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PDB ID Mentions in PubMed Central Article count: 5

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PDB ID Mentions in PubMed Central

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Algorithms for incorporating prior topological information in HMMs: application to transmembrane proteins.

(2006) BMC Bioinformatics 7

PubMed: 16597327 | PubMedCentral: PMC1523218 | DOI: 10.1186/1471-2105-7-189

We list the PDB code, the name of the protein and the number of the transmembrane segments PDB code Name Number of transmembrane segments 1RC2 :B AQUAPORIN Z 6 1J4N :A AQUAPORIN 1 6 1IWG :A MULTIDRUG ... FFLUX TRANSPORTER ACRB 12 1NEK :C SUCCINATE DEHYDROGENASE CYTOCHROME B-556 SUBUNIT 3 1NEK :D SUCCINATE_DEHYDROGENASE HYDROPHOBIC MEMBRANE ANCHOR PROTEIN 3 1Q16 :C RESPIRATORY NITRATE REDUCTASE 1 GAMMA CHAIN 5 1RH5 :B PREPROTEIN TRANSLOCASE SECE SUBUNIT 1 1RH5 :C PREPROTEIN TRANSLOCASE SECBETA SUBUNIT 1 1IZL :A PHOTOSYSTEM II SUBUNIT PSBA 5 1IZL :C PHOTOSYSTEM II SUBUNIT PSBC 5 1YCE ROTOR OF F-TYPE NA+-ATPASE 2 2BL2 ROTOR OF V-TYPE NA+-ATPASE 4 1XQF :A PROBABLE AMMONIUM TRANSPORTER 11 1KPL :A H+/CL- EXCHANGE TRANSPORTER 14 1S5L :B PHOTOSYSTEM II CORE LIGHT HARVESTING PROTEIN 6 1S5L :C PHOTOSYSTEM II CP43 PROTEIN 6 1S5L :D PHOTOSYSTEM II REACTION CENTER D2 PROTEIN 5 1S5L :E CYTOCHROME B559 ALPHA SUBUNIT 1 1FX8 :A GLPF GLYCEROL FACILITATOR CHANNEL 6 1LNQ :A MTHK POTTASIUM CHANNEL, CA-GATED 2 1MXM :A MECHANOSENSITIVE CHANNEL PROTEIN 3 1Q90 :M CYTOCHROME B6F COMPLEX SUBUNIT PETM 1 1VF5 :C CYTOCHROME F 1 1K4C :C POTASSIUM CHANNEL KCSA 2 1ZCD :A NA(+)/H(+) ANTIPORTER 1 12 2A79 :B POTASSIUM VOLTAGE-GATED CHANNEL SUBFAMILY A MEMBER 2 6

Publication Year: 2006


Prediction of transmembrane helix orientation in polytopic membrane proteins.

(2006) BMC Struct Biol 6

PubMed: 16792816 | PubMedCentral: PMC1540425 | DOI: 10.1186/1472-6807-6-13

Almost identical structures of cytochrome b 6 f complex were obtained from the thermophilic cyanobacterium Mastigocladus laminosus (PDB: 1VF5 ) [ 34 ] and the green alga Chlamydomonas reinhardtii (PDB... 1Q90 ) [ 35 ].

reinhardtii (PDB: 1Q90 ) and M. laminosus (PDB: 1VF5 ) .

Packing of PetN subunit with PetL and PetM subunits Placement of the PetN TM helix is different in 1Q90 and 1VF5 structures: it is almost completely buried within a helical bundle in 1Q90 and is exposed in 1VF5 (Figure 7 ).

In summary, we find that the conserved faces of PetN, PetL, and PetG subunits are hidden within the helical bundle in green alga structure 1Q90, while in cyanobacterium structure 1VF5, the conserved helical faces of the same subunits are often lipid-exposed.

Sequence motifs such as GG4 and SS4 in PetG, PetL and PetN subunits are found in tight helix-helix packing interactions in the green alga cytochrome b 6 f structure, while such tight packing interactions are often missing in cyanobacterium 1VF5 structure.

(B) TM helices PetN and PetM do not pack tightly in 1VF5 structure.

The first sequence in every sequence alignment is from 1Q90 structure, while the second sequence is from 1VF5 structure.

In the cyanobacterium structure (1VF5), Trp8 points towards the lipid phase (Figure 8B ), while in the green alga structure (1Q90) this residue points inside of TM bundle into the lipid-filled cavity and forms a H-bond with highly conserved Gln37 from the soluble domain of cytochrome f (Figure 8C ).

Publication Year: 2006


Correlation between amino acid residues converted by RNA editing and functional residues in protein three-dimensional structures in plant organelles.

(2008) BMC Plant Biol 8

PubMed: 18631376 | PubMedCentral: PMC2488346 | DOI: 10.1186/1471-2229-8-79

Table 1 Products of mRNAs undergoing conversion editing Protein Name # of genes # of edited nucleotide sites PDB ID (chain) Transcription machinery  RNA polymease α 2 24 (2:21:1) 2a69 ... A), 1coo (_)  RNA polymerase β 1 19 (6:13:0) 2a69 (C)  RNA polymerase β' 2 20 (9:11:0) 2a69 (D) Translation machinery  ribosomal protein S1 2 6 (1: 5: 0)  ribosomal protein S2 4 34 (12: 22: 0) 2j00 (B)  ribosomal protein S3 7 74 (20: 32: 22) 2j00 (C)  ribosomal protein S4 4 52 (18:30:4) 2j00 (D)  ribosomal protein S7 4 9 (2:7:0)  ribosomal protein S8 1 2 (1: 1: 0) 2j00 (H)  ribosomal protein S10 2 5 (2: 3: 0) 2j00 (J)  ribosomal protein S12 3 21 (4: 14: 3) 2j00 (L)  ribosomal protein S13 3 18 (5: 12: 1) 2j00 (M)  ribosomal protein S14 3 5 (1:3:1) 2j00 (N)  ribosomal protein S19 5 33 (7:19:7) 2j00 (S)  ribosomal protein L2 4 10 (3:4:3) 2j01 (D)  ribosomal protein L5 5 28 (8:20:0) 2j01 (G)  ribosomal protein L14 1 1 (1:0:0) 2j01 (O)  ribosomal protein L16 4 33 (6:19:8) 2j01 (Q)  ribosomal protein L20 1 3 (1:2:0) 2j01 (U)  ribosomal protein L21 1 2 (2:0:0) 2j01 (V)  ribosomal protein L22 1 2 (0:2:0) 2j01 (W)  ribosomal protein L23 1 3 (0:3:0) 2j01 (X)  ribosomal protein L33 1 1 (0:1:0) 2j01 (6)  ribosomal protein L36 1 1 (0:1:0)  translation initiation factor 1 1 3 (1:2:0) 1hr0 (W)  Clp protease proteolytic subunit 1 1 6 (0:6:0) 1yg6 (A) Respiratory machinery  NADH dehydrogenase subunit J 1 2 (0:2:0) 2fug (5)  NADH dehydrogenase subunit K 1 3 (1:1:1) 2fug (6)  NADH dehydrogenase subunit I 1 2 (1:1:0) 2fug (9)  NADH dehydrogenase subunit 1 23 141 (71:60:10)  NADH dehydrogenase subunit 2 25 236 (55:147:34)  NADH dehydrogenase subunit 3 7 102 (36:62:4)  NADH dehydrogenase subunit 4 10 111 (31:77:3)  NADH dehydrogenase subunit 4L 9 64 (15:48:1)  NADH dehydrogenase subunit 5 7 180 (44:94:42)  NADH dehydrogenase subunit 6 5 61 (14:40:7)  NADH dehydrogenase subunit 7 4 86 (20:49:17)  NADH dehydrogenase subunit 9 6 58 (24:33:1)  cytochrome bc 1 complex cytochrome b 7 136 (68:59:9) 1kyo (C)  cytochrome c biogenesis ccmC 5 156 (65:77:14)  cytochrome c biogenesis ccmF 15 195 (90:88:17)  cytochrome c biogenesis ccsA 1 12 (2:10:0)  cytochrome c ccmB 7 278 (108:145:25)  cytochrome c oxidase I 20 324 (107:196:21) 1v55 (A)  cytochrome c oxidase II 14 164 (64:85:15) 1v55 (B)  cytochrome c oxidase III 15 155 (42:82:31) 1v55 (C) Photosynthesis machinery  photochlorophyllide reductase subunit chlL 1 9 (5:4:0) 2afh (E)  photochlorophyllide reductase subunit chlB 8 23 (10:13:0)  photochlorophyllide reductase subunit chlN 1 3 (1:2:0)  photosystem II subunit V 2 5 (1:3:1) 2axt (E)  photosystem II subunit VI 2 7 (1:5:1) 2axt (F)  photosystem II CP47 protein 2 55 (15:34:6) 2axt (B)  photosystem II H protein 1 4 (0:4:0) 2axt (H)  photosystem II J protein 1 2 (1:1:0) 2axt (J)  photosystem II L protein 4 8 (1:7:0) 2axt (L)  photosystem II M protein 1 1 (0:1:0) 2axt (M)  photosystem II N protein 1 2 (0:2:0)  photosystem II T protein 2 5 (2:3:0) 2axt (T)  photosystem II Z protein 1 1 (0:0:1) 2axt (Z)  cytochrome b 6 f complex petG 1 1 (0:1:0) 1vf 5(G)  cytochrome b 6 f complex petL 1 2 (1:1:0) 1vf5 (E)  cytochrome b 6 f subunit 4 2 19 (4:15:0) 1vf5 (B)  cytochrome f 1 2 (2:0:0) 1vf5 (C)  photosystem I P700 apoprotein A1 1 1 (1:0:0) 1jb0 (A)  photosystem I P700 apoprotein A2 1 1 (0:1:0) 1jb0 (B)  photosystem I subunit IX 1 1 (0:1:0) 1jb0 (J)  photosystem I assembly protein Ycf3 2 9 (2:7:0)  ATPase α 21 100 (66:28:6) 2ck3 (A)  ATPase β 1 7 (1:6:0) 2ck3 (D)  ATPase ε 1 3 (1:2:0) 1fs0 (E)  ATP synthase CF0 A chain 1 11 (2:8:1)  ATP synthase CF0 B chain 1 1 (0:1:0)  ATP synthase CF0 C chain 1 7 (1:6:0)  ATP synthase subunit 6 12 38 (19:17:2)  ATP synthase subunit 9 10 58 (17:37:4)  RUBISCO large subunit 5 35 (11:23:1) 1uw9 (A) Other machinery  Chloroplast envelope membrane protein 1 5 (3:2:0)  Acetyl-coA carboxylase carboxyl transferase β 1 16 (6:9:1) 2f9i (B)  succinate dehydrogenase subunit 4 1 1 (0:1:0)  maturase K (intron-encoded protein) 1 4 (0:4:0)  maturase R (intron-encoded protein) 5 54 (13:36:5) Hypothetical organelle proteins  hypothetical protein ycf1 1 2 (0:1:1)  hypothetical protein ycf2 1 7 (4:2:1)  hypothetical protein ymf19 5 20 (4:8:8)  orf114 1 2 (0:0:2)  orf240a 1 1 (1:0:0)  orf25 5 45 (8:33:4)  orfX 4 101 (45:45:11) Total 365 3560 1219 1983 358 Detail of the data is described in Additional files 1 and 2 .

Publication Year: 2008


PubMed ID is not available.

Published in 2014

PubMedCentral: PMC4002152

773 Figure 29 Structure of the bc 1 complex from chicken (PDB ID 3H1J) and its Rieske protein and Rieske center (left) and structure of the b 6 f complex from Mastigocladus laminosus (PDB ID 1VF5) and... its Rieske protein and Rieske center (right).

Publication Year: 2014


PubMed ID is not available.

Published in 2015

PubMedCentral: PMC4453056

The following subunits and PDB files were used: All four subunits from complex II: 1NEK (bacterial) and 1ZOY (mitochondrial); cytochrome b from complex III: 1ZRT and 2FYN (bacterial), 1EZV, 1BCC, 1BGY... 1NTM (mitochondrial); cytochrome f , cytochrome b 6 , subunit IV, PetG, and PetL from cytochrome b 6 f : 1VF5 (bacterial), 1Q90 (chloroplast); and Cox1, Cox2, and Cox3 from complex IV: 1M57 and 1QLE (bacterial), 1V54 and 1OCC (mitochondrial).

Publication Year: 2015