2V8A - JenaLib

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Title :   THE STRUCTURE OF THERMOSYNECHOCOCCUS ELONGATUS ALLOPHYCOCYANIN AT 3.5 ANGSTROEMS.

Authors :   J. W. Murray, K. Maghlaoui, J. Barber

Date :   06 Aug 07 (Deposition) - 11 Dec 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.50

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

Keywords :   Antenna, Transport, Chromophore, Methylation, Bile Pigment, Phycobilisome, Photosynthesis, Light-Harvesting, Electron Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. W. Murray, K. Maghlaoui, J. Barber
The Structure Of Allophycocyanin From Thermosynechococcus Elongatus At 3. 5 A Resolution.
Acta Crystallogr. , Sect. F V. 63 998 2007
PubMed-ID: 18084078 | Reference-DOI: 10.1107/S1744309107050920

Molecule 1 - ALLOPHYCOCYANIN ALPHA CHAIN
	Chains	:	A
	Organism Scientific	:	THERMOSYNECHOCOCCUS ELONGATUS
	Organism Taxid	:	197221
	Strain	:	BP-1

Molecule 2 - ALLOPHYCOCYANIN BETA CHAIN
	Chains	:	B
	Organism Scientific	:	THERMOSYNECHOCOCCUS ELONGATUS
	Organism Taxid	:	197221
	Strain	:	BP-1

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 3)

No.	Name	Count	Type	Full Name
1	CYC	2	Ligand/Ion	PHYCOCYANOBILIN
2	MEN	1	Mod. Amino Acid	N-METHYL ASPARAGINE

Biological Unit 1 (2, 9)

No.	Name	Count	Type	Full Name
1	CYC	6	Ligand/Ion	PHYCOCYANOBILIN
2	MEN	3	Mod. Amino Acid	N-METHYL ASPARAGINE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	VAL A:65 , ASN A:71 , ALA A:72 , MET A:77 , THR A:80 , CYS A:81 , ARG A:83 , ASP A:84 , TYR A:87 , TYR A:88 , ILE A:107 , GLY A:108 , MET A:115 , TYR A:116 , THR A:121 , PRO A:122 , ALA A:125 , VAL A:126 , TYR B:62 , THR B:66 , TYR B:73 , THR B:74	BINDING SITE FOR RESIDUE CYC A1081
2	AC2	SOFTWARE	MEN B:71 , MET B:72 , ARG B:76 , ARG B:77 , CYS B:81 , ARG B:83 , ASP B:84 , LEU B:85 , ARG B:107 , VAL B:121 , PRO B:122 , THR B:126	BINDING SITE FOR RESIDUE CYC B1081

(no "SS Bond" information available for 2V8A)

(no "Cis Peptide Bond" information available for 2V8A)

(no "SAP(SNP)/Variant" information available for 2V8A)

(no "PROSITE Motif" information available for 2V8A)

(no "Exon" information available for 2V8A)

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:160
 aligned with PHAA_THEEB | P50030 from UniProtKB/Swiss-Prot  Length:161

    Alignment length:160
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161
           PHAA_THEEB     2 SVVTKSIVNADAEARYLSPGELDRIKNFVSTGERRLRIAQTLTENRERIVKQAGDQLFQKRPDVVSPGGNAYGEEMTATCLRDLDYYLRLVTYGIVAGDVTPIEEIGLVGVREMYNSLGTPIPAVAEGIRAMKNVACSLLSAEDAAEAGSYFDFVIGAMQ 161
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2v8aA00 A:2-161 Phycocyanins                                                                                                                                     CATH domains
               Pfam domains ---Phycobilisome-2v8aA01 A:5-161                                                                                                                                 Pfam domains
         Sec.struct. author hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh.hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2v8a A   2 SVVTKSIVNADAEARYLSPGELDRIKNFVSTGERRLRIAQTLTENRERIVKQAGDQLFQKRPDVVSPGGNAYGEEMTATCLRDLDYYLRLVTYGIVAGDVTPIEEIGLVGVREMYNSLGTPIPAVAEGIRAMKNVACSLLSAEDAAEAGSYFDFVIGAMQ 161
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161

Chain B from PDB  Type:PROTEIN  Length:161
 aligned with APCB_THEEB | P50031 from UniProtKB/Swiss-Prot  Length:161

    Alignment length:161
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160 
           APCB_THEEB     1 MQDAITAVINASDVQGKYLDTAAMEKLKAYFATGELRVRAASVISANAANIVKEAVAKSLLYSDITRPGGNMYTTRRYAACIRDLDYYLRYATYAMLAGDPSILDERVLNGLKETYNSLGVPIAATVQAIQAMKEVTASLVGADAGKEMGIYFDYICSGLS 161
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2v8aB00 B:1-161 Phycocyanins                                                                                                                                      CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhh..hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2v8a B   1 MQDAITAVINASDVQGKYLDTAAMEKLKAYFATGELRVRAASVISANAANIVKEAVAKSLLYSDITRPGGnMYTTRRYAACIRDLDYYLRYATYAMLAGDPSILDERVLNGLKETYNSLGVPIAATVQAIQAMKEVTASLVGADAGKEMGIYFDYICSGLS 161
                                    10        20        30        40        50        60        70|       80        90       100       110       120       130       140       150       160 
                                                                                                 71-MEN

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 2V8A)

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Globin-like (786)

Homologous Superfamily: Phycocyanins (32)

Thermosynechococcus elongatus. Organism_taxid: 197221. Strain: bp-1. (1)

1a	2v8aB00	B:1-161
1b	2v8aA00	A:2-161

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Globin (291)

Family: Phycobilisome (15)

Thermosynechococcus elongatus (strain BP-1) (4)

Phycobilisome-2v8aA01

A:5-161

Asymmetric Unit(hide GO term definitions)

Chain A (PHAA_THEEB | P50030)

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: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: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.
	GO:0042651	thylakoid membrane	The pigmented membrane of any thylakoid.

Chain B (APCB_THEEB | P50031)

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: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: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.
	GO:0042651	thylakoid membrane	The pigmented membrane of any thylakoid.

Asymmetric Unit
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