5Y6P

Structure of the phycobilisome from the red alga Griffithsia pacifica


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.5 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structure of phycobilisome from the red alga Griffithsia pacifica

Zhang, J.Ma, J.Liu, D.Qin, S.Sun, S.Zhao, J.Sui, S.F.

(2017) Nature 551: 57-63

  • DOI: 10.1038/nature24278

  • PubMed Abstract: 
  • Life on Earth depends on photosynthesis for its conversion of solar energy to chemical energy. Photosynthetic organisms have developed a variety of light-harvesting systems to capture sunlight. The largest light-harvesting complex is the phycobilisom ...

    Life on Earth depends on photosynthesis for its conversion of solar energy to chemical energy. Photosynthetic organisms have developed a variety of light-harvesting systems to capture sunlight. The largest light-harvesting complex is the phycobilisome (PBS), the main light-harvesting antenna in cyanobacteria and red algae. It is composed of phycobiliproteins and linker proteins but the assembly mechanisms and energy transfer pathways of the PBS are not well understood. Here we report the structure of a 16.8-megadalton PBS from a red alga at 3.5 Å resolution obtained by single-particle cryo-electron microscopy. We modelled 862 protein subunits, including 4 linkers in the core, 16 rod-core linkers and 52 rod linkers, and located a total of 2,048 chromophores. This structure reveals the mechanisms underlying specific interactions between linkers and phycobiliproteins, and the formation of linker skeletons. These results provide a firm structural basis for our understanding of complex assembly and the mechanisms of energy transfer within the PBS.


    Organizational Affiliation

    State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
LRC6
A1, B1
260N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
LRC4
C1, D1
192N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
LRC5
E1, F1
307N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
alpha_APC
G1, I1, K1, N1, P1, R1, T1, X1, Z1, b1, d1, f1, i1, k1, o1, q1, s1, u1, w1, y1
161N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
beta_APC
H1, J1, L1, M1, O1, S1, U1, W1, Y1, a1, c1, e1, h1, j1, l1, n1, p1, r1, t1, v1, x1, z1
161N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
ApcF
Q1, g1
174N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
ApcD
V1, m1
161N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
LCM
a2, b2
885N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
LC
c2, d2
93N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
R-phycoerythrin alpha chain
e2, g2, i2, k2, m2, o2, q2, s2, u2, w2, y2, E2, G2, I2, K2, M2, O2, Q2, S2, U2, W2, Y2, A3, C3, E3, G3, I3, K3, M3, O3, Q3, S3, U3, W3, Y3, e3, g3, i3, k3, m3, o3, q3, s3, u3, w3, y3, A4, C4, E4, G4, I4, K4, M4, O4, Q4, S4, U4, W4, Y4, m4, o4, q4, s4, u4, w4, y4, A5, C5, E5, G5, I5, K5, M5, O5, Q5, S5, U5, m5, o5, q5, s5, u5, w5, y5, i8, j8, k8, l8, m8, A6, C6, E6, G6, I6, K6, M6, O6, Q6, S6, U6, W6, Y6, f6, g6, h6, i6, j6, k6, m6, o6, q6, s6, u6, w6, q8, r8, s8, t8, u8, A7, C7, E7, G7, I7, K7, M7, O7, Q7, S7, U7, W7, Y7, f7, g7, h7, i7, j7, k7, m7, o7, q7, s7, u7, w7, v8, x8, z8, B8, D8, F8, H8, J8, L8, N8, P8, m9, o9, q9, s9, u9, w9, y9, A9, C9, E9, G9, I9, K9, M9, O9, Q9, S9, U9, am, ao, aq, as, au, aw, ay, aA, aC, aE, aG, aI, aK, aM, aO, aQ, aS, aU, bm, bt, bu, bv, bw, bx, by, bA, bC, bE, bG, bI, bK, bM, bO, bQ, bS, bU, cm, ct, cu, cv, cw, cx, cy, cA, cC, cD, cG, cI, cK, cS, cT, cU, cV, cW, cX, cZ, da, db, dc, de, dg, dk, dm, do, dq, ds, du, dA, dC, dE, dG, dI, dJ, dM, dO, dQ, dS, dU, dW, dZ, ea, ed, ef, eh, ej, ek, em, eo, eq, es, eu, eA, eC, eE, eG, eI, eK, eM, eO, eQ, eS, eU, eW, la, lc, le, lg, li, lk, lm, lo, lq, ls, lu, lw, fb, fe, fg, fh, fk, fl, fn, fp, fr, ft, fv, fx, gb, gc, gf, gh, gj, gl, gm, go, gq, gs, gu, gw, hA, hC, hE, hF, hI, hK, hM, hO, hQ, hS, hU, hW, iA, iB
164N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
R-phycoerythrin beta chain
f2, h2, j2, l2, n2, p2, r2, t2, v2, x2, z2, F2, H2, J2, L2, N2, P2, R2, T2, V2, X2, Z2, B3, D3, F3, H3, J3, L3, N3, P3, R3, T3, V3, X3, Z3, f3, h3, j3, l3, n3, p3, r3, t3, v3, x3, z3, B4, D4, F4, H4, J4, L4, N4, P4, R4, T4, V4, X4, Z4, n4, p4, r4, t4, v4, x4, z4, B5, D5, F5, H5, J5, L5, N5, P5, R5, T5, V5, n5, p5, r5, t5, v5, x5, z5, f8, g8, h8, B6, D6, F6, H6, J6, L6, N6, P6, R6, T6, V6, X6, Z6, a6, b6, c6, d6, e6, l6, n6, p6, r6, t6, v6, x6, y6, z6, n8, o8, p8, B7, D7, F7, H7, J7, L7, N7, P7, R7, T7, V7, X7, Z7, a7, b7, c7, d7, e7, l7, n7, p7, r7, t7, v7, x7, y7, z7, w8, y8, A8, C8, E8, G8, I8, K8, M8, O8, Q8, n9, p9, r9, t9, v9, x9, z9, B9, D9, F9, H9, J9, L9, N9, P9, R9, T9, V9, an, ap, ar, at, av, ax, az, aB, aD, aF, aH, aJ, aL, aN, aP, aR, aT, aV, bn, bo, bp, bq, br, bs, bz, bB, bD, bF, bH, bJ, bL, bN, bP, bR, bT, bV, cn, co, cp, cq, cr, cs, cz, cB, cE, cF, cH, cJ, cL, cM, cN, cO, cP, cQ, cR, cY, dd, df, dh, di, dj, dl, dn, dp, dr, dt, dv, dB, dD, dF, dH, dK, dL, dN, dP, dR, dT, dV, dX, dY, eb, ec, ee, eg, ei, el, en, ep, er, et, ev, eB, eD, eF, eH, eJ, eL, eN, eP, eR, eT, eV, eX, lb, ld, lf, lh, lj, ll, ln, lp, lr, lt, lv, lx, fa, fc, ff, fi, fj, fm, fo, fq, fs, fu, fw, fy, ga, gd, ge, gg, gi, gk, gn, gp, gr, gt, gv, gx, hB, hD, hG, hH, hJ, hL, hN, hP, hR, hT, hV, hX, iC, iD, iE, iF, iG, iH, jI, jJ, jK, jL, jM, jN, jO, jP, kQ, kR, kS, kT, kU, kV, kW, kX
177N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
LR_gamma4
A2, a3, 34, Y5, b8, b9, U8, Z9, aY, bY, dw, dx, ey, ez
318N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
LRC2
B2, b3
477N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
LR_gamma5
C2, D2, c3, d3, 44, Z5, c8, d8, e8, c9, d9, e9, T8, Y9, aZ, bZ
285N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
LRC1
14, W5, R8, W9, aW, bW
232N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
LR1
24, X5, S8, X9, aX, bX
371N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
alpha_PC
a4, b4, d4, f4, i4, k4, a5, b5, d5, f5, i5, k5, V8, X8, Z8, g9, i9, k9, aa, ac, ae, ag, ai, ak, ba, bc, be, bg, bi, bk, ca, cc, ce, cg, ci, ck
162N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
beta_PC
c4, e4, g4, h4, j4, l4, c5, e5, g5, h5, j5, l5, W8, Y8, f9, h9, j9, l9, ab, ad, af, ah, aj, al, bb, bd, bf, bh, bj, bl, cb, cd, cf, ch, cj, cl
172N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
LRC3
a8, a9
514N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
LR3
dy, dz
352N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
LR2
ew, ex, fd, fz
276N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
LR_gamma7
eY, eZ
352N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
LR_gamma8
ly, lz, hY, hZ
350N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
LR_gamma6
gy, gz
297N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
LR9
ka, kb
362N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PEB
Query on PEB

Download SDF File 
Download CCD File 
24, 34, 44, A1, A2, A3, a3, A4, a4, a5, A5, a6, A6, A7, a7, A8, a8, A9, a9, aa, aA, ab, aB, ac, aC, aD, ad, ae, aE, aF, af, aG, ag, aH, ah, ai, aI, aj, aJ, ak, aK, al, aL, aM, am, aN, an, aO, ao, ap, aP, aQ, aq, aR, ar, as, aS, aT, at, aU, au, av, aV, aW, aw, aX, ax, ay, aY, aZ, az, B1, B2, b3, B3, b4, B4, B5, b5, B6, b6, B7, b7, b8, B8, b9, B9, bA, ba, bb, bB, bc, bC, bD, bd, be, bE, bf, bF, bg, bG, bh, bH, bi, bI, bj, bJ, bK, bk, bL, bl, bm, bM, bn, bN, bo, bO, bp, bP, bq, bQ, br, bR, bs, bS, bT, bt, bu, bU, bV, bv, bw, bW, bX, bx, by, bY, bZ, bz, C2, c3, C3, c4, C4, C5, c5, C6, c6, C7, c7, c8, C8, c9, C9, ca, cA, cB, cb, cc, cC, cd, cD, ce, cE, cF, cf, cG, cg, cH, ch, cI, ci, cJ, cj, cK, ck, cL, cl, cM, cm, cn, cN, co, cO, cp, cP, cq, cQ, cr, cR, cS, cs, cT, ct, cu, cU, cv, cV, cW, cw, cx, cX, cY, cy, cZ, cz, D2, d3, D3, d4, D4, D5, d5, D6, d6, D7, d7, d8, D8, D9, d9, dA, da, db, dB, dC, dc, dD, dd, de, dE, dF, df, dG, dg, dH, dh, di, dI, dJ, dj, dk, dK, dl, dL, dM, dm, dN, dn, dO, do, dP, dp, dq, dQ, dR, dr, dS, ds, dt, dT, du, dU, dv, dV, dW, dw, dX, dx, dy, dY, dZ, dz, e2, E2, e3, E3, e4, E4, e5, E5, E6, e6, e7, E7, E8, e8, E9, e9, ea, eA, eb, eB, ec, eC, eD, ed, eE, ee, ef, eF, eg, eG, eh, eH, eI, ei, eJ, ej, eK, ek, el, eL, eM, em, en, eN, eo, eO, ep, eP, eq, eQ, eR, er, es, eS, et, eT, eu, eU, eV, ev, ew, eW, eX, eY, ey, eZ, ez, F2, f
PHYCOERYTHROBILIN
C33 H40 N4 O6
NKCBCVIFPXGHAV-WAVSMFBNSA-N
 Ligand Interaction
PVN
Query on PVN

Download SDF File 
Download CCD File 
34, 44, A2, a3, aY, aZ, b8, b9, bY, bZ, C2, c3, c8, c9, D2, d3, d8, d9, dw, dx, e8, e9, eY, ey, ez, eZ, gy, gz, hY, hZ, ly, lz, T8, U8, Y5, Y9, Z5, Z9
PHYCOVIOLOBILIN
Phycoviolobilin, bound form
C33 H40 N4 O6
SYEAKBPGLNVPDH-HVONXEAXSA-N
 Ligand Interaction
CYC
Query on CYC

Download SDF File 
Download CCD File 
a1, a2, b1, b2, c1, d1, d2, e1, f1, g1, G1, H1, h1, i1, I1, J1, j1, k1, K1, L1, M1, m1, N1, n1, o1, O1, p1, P1, q1, Q1, R1, r1, s1, S1, t1, U1, u1, v1, V1, w1, W1, X1, Y1, y1, Z1, z1
PHYCOCYANOBILIN
C33 H40 N4 O6
VXTXPYZGDQPMHK-GMXXPEQVSA-N
 Ligand Interaction
PUB
Query on PUB

Download SDF File 
Download CCD File 
34, 44, A2, a3, a6, a7, A8, aB, aD, aF, aH, aJ, aL, an, aN, aP, ap, ar, aR, aT, at, aV, av, ax, aY, aZ, az, B3, B4, B5, b6, B6, b7, B7, b8, B9, b9, bB, bD, bF, bH, bJ, bL, bN, bn, bo, bp, bP, bq, br, bR, bs, bT, bV, bY, bz, bZ, C2, c3, c6, c7, C8, c8, c9, cB, cE, cF, cH, cJ, cL, cM, cn, cN, co, cO, cP, cp, cQ, cq, cr, cR, cs, cY, cz, D2, D3, d3, D4, D5, D6, d6, D7, d7, d8, d9, D9, dB, dd, dD, df, dF, dH, dh, di, dj, dK, dl, dL, dN, dn, dp, dP, dr, dR, dt, dT, dV, dv, dw, dX, dx, dY, e6, e7, E8, e8, e9, eb, eB, ec, eD, ee, eF, eg, eH, ei, eJ, eL, el, en, eN, eP, ep, er, eR, eT, et, eV, ev, eX, ey, eY, ez, eZ, f2, F2, f3, F3, F4, F5, F6, F7, f8, F9, fa, fc, ff, fi, fj, fm, fo, fq, fs, fu, fw, fy, G8, g8, ga, gd, ge, gg, gi, gk, gn, gp, gr, gt, gv, gx, gy, gz, H2, h2, H3, h3, H4, H5, H6, H7, h8, H9, hB, hD, hG, hH, hJ, hL, hN, hP, hR, hT, hV, hX, hY, hZ, I8, iC, iD, iE, iF, iG, iH, j2, J2, j3, J3, J4, J5, J6, J7, J9, jI, jJ, jK, jL, jM, jN, jO, jP, K8, kQ, kR, kS, kT, kU, kV, kW, kX, l2, L2, L3, l3, L4, L5, L6, l6, l7, L7, L9, lb, ld, lf, lh, lj, ll, ln, lp, lr, lt, lv, lx, ly, lz, M8, n2, N2, n3, N3, n4, N4, n5, N5, N6, n6, N7, n7, n8, n9, N9, O8, o8, P2, p2, p3, P3, p4, P4, p5, P5, p6, P6, P7, p7, p8, p9, P9, Q8, R2, r2, R3, r3, R4, r4, R5, r5, R6, r6, r7, R7, R9, r9, s7, T2, t2, T3, t3, t4, T4, t5, T5, T6, t6, t7, T7, T8, t9, T9, u6, U8, v2, V
PHYCOUROBILIN
C33 H42 N4 O6
KDCCOOGTVSRCHX-YYVBKQGDSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.5 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-11-15
    Type: Initial release