SEGMENT PEPTIDE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 15)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (5, 5)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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Gene Ontology (18, 18)

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Related Entries

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Related Entries Specified in the PDB File