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Title :   INTRAFLAGELLAR TRANSPORT COMPLEX 25-27 FROM CHLAMYDOMONAS

Authors :   S. Bhogaraju, M. Taschner, E. Lorentzen

Date :   11 Mar 11 (Deposition) - 23 Mar 11 (Release) - 01 Jun 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.80

Chains :   Asym./Biol. Unit : A,B,C,D

Keywords :   Transport Protein, Cilium, Ift Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Bhogaraju, M. Taschner, M. Morawetz, C. Basquin, E. Lorentzen
Crystal Structure Of The Intraflagellar Transport Complex 25/27.
Embo J. V. 30 1907 2011
PubMed-ID: 21505417 | Reference-DOI: 10.1038/EMBOJ.2011.110

Molecule 1 - INTRAFLAGELLAR TRANSPORT PROTEIN 25
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Fragment	:	RESIDUES 1-135
	Organism Common	:	GREEN ALGAE
	Organism Scientific	:	CHLAMYDOMONAS REINHARDTII
	Organism Taxid	:	3055
	Synonym	:	IFT25

Molecule 2 - SMALL RAB-RELATED GTPASE
	Chains	:	C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Organism Common	:	GREEN ALGAE
	Organism Scientific	:	CHLAMYDOMONAS REINHARDTII
	Organism Taxid	:	3055
	Synonym	:	IFT27

		1	2	3	4
Asymmetric/Biological Unit	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 4)

No.	Name	Count	Type	Full Name
1	CA	2	Ligand/Ion	CALCIUM ION
2	CL	1	Ligand/Ion	CHLORIDE ION
3	MG	1	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN A:27 , ASP A:30 , LYS A:32 , THR A:35 , ASN A:127	BINDING SITE FOR RESIDUE CA A 201
2	AC2	SOFTWARE	ASN B:27 , ASP B:30 , LYS B:32 , THR B:35 , ASN B:127	BINDING SITE FOR RESIDUE CA B 201
3	AC3	SOFTWARE	VAL C:102 , SER C:103 , SER C:104 , MET C:105 , GLN C:143 , HIS C:145 , GLN C:146	BINDING SITE FOR RESIDUE MG C 301
4	AC4	SOFTWARE	ALA D:25 , GLY D:28 , LYS D:29 , SER D:30	BINDING SITE FOR RESIDUE CL D1204

(no "SS Bond" information available for 2YC4)

Asymmetric/Biological Unit

No.	Residues
1	Phe A:43	-	Pro A:44
2	Phe B:43	-	Pro B:44
3	Ala C:77	-	Gly C:78
4	Gly C:78	-	Ser C:79
5	Arg D:202	-	Asn D:203

(no "SAP(SNP)/Variant" information available for 2YC4)

Asymmetric/Biological Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RAB	PS51419	small GTPase Rab1 family profile.	IFT27_CHLRE	12-204	2	C:12-204 D:12-203

(no "Exon" information available for 2YC4)

Asymmetric/Biological 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:131
 aligned with IFT25_CHLRE | B8LIX8 from UniProtKB/Swiss-Prot  Length:189

    Alignment length:135
                                    10        20        30        40        50        60        70        80        90       100       110       120       130     
          IFT25_CHLRE     1 MKDYAREENGGLVVMASCSDERFPPENMLDGKDNTFWVTTGMFPQEFVLRLESCIRVSKITTLSLNVRKLAVEKCDQDKPDQFEKVFEVELANRGDRLQTEVHQVNIRAKYLKFILLQGHGEFATVNRVSVVGGD 135
               SCOP domains d2yc4a_ A: automated matches                                                                                                            SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee..hhhhh.ee..........hhhhhh.......ee......eeeeeeeeeeeeeeeeeeeee.eeeeeeeee........eeeeeee...----.eeeeeeeeeeeeeeeeeeeee.....eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2yc4 A   1 MKDYAREENGGLVVMASCSDERFPPENMLDGKDNTFWVTTGMFPQEFVLRLESCIRVSKITTLSLNVRKLAVEKCDQDKPDQFEKVFEVELAN----LQTEVHQVNIRAKYLKFILLQGHGEFATVNRVSVVGGD 135
                                    10        20        30        40        50        60        70        80        90  |    100       110       120       130     
                                                                                                                       93   98

Chain B from PDB  Type:PROTEIN  Length:131
 aligned with IFT25_CHLRE | B8LIX8 from UniProtKB/Swiss-Prot  Length:189

    Alignment length:133
                                    11        21        31        41        51        61        71        81        91       101       111       121       131   
          IFT25_CHLRE     2 KDYAREENGGLVVMASCSDERFPPENMLDGKDNTFWVTTGMFPQEFVLRLESCIRVSKITTLSLNVRKLAVEKCDQDKPDQFEKVFEVELANRGDRLQTEVHQVNIRAKYLKFILLQGHGEFATVNRVSVVGG 134
               SCOP domains d2yc4b_ B: automated matches                                                                                                          SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhh.ee..........hhhhhh.......ee......eeeeeeeeeeeeeeeeeeeee.eeeeeeeee........eeeeeee.....--.eeeeeeeeeeeeeeeeeeeee.....eeeeeeeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2yc4 B   2 KDYAREENGGLVVMASCSDERFPPENMLDGKDNTFWVTTGMFPQEFVLRLESCIRVSKITTLSLNVRKLAVEKCDQDKPDQFEKVFEVELANRG--LQTEVHQVNIRAKYLKFILLQGHGEFATVNRVSVVGG 134
                                    11        21        31        41        51        61        71        81        91   |  |101       111       121       131   
                                                                                                                        95 98

Chain C from PDB  Type:PROTEIN  Length:177
 aligned with IFT27_CHLRE | A8HN58 from UniProtKB/Swiss-Prot  Length:204

    Alignment length:198
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196        
          IFT27_CHLRE     7 KPIDITATLRCKVAVVGEATVGKSALISMFTSKGSKFLKDYAMTSGVEVVVAPVTIPDTTVSVELFLLDTAGSDLYKEQISQYWNGVYYAILVFDVSSMESFESCKAWFELLKSARPDRERPLRAVLVANKTDLPPQRHQVRLDMAQDWATTNTLDFFDVSANPPGKDADAPFLSIATTFYRNYEDKVAAFQDACRNY 204
               SCOP domains d2yc4c_ C: automated matches                                                                                                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eeeeeeeeee.hhhhhhhhhhhhhhh-----------------.eeeee.....eeeeeeeee...hhhhhhhh........eeeeeee..hhhhhhhhhhhhhhhhhhh.......eeeeeee.---.......hhhhhhhhhhhh..eeee..-......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----RAB  PDB: C:12-204 UniProt: 12-204                                                                                                                                                                PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2yc4 C   7 KPIDITATLRCKVAVVGEATVGKSALISMFTS-----------------VVAPVTIPDTTVSVELFLLDTAGSDLYKEQISQYWNGVYYAILVFDVSSMESFESCKAWFELLKSARPDRERPLRAVLVANK---PPQRHQVRLDMAQDWATTNTLDFFDVS-NPPGKDADAPFLSIATTFYRNYEDKVAAFQDACRNY 204
                                    16        26        36 |       -        56        66        76        86        96       106       116       126       136|   |  146       156       166| |    176       186       196        
                                                          38                56                                                                              137 141                       167 |                                   
                                                                                                                                                                                            169

Chain D from PDB  Type:PROTEIN  Length:175
 aligned with IFT27_CHLRE | A8HN58 from UniProtKB/Swiss-Prot  Length:204

    Alignment length:196
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197      
          IFT27_CHLRE     8 PIDITATLRCKVAVVGEATVGKSALISMFTSKGSKFLKDYAMTSGVEVVVAPVTIPDTTVSVELFLLDTAGSDLYKEQISQYWNGVYYAILVFDVSSMESFESCKAWFELLKSARPDRERPLRAVLVANKTDLPPQRHQVRLDMAQDWATTNTLDFFDVSANPPGKDADAPFLSIATTFYRNYEDKVAAFQDACRN 203
               SCOP domains d2yc4d_ D: automated matches                                                                                                                                                                         SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeeeee.hhhhhhhhhhhhhhhh..---------------.eeee.....eeeeeeeee.--hhhhhhhhh.......eeeeeee..hhhhhhhhhhhhhhhhhhh.......eeeeeee.....----..hhhhhhhhhhhh..eeee.........hhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----RAB  PDB: D:12-203 UniProt: 12-204                                                                                                                                                               PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2yc4 D   8 PIDITATLRCKVAVVGEATVGKSALISMFTSKGS---------------VAPVTIPDTTVSVELFLLDT--SDLYKEQISQYWNGVYYAILVFDVSSMESFESCKAWFELLKSARPDRERPLRAVLVANKTDLP----QVRLDMAQDWATTNTLDFFDVSANPPGKDADAPFLSIATTFYRNYEDKVAAFQDACRN 203
                                    17        27        37   |     -        57        67        |- |      87        97       107       117       127       137   |   147       157       167       177       187       197      
                                                            41              57                 76 79                                                           141  146

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 2YC4)

(no "Pfam Domain" information available for 2YC4)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (IFT25_CHLRE | B8LIX8)

molecular function
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	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).
cellular component
	GO:0042995	cell projection	A prolongation or process extending from a cell, e.g. a flagellum or axon.
	GO:0005929	cilium	A specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface and of some cytoplasmic parts. Each cilium is largely bounded by an extrusion of the cytoplasmic (plasma) membrane, and contains a regular longitudinal array of microtubules, anchored to a basal body.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	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:0030992	intraciliary transport particle B	The larger subcomplex of the intraciliary transport particle; characterized complexes have molecular weights around 550 kDa.
	GO:0031514	motile cilium	A cilium which may have a variable arrangement of axonemal microtubules and also contains molecular motors. It may beat with a whip-like pattern that promotes cell motility or transport of fluids and other cells across a cell surface, such as on epithelial cells that line the lumenal ducts of various tissues; or they may display a distinct twirling motion that directs fluid flow asymmetrically across the cellular surface to affect asymmetric body plan organization. Motile cilia can be found in single as well as multiple copies per cell.

Chain C,D (IFT27_CHLRE | A8HN58)

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.
	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: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: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: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:0030992	intraciliary transport particle B	The larger subcomplex of the intraciliary transport particle; characterized complexes have molecular weights around 550 kDa.
	GO:0031514	motile cilium	A cilium which may have a variable arrangement of axonemal microtubules and also contains molecular motors. It may beat with a whip-like pattern that promotes cell motility or transport of fluids and other cells across a cell surface, such as on epithelial cells that line the lumenal ducts of various tissues; or they may display a distinct twirling motion that directs fluid flow asymmetrically across the cellular surface to affect asymmetric body plan organization. Motile cilia can be found in single as well as multiple copies per cell.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Ala C:77 - Gly C:78	[ RasMol ]
		Arg D:202 - Asn D:203	[ RasMol ]
		Gly C:78 - Ser C:79	[ RasMol ]
		Phe A:43 - Pro A:44	[ RasMol ]
		Phe B:43 - Pro B:44	[ RasMol ]

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	IFT25_CHLRE \| B8LIX8	:	2yc2
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2yc2	INTRAFLAGELLAR TRANSPORT COMPLEX 25-27 FROM CHLAMYDOMONAS

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (5, 5)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (2, 4)

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Gene Ontology (11, 17)

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