7ezx

Electron Microscopy
3Å resolution

Structure of the phycobilisome from the red alga Porphyridium purpureum in Middle Light

Released:

Function and Biology Details

Structure analysis Details

Assembly composition:
hetero 658-mer (preferred)
PDBe Complex ID:
PDB-CPX-105416 (preferred)
Entry contents:
28 distinct polypeptide molecules
Macromolecules (28 distinct):
Phycobilisome 31.8 kDa linker polypeptide, phycoerythrin-associated, rod Chains: X1, X7, X9, XF, XI, XK
Molecule details ›
Chains: X1, X7, X9, XF, XI, XK
Length: 363 amino acids
Theoretical weight: 39.74 KDa
Source organism: Porphyridium purpureum
UniProt:
  • Canonical: A0A5J4YM59 (Residues: 1-363; Coverage: 100%)
Gene name: FVE85_8023
Sequence domains:
R-phycoerythrin gamma chain, chloroplastic Chains: A1, A7, A9, AF, AI, AK
Molecule details ›
Chains: A1, A7, A9, AF, AI, AK
Length: 290 amino acids
Theoretical weight: 31.79 KDa
Source organism: Porphyridium purpureum
UniProt:
  • Canonical: A0A5J4YX19 (Residues: 1-290; Coverage: 100%)
Gene name: FVE85_2041
PBS-linker domain-containing protein Chains: B1, B7, B9, BF, BI, BK
Molecule details ›
Chains: B1, B7, B9, BF, BI, BK
Length: 232 amino acids
Theoretical weight: 27 KDa
Source organism: Porphyridium purpureum
UniProt:
  • Canonical: W0RZ90 (Residues: 1-232; Coverage: 100%)
Gene name: cpcG
Sequence domains: Phycobilisome Linker polypeptide
C-phycocyanin alpha subunit Chains: C1, C7, C9, CF, CI, CK, E1, E7, E9, EF, EI, EK, G1, G7, G9, GF, GI, GK, I1, I7, I9, IF, II, IK, K1, K7, K9, KF, KI, KK, M1, M7, M9, MF, MI, MK
Molecule details ›
Chains: C1, C7, C9, CF, CI, CK, E1, E7, E9, EF, EI, EK, G1, G7, G9, GF, GI, GK, I1, I7, I9, IF, II, IK, K1, K7, K9, KF, KI, KK, M1, M7, M9, MF, MI, MK
Length: 162 amino acids
Theoretical weight: 17.48 KDa
Source organism: Porphyridium purpureum
UniProt:
  • Canonical: W0RYI4 (Residues: 1-162; Coverage: 100%)
Gene name: cpcA
Sequence domains: Phycobilisome protein
C-phycocyanin beta subunit Chains: D1, D7, D9, DF, DI, DK, F1, F7, F9, FF, FI, FK, H1, H7, H9, HF, HI, HK, J1, J7, J9, JF, JI, JK, L1, L7, L9, LF, LI, LK, N1, N7, N9, NF, NI, NK
Molecule details ›
Chains: D1, D7, D9, DF, DI, DK, F1, F7, F9, FF, FI, FK, H1, H7, H9, HF, HI, HK, J1, J7, J9, JF, JI, JK, L1, L7, L9, LF, LI, LK, N1, N7, N9, NF, NI, NK
Length: 172 amino acids
Theoretical weight: 18.24 KDa
Source organism: Porphyridium purpureum
UniProt:
  • Canonical: W0RZB2 (Residues: 1-172; Coverage: 100%)
Gene name: cpcB
Sequence domains: Phycobilisome protein
Phycoerythrin alpha subunit Chains: A3, AA, AC, AE, AG, AJ, AL, AN, AO, AQ, B4, BD, C3, CA, CB, CC, CE, CG, CJ, CL, CM, CN, CO, CQ, D4, DD, E3, EA, EB, EC, EE, EG, EJ, EL, EM, EN, EO, EQ, F4, FD, G3, GA, GB, GC, GE, GG, GJ, GL, GM, GN, GO, GQ, H4, HD, I3, IA, IB, IC, IE, IG, IJ, IL, IM, IN, IO, IQ, J4, J5, J8, JD, K3, KA, KB, KC, KE, KG, KJ, KL, KM, KN, KO, KQ, L4, LD, M2, MB, MJ, ML, MM, MR, O1, O2, O7, O9, OB, OF, OI, OJ, OK, OL, OM, OR, Q1, Q2, Q7, Q9, QB, QF, QI, QJ, QK, QL, QM, QR, S1, S2, S7, S9, SB, SF, SI, SJ, SK, SL, SM, SR, U1, U2, U7, U9, UB, UF, UI, UJ, UK, UL, UM, UR, W1, W2, W7, W9, WB, WF, WI, WJ, WK, WL, WM, WR, YB, YJ, YL, YM, Z1, Z7, Z9, ZF, ZI, ZK, aB, aJ, aL, aM, b1, b7, b9, bF, bI, bK, cJ, cL, d1, d7, d9, dB, dF, dI, dK, dM, eJ, eL, f1, f7, f9, fB, fF, fI, fK, fM, gJ, gL, h1, h7, h9, hB, hF, hI, hK, hM, iJ, iL, j1, j7, j9, jB, jF, jI, jK, jM, kJ, kL, l1, l7, l9, lB, lF, lI, lK, lM, mJ, mL, oJ, oL, qJ, qL, sJ, sL, uJ, uL
Molecule details ›
Chains: A3, AA, AC, AE, AG, AJ, AL, AN, AO, AQ, B4, BD, C3, CA, CB, CC, CE, CG, CJ, CL, CM, CN, CO, CQ, D4, DD, E3, EA, EB, EC, EE, EG, EJ, EL, EM, EN, EO, EQ, F4, FD, G3, GA, GB, GC, GE, GG, GJ, GL, GM, GN, GO, GQ, H4, HD, I3, IA, IB, IC, IE, IG, IJ, IL, IM, IN, IO, IQ, J4, J5, J8, JD, K3, KA, KB, KC, KE, KG, KJ, KL, KM, KN, KO, KQ, L4, LD, M2, MB, MJ, ML, MM, MR, O1, O2, O7, O9, OB, OF, OI, OJ, OK, OL, OM, OR, Q1, Q2, Q7, Q9, QB, QF, QI, QJ, QK, QL, QM, QR, S1, S2, S7, S9, SB, SF, SI, SJ, SK, SL, SM, SR, U1, U2, U7, U9, UB, UF, UI, UJ, UK, UL, UM, UR, W1, W2, W7, W9, WB, WF, WI, WJ, WK, WL, WM, WR, YB, YJ, YL, YM, Z1, Z7, Z9, ZF, ZI, ZK, aB, aJ, aL, aM, b1, b7, b9, bF, bI, bK, cJ, cL, d1, d7, d9, dB, dF, dI, dK, dM, eJ, eL, f1, f7, f9, fB, fF, fI, fK, fM, gJ, gL, h1, h7, h9, hB, hF, hI, hK, hM, iJ, iL, j1, j7, j9, jB, jF, jI, jK, jM, kJ, kL, l1, l7, l9, lB, lF, lI, lK, lM, mJ, mL, oJ, oL, qJ, qL, sJ, sL, uJ, uL
Length: 164 amino acids
Theoretical weight: 17.82 KDa
Source organism: Porphyridium purpureum
UniProt:
  • Canonical: E2IH77 (Residues: 1-164; Coverage: 100%)
Gene names: cpeA, peA
Sequence domains: Phycobilisome protein
B-phycoerythrin beta chain Chains: A5, A8, B3, B5, B8, BA, BC, BE, BG, BJ, BL, BN, BO, BQ, C4, C5, C8, CD, D3, DA, DB, DC, DE, DG, DJ, DL, DM, DN, DO, DQ, E4, ED, F3, F5, F8, FA, FB, FC, FE, FG, FJ, FL, FM, FN, FO, FQ, G4, G5, G8, GD, H3, H5, H8, HA, HB, HC, HE, HG, HJ, HL, HM, HN, HO, HQ, I4, I5, I8, ID, J3, JA, JB, JC, JE, JG, JJ, JL, JM, JN, JO, JQ, K4, K5, K8, KD, L3, L5, L8, LA, LB, LC, LE, LG, LJ, LL, LM, LN, LO, LQ, M3, M4, MD, MO, N2, N3, NB, NJ, NL, NM, NO, NR, P1, P2, P7, P9, PB, PF, PI, PJ, PK, PL, PM, PR, R1, R2, R7, R9, RB, RF, RI, RJ, RK, RL, RM, RR, T1, T2, T7, T9, TB, TF, TI, TJ, TK, TL, TM, TR, V1, V2, V7, V9, VB, VF, VI, VJ, VK, VL, VM, VR, X2, XB, XJ, XL, XM, XR, Y1, Y7, Y9, YF, YI, YK, ZB, ZJ, ZL, ZM, a1, a7, a9, aF, aI, aK, bJ, bL, c1, c7, c9, cB, cF, cI, cK, cM, dJ, dL, e1, e7, e9, eB, eF, eI, eK, eM, fJ, fL, g1, g7, g9, gB, gF, gI, gK, gM, hJ, hL, i1, i7, i9, iB, iF, iI, iK, iM, jJ, jL, k1, k7, k9, kB, kF, kI, kK, kM, lJ, lL, m1, m7, m9, mB, mF, mI, mK, mM, nJ, nL, pJ, pL, rJ, rL, tJ, tL, vJ, vL
Molecule details ›
Chains: A5, A8, B3, B5, B8, BA, BC, BE, BG, BJ, BL, BN, BO, BQ, C4, C5, C8, CD, D3, DA, DB, DC, DE, DG, DJ, DL, DM, DN, DO, DQ, E4, ED, F3, F5, F8, FA, FB, FC, FE, FG, FJ, FL, FM, FN, FO, FQ, G4, G5, G8, GD, H3, H5, H8, HA, HB, HC, HE, HG, HJ, HL, HM, HN, HO, HQ, I4, I5, I8, ID, J3, JA, JB, JC, JE, JG, JJ, JL, JM, JN, JO, JQ, K4, K5, K8, KD, L3, L5, L8, LA, LB, LC, LE, LG, LJ, LL, LM, LN, LO, LQ, M3, M4, MD, MO, N2, N3, NB, NJ, NL, NM, NO, NR, P1, P2, P7, P9, PB, PF, PI, PJ, PK, PL, PM, PR, R1, R2, R7, R9, RB, RF, RI, RJ, RK, RL, RM, RR, T1, T2, T7, T9, TB, TF, TI, TJ, TK, TL, TM, TR, V1, V2, V7, V9, VB, VF, VI, VJ, VK, VL, VM, VR, X2, XB, XJ, XL, XM, XR, Y1, Y7, Y9, YF, YI, YK, ZB, ZJ, ZL, ZM, a1, a7, a9, aF, aI, aK, bJ, bL, c1, c7, c9, cB, cF, cI, cK, cM, dJ, dL, e1, e7, e9, eB, eF, eI, eK, eM, fJ, fL, g1, g7, g9, gB, gF, gI, gK, gM, hJ, hL, i1, i7, i9, iB, iF, iI, iK, iM, jJ, jL, k1, k7, k9, kB, kF, kI, kK, kM, lJ, lL, m1, m7, m9, mB, mF, mI, mK, mM, nJ, nL, pJ, pL, rJ, rL, tJ, tL, vJ, vL
Length: 177 amino acids
Theoretical weight: 18.58 KDa
Source organism: Porphyridium purpureum
UniProt:
  • Canonical: P11393 (Residues: 1-177; Coverage: 100%)
Gene name: cpeB
Sequence domains: Phycobilisome protein
PBS-linker domain-containing protein Chains: e2, eR
Molecule details ›
Chains: e2, eR
Length: 303 amino acids
Theoretical weight: 32.89 KDa
Source organism: Porphyridium purpureum
UniProt:
  • Canonical: A0A5J4Z7F4 (Residues: 1-303; Coverage: 100%)
Gene name: FVE85_7221
Sequence domains: Phycobilisome Linker polypeptide
PBS-linker domain-containing protein Chains: O3, OO
Molecule details ›
Chains: O3, OO
Length: 405 amino acids
Theoretical weight: 43.97 KDa
Source organism: Porphyridium purpureum
UniProt:
  • Canonical: A0A5J4YMI8 (Residues: 22-426; Coverage: 95%)
Gene name: FVE85_8365
Sequence domains: Phycobilisome Linker polypeptide
PBS-linker domain-containing protein Chains: d4, dD
Molecule details ›
Chains: d4, dD
Length: 342 amino acids
Theoretical weight: 37.18 KDa
Source organism: Porphyridium purpureum
UniProt:
  • Canonical: A0A5J4Z162 (Residues: 1-342; Coverage: 100%)
Gene name: FVE85_0729
Sequence domains: Phycobilisome Linker polypeptide
CaRSPs2 Chains: D5, D8
Molecule details ›
Chains: D5, D8
Length: 327 amino acids
Theoretical weight: 36.4 KDa
Source organism: Porphyridium purpureum
UniProt:
  • Canonical: A0A5J4YX67 (Residues: 1-327; Coverage: 100%)
Gene name: FVE85_1715
CaRSPs1 Chains: E5, E8
Molecule details ›
Chains: E5, E8
Length: 288 amino acids
Theoretical weight: 31.17 KDa
Source organism: Porphyridium purpureum
UniProt:
  • Canonical: A0A5J4YJY8 (Residues: 1-288; Coverage: 100%)
Gene name: FVE85_9475
FAS1 domain-containing protein Chains: k6, kH
Molecule details ›
Chains: k6, kH
Length: 288 amino acids
Theoretical weight: 31.33 KDa
Source organism: Porphyridium purpureum
UniProt:
  • Canonical: A0A5J4Z027 (Residues: 48-335; Coverage: 86%)
Gene name: FVE85_0141
Sequence domains: Fasciclin domain
R-phycoerythrin gamma chain, chloroplastic Chains: MA, MG, MN, MQ
Molecule details ›
Chains: MA, MG, MN, MQ
Length: 333 amino acids
Theoretical weight: 36.92 KDa
Source organism: Porphyridium purpureum
UniProt:
  • Canonical: A0A5J4YNU6 (Residues: 1-333; Coverage: 100%)
Gene name: FVE85_9240
PBS-linker domain-containing protein Chains: bB, bM
Molecule details ›
Chains: bB, bM
Length: 490 amino acids
Theoretical weight: 53.6 KDa
Source organism: Porphyridium purpureum
UniProt:
  • Canonical: A0A5J4YX63 (Residues: 1-490; Coverage: 100%)
Gene name: FVE85_2314
Sequence domains: Phycobilisome Linker polypeptide
R-phycoerythrin gamma chain, chloroplastic Chains: AB, AM, wJ, wL, xJ, xL
Molecule details ›
Chains: AB, AM, wJ, wL, xJ, xL
Length: 273 amino acids
Theoretical weight: 29.45 KDa
Source organism: Porphyridium purpureum
UniProt:
  • Canonical: A0A5J4YZM7 (Residues: 1-273; Coverage: 100%)
Gene name: FVE85_2042
R-phycoerythrin gamma chain, chloroplastic Chains: BB, BM, yJ, yL
Molecule details ›
Chains: BB, BM, yJ, yL
Length: 290 amino acids
Theoretical weight: 31.36 KDa
Source organism: Porphyridium purpureum
UniProt:
  • Canonical: A0A5J4YZH3 (Residues: 1-290; Coverage: 100%)
Gene name: FVE85_2309
PBS-linker domain-containing protein Chains: MC, ME
Molecule details ›
Chains: MC, ME
Length: 316 amino acids
Theoretical weight: 34.96 KDa
Source organism: Porphyridium purpureum
UniProt:
  • Canonical: A0A5J4Z323 (Residues: 1-316; Coverage: 100%)
Gene name: FVE85_0816
Sequence domains: Phycobilisome Linker polypeptide
PBS-linker domain-containing protein Chains: zJ, zL
Molecule details ›
Chains: zJ, zL
Length: 498 amino acids
Theoretical weight: 55.15 KDa
Source organism: Porphyridium purpureum
UniProt:
  • Canonical: A0A5J4YI31 (Residues: 1-498; Coverage: 100%)
Gene name: FVE85_9810
Sequence domains: Phycobilisome Linker polypeptide
Allophycocyanin alpha subunit Chains: AP, CP, EP, GP, JP, KP, NP, PP, RP, TP, cP, eP, gP, iP, lP, mP, pP, rP, tP, vP
Molecule details ›
Chains: AP, CP, EP, GP, JP, KP, NP, PP, RP, TP, cP, eP, gP, iP, lP, mP, pP, rP, tP, vP
Length: 161 amino acids
Theoretical weight: 17.64 KDa
Source organism: Porphyridium purpureum
UniProt:
  • Canonical: W0RYM0 (Residues: 1-161; Coverage: 100%)
Gene name: apcA
Sequence domains: Phycobilisome protein
Allophycocyanin beta subunit Chains: BP, DP, FP, HP, IP, LP, MP, OP, QP, SP, UP, dP, fP, hP, jP, kP, nP, oP, qP, sP, uP, wP
Molecule details ›
Chains: BP, DP, FP, HP, IP, LP, MP, OP, QP, SP, UP, dP, fP, hP, jP, kP, nP, oP, qP, sP, uP, wP
Length: 161 amino acids
Theoretical weight: 17.42 KDa
Source organism: Porphyridium purpureum
UniProt:
  • Canonical: W0S279 (Residues: 1-161; Coverage: 100%)
Gene name: apcB
Sequence domains: Phycobilisome protein
Allophycocyanin gamma subunit Chains: VP, xP
Molecule details ›
Chains: VP, xP
Length: 161 amino acids
Theoretical weight: 18.13 KDa
Source organism: Porphyridium purpureum
UniProt:
  • Canonical: W0S1U6 (Residues: 1-161; Coverage: 100%)
Gene name: apcD
Sequence domains: Phycobilisome protein
Allophycocyanin beta 18 subunit Chains: WP, yP
Molecule details ›
Chains: WP, yP
Length: 173 amino acids
Theoretical weight: 19.78 KDa
Source organism: Porphyridium purpureum
UniProt:
  • Canonical: W0RZE2 (Residues: 1-173; Coverage: 100%)
Gene name: apcF
Sequence domains: Phycobilisome protein
CpcD-like domain-containing protein Chains: XP, zP
Molecule details ›
Chains: XP, zP
Length: 132 amino acids
Theoretical weight: 14.11 KDa
Source organism: Porphyridium purpureum
UniProt:
  • Canonical: A0A5J4YVZ2 (Residues: 1-132; Coverage: 100%)
Gene name: FVE85_2818
Sequence domains: CpcD/allophycocyanin linker domain
Phycobiliprotein ApcE Chains: 1P, YP
Molecule details ›
Chains: 1P, YP
Length: 879 amino acids
Theoretical weight: 99.47 KDa
Source organism: Porphyridium purpureum
UniProt:
  • Canonical: W0RZJ2 (Residues: 1-879; Coverage: 100%)
Gene name: apcE
Sequence domains:
Lrc4 Chains: 2P, ZP
Molecule details ›
Chains: 2P, ZP
Length: 159 amino acids
Theoretical weight: 16.92 KDa
Source organism: Porphyridium purpureum
UniProt:
  • Canonical: A0A5J4YTV6 (Residues: 1-159; Coverage: 100%)
Gene name: FVE85_4247
LRC5 Chains: 3P, aP
Molecule details ›
Chains: 3P, aP
Length: 288 amino acids
Theoretical weight: 30.27 KDa
Source organism: Porphyridium purpureum
UniProt:
  • Canonical: A0A5J4Z2M2 (Residues: 1-288; Coverage: 100%)
Gene name: FVE85_5140
FAS1 domain-containing protein Chains: 4P, bP
Molecule details ›
Chains: 4P, bP
Length: 253 amino acids
Theoretical weight: 26.62 KDa
Source organism: Porphyridium purpureum
UniProt:
  • Canonical: A0A5J4ZA95 (Residues: 1-253; Coverage: 100%)
Gene name: FVE85_7258
Sequence domains: Fasciclin domain

Ligands and Environments

1 modified residue:

Experiments and Validation Details

Entry percentile scores
Resolution:
Relevant EMDB volumes: EMD-31393