4H0M

X-Ray Crystal Structure of Phycocyanin from Synechococcus elongatus sp. PCC 7942

PDB DOI: https://doi.org/10.2210/pdb4H0M/pdb

Classification: PHOTOSYNTHESIS
Organism(s): Synechococcus elongatus PCC 7942 = FACHB-805
Mutation(s): No

Deposited: 2012-09-09 Released: 2013-03-06
Deposition Author(s): Marx, A., Adir, N.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.295
R-Value Work: 0.242
R-Value Observed: 0.245

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Allophycocyanin and phycocyanin crystal structures reveal facets of phycobilisome assembly.

Marx, A., Adir, N.

(2013) Biochim Biophys Acta 1827: 311-318

PubMed: 23201474 Search on PubMed
DOI: https://doi.org/10.1016/j.bbabio.2012.11.006
Primary Citation of Related Structures:
4F0T, 4F0U, 4GXE, 4GY3, 4H0M

PubMed Abstract:
X-ray crystal structures of the isolated phycobiliprotein components of the phycobilisome have provided high resolution details to the description of this light harvesting complex at different levels of complexity and detail. The linker-independent assembly of trimers into hexamers in crystal lattices of previously determined structures has been observed in almost all of the phycocyanin (PC) and allophycocyanin (APC) structures available in the Protein Data Bank. In this paper we describe the X-ray crystal structures of PC and APC from Synechococcus elongatus sp. PCC 7942, PC from Synechocystis sp. PCC 6803 and PC from Thermosynechococcus vulcanus crystallized in the presence of urea. All five structures are highly similar to other PC and APC structures on the levels of subunits, monomers and trimers. The Synechococcus APC forms a unique loose hexamer that may show the structural requirements for core assembly and rod attachment. While the Synechococcus PC assembles into the canonical hexamer, it does not further assemble into rods. Unlike most PC structures, the Synechocystis PC fails to form hexamers. Addition of low concentrations of urea to T. vulcanus PC inhibits this proteins propensity to form hexamers, resulting in a crystal lattice composed of trimers. The molecular source of these differences in assembly and their relevance to the phycobilisome structure is discussed.

Organizational Affiliation

Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa, Israel.

Macromolecule Content

Total Structure Weight: 448.45 kDa
Atom Count: 32,152
Modelled Residue Count: 4,008
Deposited Residue Count: 4,032
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
C-phycocyanin alpha chain	A, C, E, G, I A, C, E, G, I, K, M, O, Q, S, U, W	163	Synechococcus elongatus PCC 7942 = FACHB-805	Mutation(s): 0
UniProt
Find proteins for P13530 (Synechococcus elongatus (strain ATCC 33912 / PCC 7942 / FACHB-805)) Explore P13530 Go to UniProtKB: P13530
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P13530
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
C-phycocyanin beta chain	B, D, F, H, J B, D, F, H, J, L, N, P, R, T, V, X	173	Synechococcus elongatus PCC 7942 = FACHB-805	Mutation(s): 0
UniProt
Find proteins for P06539 (Synechococcus elongatus (strain ATCC 33912 / PCC 7942 / FACHB-805)) Explore P06539 Go to UniProtKB: P06539
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P06539
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CYC Query on CYC Download Ideal Coordinates CCD File SDF format, chain AB [auth T] SDF format, chain CB [auth U] SDF format, chain DA [auth D] SDF format, chain DB [auth V] SDF format, chain EA [auth E] SDF format, chain EB [auth V] SDF format, chain FB [auth W] SDF format, chain GA [auth F] SDF format, chain GB [auth X] SDF format, chain HB [auth X] SDF format, chain JA [auth H] SDF format, chain KA [auth I] SDF format, chain NA [auth K] SDF format, chain PA [auth L] SDF format, chain QA [auth M] SDF format, chain RA [auth N] SDF format, chain SA [auth N] SDF format, chain UA [auth P] SDF format, chain VA [auth P] SDF format, chain WA [auth Q] SDF format, chain Y [auth A] SDF format, chain YA [auth R] SDF format, chain ZA [auth S] SDF format, chain AA [auth B] SDF format, chain BA [auth C] SDF format, chain BB [auth T] SDF format, chain CA [auth D] SDF format, chain FA [auth F] SDF format, chain HA [auth G] SDF format, chain IA [auth H] SDF format, chain LA [auth J] SDF format, chain MA [auth J] SDF format, chain OA [auth L] SDF format, chain TA [auth O] SDF format, chain XA [auth R] SDF format, chain Z [auth B] MOL2 format, chain AB [auth T] MOL2 format, chain CB [auth U] MOL2 format, chain DA [auth D] MOL2 format, chain DB [auth V] MOL2 format, chain EA [auth E] MOL2 format, chain EB [auth V] MOL2 format, chain FB [auth W] MOL2 format, chain GA [auth F] MOL2 format, chain GB [auth X] MOL2 format, chain HB [auth X] MOL2 format, chain JA [auth H] MOL2 format, chain KA [auth I] MOL2 format, chain NA [auth K] MOL2 format, chain PA [auth L] MOL2 format, chain QA [auth M] MOL2 format, chain RA [auth N] MOL2 format, chain SA [auth N] MOL2 format, chain UA [auth P] MOL2 format, chain VA [auth P] MOL2 format, chain WA [auth Q] MOL2 format, chain Y [auth A] MOL2 format, chain YA [auth R] MOL2 format, chain ZA [auth S] MOL2 format, chain AA [auth B] MOL2 format, chain BA [auth C] MOL2 format, chain BB [auth T] MOL2 format, chain CA [auth D] MOL2 format, chain FA [auth F] MOL2 format, chain HA [auth G] MOL2 format, chain IA [auth H] MOL2 format, chain LA [auth J] MOL2 format, chain MA [auth J] MOL2 format, chain OA [auth L] MOL2 format, chain TA [auth O] MOL2 format, chain XA [auth R] MOL2 format, chain Z [auth B]	AA [auth B] AB [auth T] BA [auth C] BB [auth T] CA [auth D] AA [auth B], AB [auth T], BA [auth C], BB [auth T], CA [auth D], CB [auth U], DA [auth D], DB [auth V], EA [auth E], EB [auth V], FA [auth F], FB [auth W], GA [auth F], GB [auth X], HA [auth G], HB [auth X], IA [auth H], JA [auth H], KA [auth I], LA [auth J], MA [auth J], NA [auth K], OA [auth L], PA [auth L], QA [auth M], RA [auth N], SA [auth N], TA [auth O], UA [auth P], VA [auth P], WA [auth Q], XA [auth R], Y [auth A], YA [auth R], Z [auth B], ZA [auth S]	PHYCOCYANOBILIN C₃₃ H₄₀ N₄ O₆ VXTXPYZGDQPMHK-GMXXPEQVSA-N		Interactions Focus chain AA [auth B] Focus chain AB [auth T] Focus chain BA [auth C] Focus chain BB [auth T] Focus chain CA [auth D] Focus chain CB [auth U] Focus chain DA [auth D] Focus chain DB [auth V] Focus chain EA [auth E] Focus chain EB [auth V] Focus chain FA [auth F] Focus chain FB [auth W] Focus chain GA [auth F] Focus chain GB [auth X] Focus chain HA [auth G] Focus chain HB [auth X] Focus chain IA [auth H] Focus chain JA [auth H] Focus chain KA [auth I] Focus chain LA [auth J] Focus chain MA [auth J] Focus chain NA [auth K] Focus chain OA [auth L] Focus chain PA [auth L] Focus chain QA [auth M] Focus chain RA [auth N] Focus chain SA [auth N] Focus chain TA [auth O] Focus chain UA [auth P] Focus chain VA [auth P] Focus chain WA [auth Q] Focus chain XA [auth R] Focus chain Y [auth A] Focus chain YA [auth R] Focus chain Z [auth B] Focus chain ZA [auth S] Interactions & Density Focus chain AA [auth B] Focus chain AB [auth T] Focus chain BA [auth C] Focus chain BB [auth T] Focus chain CA [auth D] Focus chain CB [auth U] Focus chain DA [auth D] Focus chain DB [auth V] Focus chain EA [auth E] Focus chain EB [auth V] Focus chain FA [auth F] Focus chain FB [auth W] Focus chain GA [auth F] Focus chain GB [auth X] Focus chain HA [auth G] Focus chain HB [auth X] Focus chain IA [auth H] Focus chain JA [auth H] Focus chain KA [auth I] Focus chain LA [auth J] Focus chain MA [auth J] Focus chain NA [auth K] Focus chain OA [auth L] Focus chain PA [auth L] Focus chain QA [auth M] Focus chain RA [auth N] Focus chain SA [auth N] Focus chain TA [auth O] Focus chain UA [auth P] Focus chain VA [auth P] Focus chain WA [auth Q] Focus chain XA [auth R] Focus chain Y [auth A] Focus chain YA [auth R] Focus chain Z [auth B] Focus chain ZA [auth S]