6KGX

Structure of the phycobilisome from the red alga Porphyridium purpureum


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural basis of energy transfer in Porphyridium purpureum phycobilisome.

Ma, J.F.You, X.Sun, S.Wang, X.X.Qin, S.Sui, S.F.

(2020) Nature 579: 146-151

  • DOI: 10.1038/s41586-020-2020-7
  • Primary Citation of Related Structures:  
    6KGX

  • PubMed Abstract: 
  • Photosynthetic organisms have developed various light-harvesting systems to adapt to their environments 1 . Phycobilisomes are large light-harvesting protein complexes found in cyanobacteria and red algae 2-4 , although how the ...

    Photosynthetic organisms have developed various light-harvesting systems to adapt to their environments 1 . Phycobilisomes are large light-harvesting protein complexes found in cyanobacteria and red algae 2-4 , although how the energies of the chromophores within these complexes are modulated by their environment is unclear. Here we report the cryo-electron microscopy structure of a 14.7-megadalton phycobilisome with a hemiellipsoidal shape from the red alga Porphyridium purpureum. Within this complex we determine the structures of 706 protein subunits, including 528 phycoerythrin, 72 phycocyanin, 46 allophycocyanin and 60 linker proteins. In addition, 1,598 chromophores are resolved comprising 1,430 phycoerythrobilin, 48 phycourobilin and 120 phycocyanobilin molecules. The markedly improved resolution of our structure compared with that of the phycobilisome of Griffithsia pacifica 5 enabled us to build an accurate atomic model of the P. purpureum phycobilisome system. The model reveals how the linker proteins affect the microenvironment of the chromophores, and suggests that interactions of the aromatic amino acids of the linker proteins with the chromophores may be a key factor in fine-tuning the energy states of the chromophores to ensure the efficient unidirectional transfer of energy.


    Organizational Affiliation

    State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China. suisf@mail.tsinghua.edu.cn.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Phycoerythrin alpha 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 purpureumMutation(s): 0 
Gene Names: peAcpeA
Find proteins for E2IH77 (Porphyridium purpureum)
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
B-phycoerythrin beta 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 purpureumMutation(s): 0 
Gene Names: cpeB
Find proteins for P11393 (Porphyridium purpureum)
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
LR72124M1M4333Porphyridium purpureumMutation(s): 0 
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
LR2_Hbb1b4o1o4405Porphyridium purpureumMutation(s): 0 
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
LR93134288Porphyridium purpureumMutation(s): 0 
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Phycobilisome rod-core linker polypeptideB2B6B7BBBFBI232Porphyridium purpureumMutation(s): 0 
Gene Names: cpcG
Find proteins for W0RZ90 (Porphyridium purpureum)
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
C-phycocyanin alpha subunitC2C6C7CBCFCIE2E6E7EBEFEIG2G6G7GBGFGII2I6I7IBIFIIK2K6K7KBKFKIM2M6M7MBMFMI162Porphyridium purpureumMutation(s): 0 
Gene Names: cpcA
Find proteins for W0RYI4 (Porphyridium purpureum)
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
C-phycocyanin beta subunitD2D6D7DBDFDIF2F6F7FBFFFIH2H6H7HBHFHIJ2J6J7JBJFJIL2L6L7LBLFLIN2N6N7NBNFNI172Porphyridium purpureumMutation(s): 0 
Gene Names: cpcB
Find proteins for W0RZB2 (Porphyridium purpureum)
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
LR2e3eD303Porphyridium purpureumMutation(s): 0 
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
LRC2b8bA490Porphyridium purpureumMutation(s): 0 
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
LR5A8AAwEwGxExG273Porphyridium purpureumMutation(s): 0 
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
LR8B8BAyEyG290Porphyridium purpureumMutation(s): 0 
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
LR3d9dJ342Porphyridium purpureumMutation(s): 0 
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
Allophycocyanin alpha subunitAHCHEHGHJHKHNHPHRHTHcHeHgHiHlHmHpHrHtHvH161Porphyridium purpureumMutation(s): 0 
Gene Names: apcA
Find proteins for W0RYM0 (Porphyridium purpureum)
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
Allophycocyanin beta subunitBHDHFHHHIHLHMHOHQHSHUHdHfHhHjHkHnHoHqHsHuHwH161Porphyridium purpureumMutation(s): 0 
Gene Names: apcB
Find proteins for W0S279 (Porphyridium purpureum)
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
Allophycocyanin gamma subunitVHxH161Porphyridium purpureumMutation(s): 0 
Gene Names: apcD
Find proteins for W0S1U6 (Porphyridium purpureum)
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
LCXHzH93Porphyridium purpureumMutation(s): 0 
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
Phycobilisome linker polypeptide1HYH879Porphyridium purpureumMutation(s): 0 
Gene Names: apcE
Find proteins for W0RZJ2 (Porphyridium purpureum)
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
LRC53HaH288Porphyridium purpureumMutation(s): 0 
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
LRC3zEzG498Porphyridium purpureumMutation(s): 0 
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
Allophycocyanin beta 18 subunitWHyH173Porphyridium purpureumMutation(s): 0 
Gene Names: apcF
Find proteins for W0RZE2 (Porphyridium purpureum)
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
LRC42HZH159Porphyridium purpureumMutation(s): 0 
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
LRC64HbH253Porphyridium purpureumMutation(s): 0 
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
LR1X2X6X7XBXFXI363Porphyridium purpureumMutation(s): 0 
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
LR4A2A6A7A9ABAFAIAJY3YD290Porphyridium purpureumMutation(s): 0 
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PUB
Query on PUB

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21, 24, A1, A2, A4, A6, A7, A8, A9, AA, AB, AF, AI, AJ, B8, BA, K1, K3, K4, KD, N9, NJ, Q8, QA, Y3, YD, wE, wG, xE, xG, yE, yG
PHYCOUROBILIN
C33 H42 N4 O6
KDCCOOGTVSRCHX-YYVBKQGDSA-N
 Ligand Interaction
PEB
Query on PEB

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11, 14, 21, 24, A1, A2, A3, A4, A5, A6, A7, A8, A9, AA, AB, AC, AD, AE, AF, AG, AI, AJ, B1, B3, B4, B5, B8, B9, BA, BC, BD, BE, BG, BJ, C1, C3, C4, C5, C8, C9, CA, CC, CD, CE, CG, CJ, D1, D2, D3, D4, D6, D7, D8, D9, DA, DB, DD, DE, DF, DG, DI, DJ, E1, E3, E4, E8, E9, EA, ED, EE, EG, EJ, F1, F2, F3, F4, F5, F7, F8, F9, FA, FC, FD, FE, FF, FG, FI, FJ, G1, G3, G4, G5, G6, G8, G9, GA, GB, GC, GD, GE, GG, GJ, H1, H2, H3, H4, H5, H6, H7, H8, H9, HA, HB, HC, HD, HE, HF, HG, HI, HJ, I1, I3, I4, I5, I8, I9, IA, IC, ID, IE, IG, IJ, J1, J2, J3, J4, J5, J7, J8, J9, JA, JC, JD, JE, JF, JG, JI, JJ, K1, K3, K4, K5, K6, K8, K9, KA, KB, KC, KD, KE, KG, KJ, L1, L2, L3, L4, L5, L6, L7, L8, L9, LA, LB, LC, LD, LE, LF, LG, LI, LJ, M1, M3, M4, M8, M9, MA, MD, ME, MG, MJ, N1, N2, N3, N4, N6, N7, N8, N9, NA, NB, ND, NE, NF, NG, NI, NJ, O1, O2, O3, O4, O6, O7, O8, O9, OA, OB, OD, OE, OF, OG, OI, OJ, P1, P2, P3, P4, P6, P7, P8, P9, PA, PB, PD, PE, PF, PG, PI, PJ, Q1, Q2, Q3, Q4, Q6, Q7, Q8, Q9, QA, QB, QD, QE, QF, QG, QI, QJ, R1, R2, R3, R4, R6, R7, R8, R9, RA, RB, RD, RE, RF, RG, RI, RJ, S1, S2, S3, S4, S6, S7, S8, S9, SA, SB, SD, SE, SF, SG, SI, SJ, T1, T2, T3, T4, T6, T7, T8, T9, TA, TB, TD, TE, TF, TG, TI, TJ, U1, U2, U3, U4, U6, U7, U8, U9, UA, UB, UD, UE, UF, UG, UI, UJ, V1, V2, V3, V4, V6, V7, V8, V9, VA, VB, VD, VE, VF, VG, VI, VJ, W1, W2, W3, W4, W6, W7, W8, W9, WA, WB, WD, WE, WF, WG, WI, WJ, X1, X3, X4, X8, X9, XA, XD, XE, XG, XJ, Y1, Y2, Y3, Y4, Y6, Y7, Y8, Y9, YA, YB, YD, YE, YF, YG, YI, YJ, Z1, Z2, Z4, Z6, Z7, Z8, ZA, ZB, ZE, ZF, ZG, ZI, a1, a2, a4, a6, a7, a8, aA, aB, aE, aF, aG, aI, b1, b2, b4, b6, b7, bB, bE, bF, bG, bI, c1, c2, c4, c6, c7, c8, cA, cB, cE, cF, cG, cI, d1, d2, d4, d6, d7, d8, dA, dB, dE, dF, dG, dI, e1, e2, e3, e4, e6, e7, e8, eA, eB, eD, eE, eF, eG, eI, f1, f2, f4, f6, f7, f8, fA, fB, fE, fF, fG, fI, g1, g2, g4, g6, g7, g8, gA, gB, gE, gF, gG, gI, h1, h2, h4, h6, h7, h8, hA, hB, hE, hF, hG, hI, i1, i2, i4, i6, i7, i8, iA, iB, iE, iF, iG, iI, j1, j2, j4, j6, j7, j8, jA, jB, jE, jF, jG, jI, k1, k2, k4, k6, k7, k8, kA, kB, kE, kF, kG, kI, l1, l2, l4, l6, l7, l8, lA, lB, lE, lF, lG, lI, m1, m2, m4, m6, m7, m8, mA, mB, mE, mF, mG, mI, n1, n4, nE, nG, o1, oE, oG, p1, p4, pE, pG, q1, q4, qE, qG, r1, r4, rE, rG, s1, s4, sE, sG, t1, t4, tE, tG, u1, u4, uE, uG, v1, v4, vE, vG, w1, w4, wE, wG, x1, x4, xE, xG, y1, y4, yE, yG, z1, z4, zE, zG
PHYCOERYTHROBILIN
C33 H40 N4 O6
NKCBCVIFPXGHAV-WAVSMFBNSA-N
 Ligand Interaction
CYC
Query on CYC

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1H, AH, B6, BB, C2, C6, C7, CB, CF, CH, CI, D2, D6, D7, DB, DF, DI, E2, E6, E7, EB, EF, EH, EI, F2, F6, F7, FB, FF, FH, FI, G2, G6, G7, GB, GH, GI, H2, H6, H7, HB, HF, HI, I2, I6, I7, IB, IF, IH, II, J2, J7, JF, JH, JI, K2, K6, K7, KB, KF, KH, KI, L2, L6, L7, LB, LF, LH, LI, M2, M6, MB, MH, MI, N2, N7, NB, NF, NH, NI, OH, PH, QH, RH, SH, TH, UH, VH, WH, YH, cH, dH, eH, fH, gH, hH, iH, jH, kH, lH, mH, nH, oH, pH, qH, rH, sH, tH, uH, vH, wH, yH
PHYCOCYANOBILIN
C33 H40 N4 O6
VXTXPYZGDQPMHK-GMXXPEQVSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MEN
Query on MEN
11,14,A5,AC,B1,B3,B4,B5,BC,BD,BE,BG,C5,C9,CC,CJ,D1,D3,D4,D8,DA,DD,DE,DG,E9,EJ,F1,F3,F4,F5,F8,FA,FC,FD,FE,FG,G5,G9,GC,GJ,H1,H3,H4,H5,H8,HA,HC,HD,HE,HG,I5,I9,IC,IJ,J1,J3,J4,J8,JA,JD,JE,JG,K5,K9,KC,KJ,L1,L3,L4,L5,L8,LA,LC,LD,LE,LG,M9,MJ,N3,N8,NA,ND,NE,NG,O1,O4,O9,OJ,P2,P3,P6,P7,P8,PA,PB,PD,PE,PF,PG,PI,Q1,Q4,Q9,QJ,R2,R3,R6,R7,R8,RA,RB,RD,RE,RF,RG,RI,S1,S4,S9,SJ,T2,T3,T6,T7,T8,TA,TB,TD,TE,TF,TG,TI,U1,U4,U9,UJ,V2,V3,V6,V7,V8,VA,VB,VD,VE,VF,VG,VI,W1,W4,W9,WJ,X3,X8,XA,XD,XE,XG,Y1,Y2,Y4,Y6,Y7,Y9,YB,YF,YI,YJ,Z1,Z4,Z8,ZA,ZE,ZG,a1,a2,a4,a6,a7,aB,aF,aI,bE,bG,c2,c6,c7,c8,cA,cB,cF,cI,d1,d4,dE,dG,e2,e6,e7,e8,eA,eB,eF,eI,f1,f4,fE,fG,g2,g6,g7,g8,gA,gB,gF,gI,h1,h4,hE,hG,i2,i6,i7,i8,iA,iB,iF,iI,j1,j4,jE,jG,k2,k6,k7,k8,kA,kB,kF,kI,l1,l4,lE,lG,m2,m6,m7,m8,mA,mB,mF,mI,n1,n4,nE,nG,pE,pG,q1,q4,rE,rG,s1,s4,tE,tG,u1,u4,vE,vG,w1,w4,y1,y4L-PEPTIDE LINKINGC5 H10 N2 O3ASN
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-12-11
    Type: Initial release
  • Version 1.1: 2020-03-18
    Changes: Database references