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Title :   CRYSTAL STRUCTURE OF C-PHYCOCYANIN FROM GALDIERIA SULPHURARIA

Authors :   R. Fromme

Date :   21 Dec 07 (Deposition) - 24 Feb 09 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.85

Chains :   Asym. Unit : A,B
Biol. Unit 1: A,B  (6x)
Biol. Unit 2: A (3x),B (3x)

Keywords :   Photosynthesis, Photosystem Ii, Light Harvesting Proteins, Red Algae, Thermostability, Bile Pigment, Chloroplast, Chromophore, Electron Transport, Membrane, Phycobilisome, Plastid, Thylakoid, Transport, Methylation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. Fromme, B. Thangaraj, C. Vanselow, P. Fromme
Crystal Structure Of C-Phycocyanin From Galdieria Sulphuraria At 1. 85 A
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - C-PHYCOCYANIN ALPHA CHAIN
	Chains	:	A
	Organism Common	:	RED ALGA
	Organism Scientific	:	GALDIERIA SULPHURARIA

Molecule 2 - C-PHYCOCYANIN BETA CHAIN
	Chains	:	B
	Organism Common	:	RED ALGA
	Organism Scientific	:	GALDIERIA SULPHURARIA

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (6x)	:	A	B
Biological Unit 2 (3x)	:	A (3x)	B (3x)

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 4)

No.	Name	Count	Type	Full Name
1	BLA	3	Ligand/Ion	BILIVERDINE IX ALPHA
2	MEN	1	Mod. Amino Acid	N-METHYL ASPARAGINE

Biological Unit 1 (2, 24)

No.	Name	Count	Type	Full Name
1	BLA	18	Ligand/Ion	BILIVERDINE IX ALPHA
2	MEN	6	Mod. Amino Acid	N-METHYL ASPARAGINE

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	BLA	-1	Ligand/Ion	BILIVERDINE IX ALPHA
2	MEN	-1	Mod. Amino Acid	N-METHYL ASPARAGINE

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	THR A:66 , PRO A:72 , GLN A:73 , TYR A:74 , ALA A:75 , LYS A:83 , CYS A:84 , ARG A:86 , ASP A:87 , TYR A:90 , TYR A:110 , PHE A:122 , TRP A:128 , TYR A:129 , HOH A:485 , HOH A:486 , HOH A:492 , HOH A:511 , HOH A:583 , ARG B:57 , ILE B:67 , THR B:75 , ASN B:76	BINDING SITE FOR RESIDUE BLA A 484
2	AC2	SOFTWARE	LEU B:59 , LEU B:66 , ALA B:73 , ARG B:78 , ALA B:81 , CYS B:82 , ARG B:84 , ASP B:85 , ILE B:88 , TYR B:92 , LEU B:113 , LEU B:120 , HOH B:709	BINDING SITE FOR RESIDUE BLA B 584
3	AC3	SOFTWARE	LEU A:24 , GLN A:25 , ASN A:28 , ARG A:33 , GLN A:145 , ASN A:148 , ASN B:35 , LEU B:38 , ASP B:39 , ALA B:142 , ASN B:143 , ILE B:148 , THR B:149 , THR B:150 , GLY B:151 , CYS B:153 , HOH B:672 , HOH B:684 , HOH B:716 , HOH B:723	BINDING SITE FOR RESIDUE BLA B 555

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

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

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

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

(no "Exon" information available for 3BRP)

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
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Chain A from PDB  Type:PROTEIN  Length:159
 aligned with PHCA_GALSU | P00306 from UniProtKB/Swiss-Prot  Length:162

    Alignment length:159
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151         
           PHCA_GALSU     2 KTPITEAIAAADNQGRFLSNTELQAVNGRYQRAAASLEAARSLTSNAERLINGAAQAVYSKFPYTSQMPGPQYASSAVGKAKCARDIGYYLRMVTYCLVVGGTGPMDEYLIAGLEEINRTFDLSPSWYVEALNYIKANHGLSGQAANEANTYIDYAINA 160
               SCOP domains d3brpa_ A: automated matches                                                                                                                                    SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhh..hhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3brp A   2 KTPITEAIAAADNQGRFLSNTELQAVNGRYQRAAASLEAARSLTSNAQRLINGAAQAVYSKFPYTSQMPGPQYASSAVGKAKCARDIGYYLRMVTYCLVVGGTGPMDEYLIAGLEEINRTFDLSPSWYVEALNYVKSNHGLSGQAANEANTYIDYAINA 160
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151

Chain B from PDB  Type:PROTEIN  Length:170
 aligned with PHCB_GALSU | P00311 from UniProtKB/Swiss-Prot  Length:172

    Alignment length:170
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171
           PHCB_GALSU     2 LDAFAKVVAQADARGEFLSNTQLDALSKMVSEGNKRLDVVNRITSNASAIVTNAARALFSEQPQLIQPGGNAYTNRRMAACLRDMEIILRYVSYAIIAGDSSILDDRCLNGLRETYQALGVPGASVAVGIEKMKDSAIAIANDPSGITTGDCSALMAEVGTYFDRAATAV 171
               SCOP domains d3brpb_ B: automated matches                                                                                                                                               SCOP domains
               CATH domains 3brpB00 B:2-171 Phycocyanins                                                                                                                                               CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhh..hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3brp B   2 LDAFAKVVAQADARGEFLSNTQLDALSKMVSEGNKRLDVVNRITSNASAIVTNAARALFSEQPQLIQPGGnAYTNRRMAACLRDMEIILRYVSYAIIAGDSSVLDDRCLNGLRETYQALGVPGASVAVGVEKMKDSAIAIANDPSGITTGDCSALMAEVGTYFDRAATAV 171
                                    11        21        31        41        51        61        71|       81        91       101       111       121       131       141       151       161       171
                                                                                                 72-MEN

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	-	→ 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(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All alpha proteins (14657)

Fold: Globin-like (1351)

Superfamily: Globin-like (1308)

Family: Phycocyanin-like phycobilisome proteins (65)

Protein domain: automated matches (19)

Red algae (Galdieria sulphuraria) [TaxId: 130081] (2)

1a	d3brpa_	A:
1b	d3brpb_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

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Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Globin-like (786)

Homologous Superfamily: Phycocyanins (32)

Red alga (Galdieria sulphuraria) (1)

3brpB00

B:2-171

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

Asymmetric Unit(hide GO term definitions)

Chain A (PHCA_GALSU | P00306)

biological process
	GO:0055114	oxidation-reduction process	A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
	GO:0015979	photosynthesis	The synthesis by organisms of organic chemical compounds, especially carbohydrates, from carbon dioxide (CO2) using energy obtained from light rather than from the oxidation of chemical compounds.
	GO:0018298	protein-chromophore linkage	The covalent or noncovalent attachment of a chromophore to a protein.
cellular component
	GO:0009507	chloroplast	A chlorophyll-containing plastid with thylakoids organized into grana and frets, or stroma thylakoids, and embedded in a stroma.
	GO:0009535	chloroplast thylakoid membrane	The pigmented membrane of a chloroplast thylakoid. An example of this component is found in Arabidopsis thaliana.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0030089	phycobilisome	Any of the granules, approximately 32 nm x 48 nm and consisting of highly aggregated phycobiliproteins, that are attached in arrays to the external face of a thylakoid membrane in algae of the phyla Cyanophyta and Rhodophyta, where they function as light-harvesting devices in photosynthesis. Excitation energy in the phycobilisome flows in the sequence: phycoerythrin, phycocyanin, allophycocyanin before passing to the antenna chlorophyll of photosystem II.
	GO:0009536	plastid	Any member of a family of organelles found in the cytoplasm of plants and some protists, which are membrane-bounded and contain DNA. Plant plastids develop from a common type, the proplastid.
	GO:0009579	thylakoid	A membranous cellular structure that bears the photosynthetic pigments in plants, algae, and cyanobacteria. In cyanobacteria thylakoids are of various shapes and are attached to, or continuous with, the plasma membrane. In eukaryotes they are flattened, membrane-bounded disk-like structures located in the chloroplasts; in the chloroplasts of higher plants the thylakoids form dense stacks called grana. Isolated thylakoid preparations can carry out photosynthetic electron transport and the associated phosphorylation.

Chain B (PHCB_GALSU | P00311)

biological process
	GO:0055114	oxidation-reduction process	A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
	GO:0015979	photosynthesis	The synthesis by organisms of organic chemical compounds, especially carbohydrates, from carbon dioxide (CO2) using energy obtained from light rather than from the oxidation of chemical compounds.
	GO:0018298	protein-chromophore linkage	The covalent or noncovalent attachment of a chromophore to a protein.
cellular component
	GO:0009507	chloroplast	A chlorophyll-containing plastid with thylakoids organized into grana and frets, or stroma thylakoids, and embedded in a stroma.
	GO:0009535	chloroplast thylakoid membrane	The pigmented membrane of a chloroplast thylakoid. An example of this component is found in Arabidopsis thaliana.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0030089	phycobilisome	Any of the granules, approximately 32 nm x 48 nm and consisting of highly aggregated phycobiliproteins, that are attached in arrays to the external face of a thylakoid membrane in algae of the phyla Cyanophyta and Rhodophyta, where they function as light-harvesting devices in photosynthesis. Excitation energy in the phycobilisome flows in the sequence: phycoerythrin, phycocyanin, allophycocyanin before passing to the antenna chlorophyll of photosystem II.
	GO:0009536	plastid	Any member of a family of organelles found in the cytoplasm of plants and some protists, which are membrane-bounded and contain DNA. Plant plastids develop from a common type, the proplastid.
	GO:0009579	thylakoid	A membranous cellular structure that bears the photosynthetic pigments in plants, algae, and cyanobacteria. In cyanobacteria thylakoids are of various shapes and are attached to, or continuous with, the plasma membrane. In eukaryotes they are flattened, membrane-bounded disk-like structures located in the chloroplasts; in the chloroplasts of higher plants the thylakoids form dense stacks called grana. Isolated thylakoid preparations can carry out photosynthetic electron transport and the associated phosphorylation.

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	PHCA_GALSU \| P00306	:	1phn 3kvs
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1f99	POLYSIPHONIA AT 2.4 A
1gh0	SPIRULINA PLATENSIS AT 2.2 A
1jbo	SYNECHOCOCCUS ELONGATUS AT 1.45A
1ktp	SYNECHOCOCCUS VULCANUS AT 1.6 A
1phn	CYANIDIUM CALDARIUM AT 1.65 A
2bv8	PHYCOCYANIN FROM GRACILARIA CHILENSIS AT 2 A

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