Citations in PubMed

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PDB ID Mentions in PubMed Central Article count: 9

Citations in PubMed

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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

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 expos... d in 1VF5 (Figure 7 ).

(C) Highly conserved residues Ser87 and Val91 are buried within the helical bundle in 1Q90 structure.

Trp77 in 1Q90 has a more favorable phi angle of -54.2° (Dihedral angle data are obtained from PDB).

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.

Residue Trp77 forms a hydrogen bond with conserved Gln37 from the soluble domain of cytochrome f. (D) Interhelical intersubunit hydrogen bond between Arg95 from PetN and Asp35 from subunit IV in 1Q90 (only TM domain is shown for clarity).

Residues Ser85 and Ser89 form an SS4 motif (following the nomenclature of Senes et al [ 39 ]) on the PetN TM helix, and pack tightly against Gly80 and Gly84 (GG4 motif [ 39 ]) on the subunit PetM in 1Q90, as shown on Figure 10A .

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 ).

(A) AGG triplet is formed by highly conserved residues Gly8 and Gly12 from PetG and Ala70 from PetM in 1Q90 structure.

The analogous faces with conserved residues in the PetN TM helix from 1Q90 are buried within a helical bundle and are mainly involved in helix-helix interactions with helix I from subunit IV (Figure 8C ).

Helix boundaries are based on 1Q90 structure assignment.

PDB Helix count 1 L ¯ f MathType@MTEF@5@5@+=feaafiart1ev1aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacH8akY=wiFfYdH8Gipec8Eeeu0xXdbba9frFj0=OqFfea0dXdd9vqai=hGuQ8kuc9pgc9s8qqaq=dirpe0xb9q8qiLsFr0=vr0=vr0dc8meaabaqaciaacaGaaeqabaqabeGadaaakeaacuWGmbatgaqeamaaBaaaleaacqWGMbGzaeqaaaaa@2F66@ Exp 2 L ¯ f MathType@MTEF@5@5@+=feaafiart1ev1aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacH8akY=wiFfYdH8Gipec8Eeeu0xXdbba9frFj0=OqFfea0dXdd9vqai=hGuQ8kuc9pgc9s8qqaq=dirpe0xb9q8qiLsFr0=vr0=vr0dc8meaabaqaciaacaGaaeqabaqabeGadaaakeaacuWGmbatgaqeamaaBaaaleaacqWGMbGzaeqaaaaa@2F66@ Brd 3 E ¯ f MathType@MTEF@5@5@+=feaafiart1ev1aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacH8akY=wiFfYdH8Gipec8Eeeu0xXdbba9frFj0=OqFfea0dXdd9vqai=hGuQ8kuc9pgc9s8qqaq=dirpe0xb9q8qiLsFr0=vr0=vr0dc8meaabaqaciaacaGaaeqabaqabeGadaaakeaacuWGfbqrgaqeamaaBaaaleaacqWGMbGzaeqaaaaa@2F58@ Exp 2 E ¯ f MathType@MTEF@5@5@+=feaafiart1ev1aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacH8akY=wiFfYdH8Gipec8Eeeu0xXdbba9frFj0=OqFfea0dXdd9vqai=hGuQ8kuc9pgc9s8qqaq=dirpe0xb9q8qiLsFr0=vr0=vr0dc8meaabaqaciaacaGaaeqabaqabeGadaaakeaacuWGfbqrgaqeamaaBaaaleaacqWGMbGzaeqaaaaa@2F58@ Brd 3 S f Exp 2 S f Brd 3 1C3W 7 2 2 7 7 7 6 1EUL 9 4 4 8 7 9 7 1FX8 4 1 0 3 3 3 3 1IWG 10 4 4 8 6 7 6 1J4N 4 4 2 3 4 4 4 1KPL 10 4 6 7 8 8 9 1KQF 5 4 2 4 3 5 3 1L9H 7 5 5 7 7 7 7 1M3X 11 7 6 9 6 10 8 1NEK 5 5 2 5 4 5 3 1OCR 24 14 11 18 13 21 11 1OKC 6 2 1 4 3 5 3 1PV6 12 6 3 9 4 9 6 1PW4 12 8 9 8 7 10 11 1Q16 5 3 5 5 3 5 5 1Q90 12 6 4 10 7 11 11 1RH5 9 6 2 7 3 7 3 1ZCD 10 5 3 9 6 10 8 Total 162 100% 90 56% 71 44% 131 81% 102 63% 143 88% 114 70% 1 Number count of lipid-exposed TM helices.

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

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 ].

The PDB names for the protein structures used: 1C3W , 1E12 , 1EHK , 1EUL , 1FX8 , 1H2S , 1IWG , 1J4N , 1JB0 , 1K4C , 1KB9 , 1KF6 , 1KPL , 1KQF , 1L7V , 1L9H , 1M3X , 1M56 , 1MSL , 1NEK , 1OCR , 1OKC , 1PP9 , 1PV6 , 1PW4 , 1Q16 , 1QLA , 1Q90 , 1RH5 .

Publication Year: 2006


Analysis of an optimal hidden Markov model for secondary structure prediction.

(2006) BMC Struct Biol 6

PubMed: 17166267 | PubMedCentral: PMC1769381 | DOI: 10.1186/1472-6807-6-25

EVA dataset includes 20 membrane protein chains : 1pv6:A, 1pw4:A, 1rhz:A, 1zcd:A, 1zhh:B, 2a65:A, 1q90:N, 1q90:L, 1q90:M, 1s51:I, 1s51:J, 1s51:L, 1s51:M, 1s51:T, 1s51:X, 1s51:Z, 1rh5:B, 1rkl:A, 1u4h:A... and ls7b:A.

Publication Year: 2006


Biogenesis of cytochrome b6 in photosynthetic membranes.

(2009) J Cell Biol 185

PubMed: 19564403 | PubMedCentral: PMC2712960 | DOI: 10.1083/jcb.200812025

Images in c and d were generated using PyMol and the coordinates from pdb file 1Q90 with α- b 6 N peptide antigen in red, α- b 6 C peptide antigen in green, b L and b H -hemes in brown... c i -heme in orange, and Cys35 in yellow.

Publication Year: 2009


Structure of the first representative of Pfam family PF04016 (DUF364) reveals enolase and Rossmann-like folds that combine to form a unique active site with a possible role in heavy-metal chelation.

(2010) Acta Crystallogr Sect F Struct Biol Cryst Commun 66

PubMed: 20944207 | PubMedCentral: PMC2954201 | DOI: 10.1107/S1744309110007517

A search against a database of nonredundant cognate binding sites using IsoCleft (Najmanovich et al. , 2008 ▶ ), a graph-matching algorithm that searches for both geometrical and chemical comp... sition similarities, identified shared features between the Dhaf4260 cavity and the binding sites of proteins implicated in binding vitamin B 12 (B 12 -dependent glutamate mutase; PDB code 1ccw ; 40 atoms in common, Tanimoto similarity score 0.13, Z score 3.96, P -value 1.11 × 10 −2 ; Reitzer et al. , 1999 ▶ ), typical hemes (PDB code 2nap ; 37 atoms in common; Tanimoto similarity score 0.160, Z score 3.48, P -value 2.04 × 10 −2 ; Dias et al. , 1999 ▶ ), atypical hemes (PDB code 1q90 ; 37 atoms in common; Tanimoto similarity score 0.178, Z score 3.48, P -value 2.04 × 10 −2 ; Stroebel et al. , 2003 ▶ ), factor F430 (PDB code 1e6v ; 37 atoms in common; Tanimoto similarity score 0.151, Z score 3.48, P -value 2.04 × 10 −2 ; Grabarse et al. , 2000 ▶ ) and both heme and FAD (flavohemoglobin; PDB code 1cqx ; 36 atoms in common; Tanimoto similarity score 0.187, Z score 3.32, P -value 2.50 × 10 −2 ; Ermler et al. , 1995 ▶ ).

Publication Year: 2010


Probabilistic grammatical model for helix-helix contact site classification.

(2013) Algorithms Mol Biol 8

PubMed: 24350601 | PubMedCentral: PMC3892132 | DOI: 10.1186/1748-7188-8-31

Table 1 Datasets summary Dataset/Class Centroid (PDB) Size Fraction WDG150NR   140 100% c1 1Q90 B119‐128 B194‐203 67 48% c2 1OKC A114‐123 A180‐189 35 25% c3 1J4... A18‐27 A101‐110 23 16% c4 1RH5 A29‐38 C34‐42 15 11% PDBTM150NR   227 100% c1 1Q90 B119‐128 B194‐203 100 44% c2 1OKC A114‐123 A180‐189 60 26% c3 1J4N A18‐27 A101‐110 25 11% c4 1RH5 A29‐38 C34‐42 42 19% Results Cross‐validation of grammar classifiers Leave‐one‐out cross‐validation Performance of single grammar classifiers was analysed in the Leave‐One‐Out Cross‐Validation scheme with the WDG150NR dataset.

Terminal symbols on the tree branches represent residues of two helix pairs (panels A,B ) from chain A of cytochrome b6f from C.reinhardtii (PDB code: 1Q90).

Publication Year: 2013


The molecular evolution of the Qo motif.

(2014) Genome Biol Evol 6

PubMed: 25115012 | PubMedCentral: PMC4122944 | DOI: null

In cyt b 6 f complexes, these two regions are encoded as two separate polypeptides (right, pdb 1q90) and are denoted cyt b 6 and SUIV.

Publication Year: 2014


Comparative studies on detergent-assisted apocytochrome b6 reconstitution into liposomal bilayers monitored by Zetasizer instruments.

(2014) PLoS One 9

PubMed: 25423011 | PubMedCentral: PMC4244035 | DOI: 10.1371/journal.pone.0111341

Secondary structure type Helix Sheet Turn Unordered Calculated from the crystal structure of cytochrome b 6 (PDB code 1Q90) and MBP (PDB code 1PEB) 54,7 20,7 3,8 20,8 MBP-b 6 in DM 44,7 19,1 3,1 33,1 ... BP-b 6 in Triton X-100 41,9 18,7 3,4 36,0 MBP-b 6 in in SDS 27,3 25,4 5,1 42,2 The percent secondary structure of the CD spectra was predicted using the CDSSTR algorithm found in the CDPro software suite.

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