6KGX

Structure of the phycobilisome from the red alga Porphyridium purpureum


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.8 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 at 2.8 Angstroms resolution.

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

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Phycoerythrin alpha subunit
A1, C1, E1, G1, I1, K1, N1, P1, R1, T1, V1, X1, c1, e1, g1, i1, k1, m1, p1, r1, t1, v1, x1, z1, O2, Q2, S2, U2, W2, Z2, b2, d2, f2, h2, j2, l2, A3, C3, E3, G3, I3, K3, M3, O3, Q3, S3, U3, W3, A4, C4, E4, G4, I4, K4, N4, P4, R4, T4, V4, X4, c4, e4, g4, i4, k4, m4, p4, r4, t4, v4, x4, z4, J5, O6, Q6, S6, U6, W6, Z6, b6, d6, f6, h6, j6, l6, O7, Q7, S7, U7, W7, Z7, b7, d7, f7, h7, j7, l7, C8, E8, G8, I8, K8, M8, O8, Q8, S8, U8, W8, Y8, a8, d8, f8, h8, j8, l8, B9, D9, F9, H9, J9, L9, N9, P9, R9, T9, V9, X9, CA, EA, GA, IA, KA, MA, OA, QA, SA, UA, WA, YA, aA, dA, fA, hA, jA, lA, OB, QB, SB, UB, WB, ZB, bB, dB, fB, hB, jB, lB, JC, AD, CD, ED, GD, ID, KD, MD, OD, QD, SD, UD, WD, AE, CE, EE, GE, IE, KE, ME, OE, QE, SE, UE, WE, YE, aE, cE, eE, gE, iE, kE, mE, oE, qE, sE, uE, OF, QF, SF, UF, WF, ZF, bF, dF, fF, hF, jF, lF, AG, CG, EG, GG, IG, KG, MG, OG, QG, SG, UG, WG, YG, aG, cG, eG, gG, iG, kG, mG, oG, qG, sG, uG, OI, QI, SI, UI, WI, ZI, bI, dI, fI, hI, jI, lI, BJ, DJ, FJ, HJ, JJ, LJ, NJ, PJ, RJ, TJ, VJ, XJ
164Porphyridium purpureumMutation(s): 0 
Gene Names: peA (cpeA)
Find proteins for E2IH77 (Porphyridium purpureum)
Go to UniProtKB:  E2IH77
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
B-phycoerythrin beta chain
B1, D1, F1, H1, J1, L1, O1, Q1, S1, U1, W1, Y1, Z1, a1, d1, f1, h1, j1, l1, n1, q1, s1, u1, w1, y1, 11, P2, R2, T2, V2, Y2, a2, c2, e2, g2, i2, k2, m2, B3, D3, F3, H3, J3, L3, N3, P3, R3, T3, V3, X3, B4, D4, F4, H4, J4, L4, O4, Q4, S4, U4, W4, Y4, Z4, a4, d4, f4, h4, j4, l4, n4, q4, s4, u4, w4, y4, 14, A5, B5, C5, F5, G5, H5, I5, K5, L5, P6, R6, T6, V6, Y6, a6, c6, e6, g6, i6, k6, m6, P7, R7, T7, V7, Y7, a7, c7, e7, g7, i7, k7, m7, D8, F8, H8, J8, L8, N8, P8, R8, T8, V8, X8, Z8, c8, e8, g8, i8, k8, m8, C9, E9, G9, I9, K9, M9, O9, Q9, S9, U9, W9, Y9, DA, FA, HA, JA, LA, NA, PA, RA, TA, VA, XA, ZA, cA, eA, gA, iA, kA, mA, PB, RB, TB, VB, YB, aB, cB, eB, gB, iB, kB, mB, AC, BC, CC, FC, GC, HC, IC, KC, LC, BD, DD, FD, HD, JD, LD, ND, PD, RD, TD, VD, XD, BE, DE, FE, HE, JE, LE, NE, PE, RE, TE, VE, XE, ZE, bE, dE, fE, hE, jE, lE, nE, pE, rE, tE, vE, PF, RF, TF, VF, YF, aF, cF, eF, gF, iF, kF, mF, BG, DG, FG, HG, JG, LG, NG, PG, RG, TG, VG, XG, ZG, bG, dG, fG, hG, jG, lG, nG, pG, rG, tG, vG, PI, RI, TI, VI, YI, aI, cI, eI, gI, iI, kI, mI, CJ, EJ, GJ, IJ, KJ, MJ, OJ, QJ, SJ, UJ, WJ, YJ
177Porphyridium purpureumMutation(s): 0 
Gene Names: cpeB
Find proteins for P11393 (Porphyridium purpureum)
Go to UniProtKB:  P11393
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
LR7
M1, 21, M4, 24
333N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
LR2_Hb
b1, o1, b4, o4
405N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
LR9
31, 34
288N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
LR1
X2, X6, X7, XB, XF, XI
363N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
LR4
A2, Y3, A6, A7, A9, AB, YD, AF, AI, AJ
290N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Phycobilisome rod-core linker polypeptide
B2, B6, B7, BB, BF, BI
232Porphyridium purpureumMutation(s): 0 
Gene Names: cpcG
Find proteins for W0RZ90 (Porphyridium purpureum)
Go to UniProtKB:  W0RZ90
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
C-phycocyanin alpha subunit
C2, E2, G2, I2, K2, M2, C6, E6, G6, I6, K6, M6, C7, E7, G7, I7, K7, M7, CB, EB, GB, IB, KB, MB, CF, EF, GF, IF, KF, MF, CI, EI, GI, II, KI, MI
162Porphyridium purpureumMutation(s): 0 
Gene Names: cpcA
Find proteins for W0RYI4 (Porphyridium purpureum)
Go to UniProtKB:  W0RYI4
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
C-phycocyanin beta subunit
D2, F2, H2, J2, L2, N2, D6, F6, H6, J6, L6, N6, D7, F7, H7, J7, L7, N7, DB, FB, HB, JB, LB, NB, DF, FF, HF, JF, LF, NF, DI, FI, HI, JI, LI, NI
172Porphyridium purpureumMutation(s): 0 
Gene Names: cpcB
Find proteins for W0RZB2 (Porphyridium purpureum)
Go to UniProtKB:  W0RZB2
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
LR2
e3, eD
303N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
LRC2
b8, bA
490N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
LR5
A8, AA, wE, xE, wG, xG
273N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
LR8
B8, BA, yE, yG
290N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
LR3
d9, dJ
342N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
LRC3
zE, zG
498N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
Allophycocyanin alpha subunit
AH, CH, EH, GH, JH, KH, NH, PH, RH, TH, cH, eH, gH, iH, lH, mH, pH, rH, tH, vH
161Porphyridium purpureumMutation(s): 0 
Gene Names: apcA
Find proteins for W0RYM0 (Porphyridium purpureum)
Go to UniProtKB:  W0RYM0
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
Allophycocyanin beta subunit
DH, FH, BH, HH, IH, LH, MH, OH, QH, SH, UH, dH, fH, hH, jH, kH, nH, oH, qH, sH, uH, wH
161Porphyridium purpureumMutation(s): 0 
Gene Names: apcB
Find proteins for W0S279 (Porphyridium purpureum)
Go to UniProtKB:  W0S279
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
Allophycocyanin gamma subunit
VH, xH
161Porphyridium purpureumMutation(s): 0 
Gene Names: apcD
Find proteins for W0S1U6 (Porphyridium purpureum)
Go to UniProtKB:  W0S1U6
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
Allophycocyanin beta 18 subunit
WH, yH
173Porphyridium purpureumMutation(s): 0 
Gene Names: apcF
Find proteins for W0RZE2 (Porphyridium purpureum)
Go to UniProtKB:  W0RZE2
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
LC
XH, zH
93N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
Phycobilisome linker polypeptide
YH, 1H
879Porphyridium purpureumMutation(s): 0 
Gene Names: apcE
Find proteins for W0RZJ2 (Porphyridium purpureum)
Go to UniProtKB:  W0RZJ2
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
LRC4
ZH, 2H
159N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
LRC5
aH, 3H
288N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
LRC6
bH, 4H
253N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PEB
Query on PEB

Download SDF File 
Download CCD File 
11, 14, 21, 24, A1, a1, A2, a2, A3, A4, a4, A5, A6, a6, a7, A7, a8, A8, A9, aA, AA, aB, AB, AC, AD, AE, aE, aF, AF, AG, aG, aI, AI, AJ, b1, B1, b2, B3, b4, B4, B5, b6, b7, B8, B9, BA, bB, BC, BD, BE, bE, bF, bG, BG, bI, BJ, c1, C1, c2, C3, C4, c4, C5, c6, c7, c8, C8, C9, cA, CA, cB, CC, CD, cE, CE, cF, CG, cG, cI, CJ, d1, D1, D2, d2, D3, D4, d4, D6, d6, D7, d7, d8, D8, D9, dA, DA, dB, DB, DD, DE, dE, DF, dF, dG, DG, DI, dI, DJ, e1, E1, e2, E3, e3, e4, E4, e6, e7, E8, e8, E9, eA, EA, eB, ED, eD, EE, eE, eF, EG, eG, eI, EJ, f1, F1, F2, f2, F3, f4, F4, F5, f6, f7, F7, f8, F8, F9, FA, fA, fB, FC, FD, fE, FE, fF, FF, FG, fG, FI, fI, FJ, G1, g1, g2, G3, G4, g4, G5, G6, g6, g7, g8, G8, G9, gA, GA, GB, gB, GC, GD, GE, gE, gF, gG, GG, gI, GJ, H1, h1, H2, h2, H3, H4, h4, H5, h6, H6, h7, H7, H8, h8, H9, HA, hA, hB, HB, HC, HD, hE, HE, HF, hF, hG, HG, HI, hI, HJ, I1, i1, i2, I3, i4, I4, I5, i6, i7, I8, i8, I9, IA, iA, iB, IC, ID, iE, IE, iF, IG, iG, iI, IJ, j1, J1, J2, j2, J3, j4, J4, J5, j6, j7, J7, j8, J8, J9, jA, JA, jB, JC, JD, JE, jE, jF, JF, jG, JG, JI, jI, JJ, k1, K1, k2, K3, K4, k4, K5, K6, k6, k7, K8, k8, K9, KA, kA, KB, kB, KC, KD, KE, kE, kF, kG, KG, kI, KJ, l1, L1, L2, l2, L3, l4, L4, L5, L6, l6, L7, l7, L8, l8, L9, lA, LA, lB, LB, LC, LD, lE, LE, lF, LF, lG, LG, LI, lI, LJ, m1, M1, m2, M3, M4, m4, m6, m7, M8, m8, M9, mA, MA, mB, MD, mE, ME, m
PHYCOERYTHROBILIN
C33 H40 N4 O6
NKCBCVIFPXGHAV-WAVSMFBNSA-N
 Ligand Interaction
CYC
Query on CYC

Download SDF File 
Download CCD File 
1H, AH, B6, BB, C2, C6, C7, CB, CF, CH, cH, CI, D2, D6, D7, DB, DF, dH, DI, E2, E6, E7, EB, EF, eH, EH, EI, F2, F6, F7, FB, FF, fH, FH, FI, G2, G6, G7, GB, gH, GH, GI, H2, H6, H7, HB, HF, hH, HI, I2, I6, I7, IB, IF, iH, IH, II, J2, J7, JF, jH, JH, JI, K2, K6, K7, KB, KF, KH, kH, KI, L2, L6, L7, LB, LF, lH, LH, LI, M2, M6, MB, MH, mH, MI, N2, N7, NB, NF, NH, nH, NI, oH, OH, pH, PH, qH, QH, RH, rH, sH, SH, TH, tH, UH, uH, vH, VH, wH, WH, YH, yH
PHYCOCYANOBILIN
C33 H40 N4 O6
VXTXPYZGDQPMHK-GMXXPEQVSA-N
 Ligand Interaction
PUB
Query on PUB

Download SDF File 
Download CCD File 
21, 24, A1, A2, A4, A6, A7, A8, A9, AA, AB, AF, AI, AJ, B8, BA, K1, K3, K4, KD, N9, NJ, Q8, QA, wE, wG, xE, xG, Y3, YD, yE, yG
PHYCOUROBILIN
C33 H42 N4 O6
KDCCOOGTVSRCHX-YYVBKQGDSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MEN
Query on MEN
11, 14, a1, a2, a4, A5, a6, a7, aB, AC, aF, aI, B1, B3, B4, B5, BC, BD, BE, bE, bG, BG, BH, c2, C5, c6, c7, c8, C9, cA, cB, CC, cF, cI, CJ, d1, D1, D2, D3, D4, d4, D6, D7, D8, DA, DB, DD, DE, dE, DF, dG, DG, dH, DH, DI, e2, e6, e7, e8, E9, eA, eB, eF, eI, EJ, F1, f1, F2, F3, F4, f4, F5, F6, F7, F8, FA, FB, FC, FD, FE, fE, FF, fG, FG, fH, FH, FI, g2, G5, g6, g7, g8, G9, gA, gB, GC, gF, gI, GJ, h1, H1, H2, H3, h4, H4, H5, H6, H7, H8, HA, HB, HC, HD, HE, hE, HF, hG, HG, hH, HH, HI, i2, I5, i6, i7, i8, I9, iA, iB, IC, iF, IH, iI, IJ, j1, J1, J2, J3, J4, j4, J6, J7, J8, JA, JB, JD, jE, JE, JF, jG, JG, jH, JI, k2, K5, k6, k7, k8, K9, kA, kB, KC, kF, kH, kI, KJ, L1, l1, L2, L3, L4, l4, L5, L6, L7, L8, LA, LB, LC, LD, LE, lE, LF, LG, lG, LH, LI, m2, m6, m7, m8, M9, mA, mB, mF, MH, mI, MJ, n1, N2, N3, n4, N6, N7, N8, NA, NB, ND, nE, NE, NF, nG, NG, nH, NI, O1, O4, O9, OH, oH, OJ, P2, P3, P6, P7, P8, PA, PB, PD, PE, pE, PF, pG, PG, PI, Q1, q1, q4, Q4, Q9, QH, qH, QJ, R2, R3, R6, R7, R8, RA, RB, RD, rE, RE, RF, rG, RG, RI, S1, s1, s4, S4, S9, sH, SH, SJ, T2, T3, T6, T7, T8, TA, TB, TD, tE, TE, TF, TG, tG, TI, u1, U1, U4, u4, U9, uH, UH, UJ, V2, V3, V6, V7, V8, VA, VB, VD, VE, vE, VF, VG, vG, VI, w1, W1, w4, W4, W9, wH, WJ, X3, X8, XA, XD, XE, XG, y1, Y1, Y2, Y4, y4, Y6, Y7, Y9, YB, YF, YI, YJ, Z1, Z4, Z8, ZA, ZE, ZG
L-PEPTIDE LINKINGC5 H10 N2 O3ASN
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.8 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: 2019-12-11
    Type: Initial release