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PDB ID Mentions in PubMed Central Article count: 18

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PDB ID Mentions in PubMed Central

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EMatch: an efficient method for aligning atomic resolution subunits into intermediate-resolution cryo-EM maps of large macromolecular assemblies.

(2007) Acta Crystallogr D Biol Crystallogr 63

PubMed: 17164525 | PubMedCentral: PMC2483490 | DOI: 10.1107/S0907444906041059

( a ) A quasi-atomic structural model of a GroEL ring (coloured as in Fig. 2 ▶ ) superimposed on its X-­ray crystal structure (PDB code 1oel ; grey) with a minimum r.m.s.d. of 5.17�... 005;Å.

Table 1 A priori known domain reconstruction For each domain, the data appearing in the columns are the domain name, the number of matched helices of the top-ranking alignment between the high-resolution domain and the cryo-EM map, the r.m.s.d. between the axial midpoints of the matched helices, the average angle and average line distance between the matched helices, the Z score of the top-ranking alignment, the running time of the fold-alignment stage and the r.m.s.d. between the domain ring in the suggested atomic quasi-structural model and the corresponding domain ring in the X-ray crystal structure of the complex (PDB code 1oel ) after superimposing the two structures with minimum r.m.s.d.   Matched helices       Domain No.

A priori known domain reconstruction The goal of this experiment is to suggest a quasi-atomic structural model of the GroEL complex given its C 7 global symmetry and the atomic structures of the three domains of its monomer [taken from PDB code 1oel (Braig et al. , 1995 ▶ )].

The model has been successfully evaluated by comparing it with the X-ray crystal structure of one of the GroEL rings at 2.8 Å resolution (PDB code 1oel ; Braig et al. , 1995 ▶ ).

Publication Year: 2007


Alignment of protein structures in the presence of domain motions.

(2008) BMC Bioinformatics 9

PubMed: 18727838 | PubMedCentral: PMC2535786 | DOI: 10.1186/1471-2105-9-352

(a) Superposition of the two structures on the first rigid body identified by RAPIDO (in blue, 1we3 is in darker colors while 1oel is in lighter colors).

Scissor symbols indicate the points in which the 1oel was divided in order to separately superpose the regions identified as rigid bodies (1 st rigid body: 220 atoms, RMSD 0.81 Å; 2 nd rigid body: 178 atoms, RMSD 0.93 Å; 3 rd rigid body: 71 atoms, RMSD 1.04 Å; 4 th rigid body: 20 atoms, RMSD 0.68 Å).

Residue numbers of domain boundaries in the E. Coli structure ( 1oel ) as determined by RAPIDO are indicated; small flexible insertions within the domains have been left out for clarity.

Here we align the structure of one GroEL subunit from Escherichia coli (PDB id 1OEL , [ 38 ]) with one from Thermus termophilus in complex with ADP (PDB id 1WE3 , [ 39 ]).

Figure 3 Alignment of two structures of GroEL from Thermus Thermophilus ( 1we3 ) and Escherichia Coli ( 1oel ).

Publication Year: 2008


Decision-making in structure solution using Bayesian estimates of map quality: the PHENIX AutoSol wizard.

(2009) Acta Crystallogr D Biol Crystallogr 65

PubMed: 19465773 | PubMedCentral: PMC2685735 | DOI: 10.1107/S0907444909012098

( c ) Structures determined using MIR: flr (1bkj; Tanner et al. , 1996 ▶ ), granulocyte (2gmf; Rozwarski et al. , 1996 ▶ ), groEL (1oel; Braig et al. , 1995 ▶ ), hn-rnp (1ha1; ... hamoo et al. , 1997 ▶ ), penicillopepsin (3app; James & Sielecki, 1983 ▶ ), qaprtase (1qpo; Sharma et al. , 1998 ▶ ), rh-dehalogenase (1bn7; Newman et al. , 1999 ▶ ), rnase-s (1rge; Sevcik et al. , 1996 ▶ ), rop (1f4n; Willis et al. , 2000 ▶ ) and synaptotagmin (1dqv; Sutton et al. , 1999 ▶ ).

The structures from the PHENIX library included 1029B (PDB code 1n0e; Chen et al. , 2004 ▶ ), 1038B (1lql; Choi et al. , 2003 ▶ ), 1063B (1lfp; Shin et al. , 2002 ▶ ), 1071B (1nf2; Shin, Roberts et al. , 2003 ▶ ), 1102B (1l2f; Shin, Nguyen et al. , 2003 ▶ ), 1167B (1s12; Shin et al. , 2005 ▶ ), aep-transaminase (1m32; Chen et al. , 2002 ▶ ), armadillo (3bct; Huber et al. , 1997 ▶ ), calmodulin (1exr; Wilson & Brunger, 2000 ▶ ), cobd (1kus; Cheong et al. , 2002 ▶ ), cp-synthase (1l1e; Huang et al. , 2002 ▶ ), cyanase (1dw9; Walsh et al. , 2000 ▶ ), epsin (1edu; Hyman et al. , 2000 ▶ ), flr (1bkj; Tanner et al. , 1996 ▶ ), fusion-complex (1sfc; Sutton et al. , 1998 ▶ ), gene-5 (1vqb; Skinner et al. , 1994 ▶ ), gere (1fse; Ducros et al. , 2001 ▶ ), gpatase (1ecf; Muchmore et al. , 1998 ▶ ), granulocyte (2gmf; Rozwarski et al. , 1996 ▶ ), groEL (1oel; Braig et al. , 1995 ▶ ), group2-intron (1kxk; Zhang & Doudna, 2002 ▶ ), hn-rnp (1ha1; Shamoo et al. , 1997 ▶ ), ic-lyase (1f61; Sharma et al. , 2000 ▶ ), insulin (2bn3; Nanao et al. , 2005 ▶ ), lysozyme (unpublished results; CSHL Macromolecular Crystallo­graphy Course), mbp (1ytt; Burling et al. , 1996 ▶ ), mev-kinase (1kkh; Yang et al. , 2002 ▶ ), myoglobin (A. Gonzales, personal communication), nsf-d2 (1nsf; Yu et al. , 1998 ▶ ), nsf-n (1qcs; Yu et al. , 1999 ▶ ), p32 (1p32; Jiang et al. , 1999 ▶ ), p9 (1bkb; Peat et al. , 1998 ▶ ), pdz (1kwa; Daniels et al. , 1998 ▶ ), penicillopepsin (3app; James & Sielecki, 1983 ▶ ), psd-95 (1jxm; Tavares et al. , 2001 ▶ ), qaprtase (1qpo; Sharma et al. , 1998 ▶ ), rab3a (1zbd; Ostermeier & Brunger, 1999 ▶ ), rh-dehalogenase (1bn7; Newman et al. , 1999 ▶ ), rnase-p (1nz0; Kazantsev et al. , 2003 ▶ ), rnase-s (1rge; Sevcik et al. , 1996 ▶ ), rop (1f4n; Willis et al. , 2000 ▶ ), s-hydrolase (1a7a; Turner et al. , 1998 ▶ ), sec17 (1qqe; Rice & Brunger, 1999 ▶ ), synapsin (1auv; Esser et al. , 1998 ▶ ), synaptotagmin (1dqv; Sutton et al. , 1999 ▶ ), tryparedoxin (1qk8; Alphey et al. , 1999 ▶ ), ut-synthase (1e8c; Gordon et al. , 2001 ▶ ) and vmp ( l8w; Eicken et al. , 2002 ▶ ).

Publication Year: 2009


GroEL-assisted protein folding: does it occur within the chaperonin inner cavity?

(2009) Int J Mol Sci 10

PubMed: 19564940 | PubMedCentral: PMC2695268 | DOI: 10.3390/ijms10052066

The figure was plotted using the SwissPdb Viewer [ 109 ] and POV-Ray ( www.povray.org ) freeware and files 1OEL [ 20 , 21 ] and 1AON [ 32 ] which are available in PDB.

Publication Year: 2009


UROX 2.0: an interactive tool for fitting atomic models into electron-microscopy reconstructions.

(2009) Acta Crystallogr D Biol Crystallogr 65

PubMed: 19564685 | PubMedCentral: PMC2703571 | DOI: 10.1107/S0907444909008671

We fitted the crystal structure of GroEL (PDB code 1oel ; Braig et al. , 1995 ▶ ) into a cryo negative-stain EM reconstruction of GroEL (DeCarlo et al. , 2002 ▶ ).

Publication Year: 2009


Automatic multiple-zone rigid-body refinement with a large convergence radius.

(2009) J Appl Crystallogr 42

PubMed: 19649324 | PubMedCentral: PMC2712840 | DOI: 10.1107/S0021889809023528

NA PDB ID NB group2-intron 3.5 1497 1kxk 1 synaptotagmin 3.2 2186 1dqv   1029B 3.0 9230 1n0e   1038B 3.0 11038 1lql 5 1071B 3.0 6558 1nf2 6 proteasome 2.9 24927 1q5q   sec17 2.... 2217 1qqe   cp-synthase 2.8 4331 1l1e   penicillopepsin 2.8 2366 3app   s-hydrolase 2.8 6666 1a7a   ut-synthase 2.8 7504 1e8c   gere 2.7 3060 1fse   groel 2.7 26957 1oel   aep-transaminase 2.6 16698 1m32 4 rab3a 2.6 2431 1zbd   a2u-globulin 2.5 5148 2a2u 4 flavin-reductase 2.5 3385 1bkj   p32 2.5 4265 1p32   psd-95 2.5 2180 1jxm   qaprtase 2.5 12570 1qpo 1 rnase-s 2.5 1488 1rge   1102B 2.5 2662 1l2f   rh-dehalogenase 2.45 2336 1bn7   armadillo 2.4 3458 3bct   cyanase 2.4 11970 1dw9   fusion-complex 2.4 7025 1sfc   human-otc 2.4 2528 1ep9   mev-kinase 2.4 2506 1kkh   nsf-d2 2.4 1943 1nsf   granulocyte 2.35 1908 2gmf   oat-gabaculine 2.3 9450 1gbn 2 vmp 2.3 7992 1l8w   gpatase 2.25 7786 1ecf   hn-rnp 2.2 1338 1ha1   antitrypsin 2.1 2985 1hp7   pdz 2.1 1372 1kwa   1167B 2.0 2920 1s12   apoferritin 2.0 1354 1gwg   cobd 2.0 2738 1lkc   synapsin 2.0 4636 1auv 1 tryparedoxin 2.0 1145 1qk8   myoglobin 1.9 1227 1n9x   nsf-n 1.9 1518 1qcs   rop 1.9 850 1f4n   epsin 1.8 1210 1edu   gene-5 1.8 673 1vqb 2 ic lyase 1.8 6484 1f61   mbp 1.8 1760 1ytt   p9 1.75 1062 1bkb   1063B 1.7 1926 1lfp   nitrite-reduct 1.7 2582 1et7   insulin 1.7 400 2bn3   lysozyme 1.5 982 1aki   rnase-p 1.5 3607 1nz0   calmodulin 1.1 1150 1exr 2 hipip 0.8 616 1iua   Table 2 Comparison of success rates for different values of the n_ref(1) 1 parameter (§3.2.1 ) The first row and the first column show the parameter values.

Publication Year: 2009


Perturbation-based Markovian transmission model for probing allosteric dynamics of large macromolecular assembling: a study of GroEL-GroES.

(2009) PLoS Comput Biol 5

PubMed: 19798437 | PubMedCentral: PMC2741606 | DOI: 10.1371/journal.pcbi.1000526

Responses are calculated using (A) the T state conformation (pdb 1oel), (B) the R state conformation (2c7e), and (C) the R″ state conformation (1aon) of the chaperon complex structures.

Publication Year: 2009


Rapid model building of alpha-helices in electron-density maps.

(2010) Acta Crystallogr D Biol Crystallogr 66

PubMed: 20179338 | PubMedCentral: PMC2827347 | DOI: 10.1107/S0907444910000314

Table 1 Helix identification in experimental electron-density maps   Residues         Structure Total Helix Built Correct d min () Map quality (CC to model map)... R.m.s.d. () Helixmap CC RNase P ( 1nz0 ; Kazantsev et al. , 2003 ▶ ) 416 177 6 6 1.5 0.53 0.85 0.41 1063B ( 1lfp ; Shin et al. , 2002 ▶ ) 243 92 65 58 1.7 0.68 1.57 0.42 Epsin ( 1edu ; Hyman et al. , 2000 ▶ ) 149 100 98 83 1.8 0.89 0.97 0.62 Isocitrate lyase ( 1f61 ; Sharma et al. , 2000 ▶ ) 836 387 385 286 1.8 0.65 1.44 0.51 MBP ( 1ytt ; Burling et al. , 1996 ▶ ) 227 42 30 17 1.8 0.89 1.31 0.52 P9 ( 1bkb ; Peat et al. , 1998 ▶ ) 136 4 27 0 1.8 0.81 2.11 0.30 Penicillopepsin ( 3app ; James Sielecki, 1983 ▶ ) 323 30 33 0 1.8 0.84 2.06 0.28 Myoglobin (Ana Gonzlez, personal communication) 154 110 59 54 1.9 0.73 0.86 0.51 ROP ( 1f4n ; Willis et al. , 2000 ▶ ) 108 92 97 86 1.9 0.84 0.89 0.54 1167B ( 1s12 ; Shin et al. , 2005 ▶ ) 370 160 142 118 2.0 0.72 1.12 0.50 CobD ( 1kus ; Cheong et al. , 2002 ▶ ) 355 129 61 45 2.0 0.80 1.29 0.46 NSF-N ( 1qcs ; Yu et al. , 1999 ▶ ) 195 29 24 2 2.0 0.80 2.21 0.22 Synapsin ( 1auv ; Esser et al. , 1998 ▶ ) 585 149 74 45 2.0 0.78 1.58 0.42 Tryparedoxin ( 1qk8 ; Alphey et al. , 1999 ▶ ) 143 40 8 0 2.0 0.79 2.12 0.18 PDZ ( 1kwa ; Daniels et al. , 1998 ▶ ) 174 30 19 0 2.1 0.67 2.16 0.22 Fusion complex ( 1sfc ; Sutton et al. , 1998 ▶ ) 867 789 716 702 2.3 0.73 1.02 0.62 GPATase ( 1ecf ; Muchmore et al. , 1998 ▶ ) 992 318 191 129 2.3 0.82 1.30 0.48 Granulocyte ( 2gmf ; Rozwarski et al. , 1996 ▶ ) 241 117 87 76 2.3 0.62 1.04 0.50 VMP ( 1l8w ; Eicken et al. , 2002 ▶ ) 1141 654 621 528 2.3 0.76 1.01 0.61 Armadillo ( 3bct ; Huber et al. , 1997 ▶ ) 457 329 232 197 2.4 0.86 0.88 0.59 Cyanase ( 1dw9 ; Walsh et al. , 2000 ▶ ) 1560 710 462 364 2.4 0.82 1.30 0.47 Mev kinase ( 1kkh ; Yang et al. , 2002 ▶ ) 317 123 133 96 2.4 0.83 1.28 0.54 NSF D2 ( 1nsf ; Yu et al. , 1998 ▶ ) 247 110 52 45 2.4 0.84 0.78 0.56 1102B ( 1l2f ; Shin, Nguyen et al. , 2003 ▶ ) 344 118 137 79 2.5 0.78 1.49 0.49 AEP transaminase ( 1m32 ; Chen et al. , 2002 ▶ ) 2169 849 792 609 2.5 0.81 1.23 0.49 FLR ( 1bkj ; Tanner et al. , 1996 ▶ ) 460 209 64 45 2.5 0.77 1.74 0.41 P32 ( 1p32 ; Jiang et al. , 1999 ▶ ) 529 190 235 172 2.5 0.86 1.15 0.56 PSD-95 ( 1jxm ; Tavares et al. , 2001 ▶ ) 264 87 72 34 2.5 0.76 1.66 0.49 QAPRTase ( 1qpo ; Sharma et al. , 1998 ▶ ) 1704 737 525 399 2.5 0.71 1.27 0.51 RNase S ( 1rge ; Sevcik et al. , 1996 ▶ ) 192 23 32 11 2.5 0.65 2.16 0.34 Gene V ( 1vqb ; Skinner et al. , 1994 ▶ ) 86 0 26 0 2.6 0.74 2.19 0.27 Rab3A ( 1zbd ; Ostermeier Brnger, 1999 ▶ ) 301 110 104 89 2.6 0.82 1.03 0.55 GerE ( 1fse ; Ducros et al. , 2001 ▶ ) 384 251 179 145 2.7 0.70 1.07 0.60 CP synthase ( 1l1e ; Huang et al. , 2002 ▶ ) 534 220 186 150 2.8 0.75 0.99 0.54 Rh dehalogenase ( 1bn7 ; Newman et al. , 1999 ▶ ) 291 109 138 86 2.8 0.78 1.44 0.46 S-hydrolase ( 1a7a ; Turner et al. , 1998 ▶ ) 861 349 343 240 2.8 0.81 1.30 0.48 UT synthase ( 1e8c ; Gordon et al. , 2001 ▶ ) 990 306 293 180 2.8 0.78 1.46 0.45 1029B ( 1n0e ; Chen et al. , 2004 ▶ ) 1130 379 255 116 3.0 0.73 1.71 0.44 1038B ( 1lql ; Choi et al. , 2003 ▶ ) 1432 440 628 367 3.0 0.71 1.58 0.48 1071B ( 1nf2 ; Shin, Roberts et al. , 2003 ▶ ) 801 286 215 136 3.0 0.65 1.69 0.49 Synaptotagmin ( 1dqv ; Sutton et al. , 1999 ▶ ) 275 8 71 3 3.2 0.67 2.08 0.41 GroEL ( 1oel ; Braig et al. , 1995 ▶ ) 3668 1841 1443 1291 3.8 0.55 1.52 0.57

Publication Year: 2010


Rapid model building of beta-sheets in electron-density maps.

(2010) Acta Crystallogr D Biol Crystallogr 66

PubMed: 20179339 | PubMedCentral: PMC2827348 | DOI: 10.1107/S0907444910000302

One structure for which most β-strand residues were missed was the GroEL structure (PDB entry 1oel ; Braig et al. , 1995 ▶ ; Berman et al. , 2000 ▶ ; Bernstein et al. , 1977 &#... 025b6; ).

Table 1 -Strand identification in experimental electron-density maps   Residues         Structure Total Strand Built Correct d min () Map quality (CC to model map) R.m.s.d. () Strandmap CC RNase P ( 1nz0 ; Kazantsev et al. , 2003 ▶ ) 416 88 18 11 1.5 0.53 1.90 0.30 1063B ( 1lfp ; Shin et al. , 2002 ▶ ) 243 57 42 33 1.7 0.68 1.58 0.41 Epsin ( 1edu ; Hyman et al. , 2000 ▶ ) 149 0 15 0 1.8 0.89 2.24 0.35 Isocitrate lyase ( 1f61 ; Sharma et al. , 2000 ▶ ) 836 98 161 67 1.8 0.65 1.75 0.42 MBP ( 1ytt ; Burling et al. , 1996 ▶ ) 227 61 60 33 1.8 0.89 1.48 0.39 P9 ( 1bkb ; Peat et al. , 1998 ▶ ) 136 73 59 50 1.8 0.81 1.02 0.48 Penicillopepsin ( 3app ; James Sielecki, 1983 ▶ ) 323 147 122 94 1.8 0.84 1.10 0.45 Myoglobin (Ana Gonzlez, personal communication) 154 0 17 0 1.9 0.73 3.34 0.24 ROP ( 1f4n ; Willis et al. , 2000 ▶ ) 108 0 20 0 1.9 0.84 2.80 0.25 1167B ( 1s12 ; Shin et al. , 2005 ▶ ) 370 108 93 69 2.0 0.72 1.50 0.47 CobD ( 1kus ; Cheong et al. , 2002 ▶ ) 355 56 80 32 2.0 0.80 1.97 0.35 NSF-N ( 1qcs ; Yu et al. , 1999 ▶ ) 195 83 60 42 2.0 0.80 1.50 0.37 Synapsin ( 1auv ; Esser et al. , 1998 ▶ ) 585 179 165 122 2.0 0.78 1.14 0.48 Tryparedoxin ( 1qk8 ; Alphey et al. , 1999 ▶ ) 143 33 39 21 2.0 0.79 1.87 0.37 PDZ ( 1kwa ; Daniels et al. , 1998 ▶ ) 174 66 36 30 2.1 0.67 1.41 0.43 Fusion complex ( 1sfc ; Sutton et al. , 1998 ▶ ) 867 0 32 0 2.3 0.73 2.95 0.41 GPATase ( 1ecf ; Muchmore et al. , 1998 ▶ ) 992 223 248 179 2.3 0.82 1.28 0.52 Granulocyte ( 2gmf ; Rozwarski et al. , 1996 ▶ ) 241 20 14 0 2.3 0.62 2.61 0.35 VMP ( 1l8w ; Eicken et al. , 2002 ▶ ) 1141 16 89 8 2.3 0.76 1.80 0.35 Armadillo ( 3bct ; Huber et al. , 1997 ▶ ) 457 0 38 0 2.4 0.86 2.66 0.33 Cyanase ( 1dw9 ; Walsh et al. , 2000 ▶ ) 1560 290 294 168 2.4 0.82 1.76 0.40 Mev kinase ( 1kkh ; Yang et al. , 2002 ▶ ) 317 77 91 62 2.4 0.83 1.46 0.47 NSF D2 ( 1nsf ; Yu et al. , 1998 ▶ ) 247 37 70 28 2.4 0.84 1.81 0.44 1102B ( 1l2f ; Shin, Nguyen et al. , 2003 ▶ ) 344 96 82 70 2.5 0.78 1.12 0.50 AEP transaminase ( 1m32 ; Chen et al. , 2002 ▶ ) 2169 354 423 264 2.5 0.81 1.46 0.42 FLR ( 1bkj ; Tanner et al. , 1996 ▶ ) 460 62 91 44 2.5 0.77 1.81 0.36 P32 ( 1p32 ; Jiang et al. , 1999 ▶ ) 529 144 154 115 2.5 0.86 1.58 0.51 PSD-95 ( 1jxm ; Tavares et al. , 2001 ▶ ) 264 68 69 47 2.5 0.76 1.42 0.46 QAPRTase ( 1qpo ; Sharma et al. , 1998 ▶ ) 1704 324 275 166 2.5 0.71 1.43 0.42 RNase S ( 1rge ; Sevcik et al. , 1996 ▶ ) 192 49 45 25 2.5 0.65 2.42 0.29 Gene V ( 1vqb ; Skinner et al. , 1994 ▶ ) 86 40 24 17 2.6 0.74 1.11 0.46 Rab3A ( 1zbd ; Ostermeier Brnger, 1999 ▶ ) 301 58 57 37 2.6 0.82 1.49 0.49 GerE ( 1fse ; Ducros et al. , 2001 ▶ ) 384 0 16 0 2.7 0.70 2.22 0.42 CP synthase ( 1l1e ; Huang et al. , 2002 ▶ ) 534 86 138 72 2.8 0.75 1.86 0.41 Rh dehalogenase ( 1bn7 ; Newman et al. , 1999 ▶ ) 291 53 67 37 2.8 0.78 1.71 0.42 S-hydrolase ( 1a7a ; Turner et al. , 1998 ▶ ) 861 135 247 83 2.8 0.81 1.86 0.37 UT synthase ( 1e8c ; Gordon et al. , 2001 ▶ ) 990 213 248 157 2.8 0.78 1.49 0.43 1029B ( 1n0e ; Chen et al. , 2004 ▶ ) 1130 232 267 139 3.0 0.73 1.36 0.49 1038B ( 1lql ; Choi et al. , 2003 ▶ ) 1432 483 472 399 3.0 0.71 1.32 0.54 1071B ( 1nf2 ; Shin, Roberts et al. , 2003 ▶ ) 801 184 232 143 3.0 0.65 1.39 0.54 Synaptotagmin ( 1dqv ; Sutton et al. , 1999 ▶ ) 275 87 49 29 3.2 0.67 1.39 0.42 GroEL ( 1oel ; Braig et al. , 1995 ▶ ) 3668 644 26 18 3.8 0.55 1.37 0.40

Publication Year: 2010


Rapid chain tracing of polypeptide backbones in electron-density maps.

(2010) Acta Crystallogr D Biol Crystallogr 66

PubMed: 20179340 | PubMedCentral: PMC2827349 | DOI: 10.1107/S0907444910000272

Table 1 Chain-tracing in experimental electron-density maps Structure d min (Å) Map quality (CC to model map using data to 3 Å) Residues Residues built C α r.m.s.d. (&#... 000c5;) Residues in secondary structure (%) CPU time (s) RNase P ( 1nz0 ; Kazantsev et al. , 2003 ▶ ) 1.5 0.53 416 284 2.53 8 14 1063B ( 1lfp ; Shin et al. , 2002 ▶ ) 1.7 0.68 243 132 1.98 17 7 Epsin ( 1edu ; Hyman et al. , 2000 ▶ ) 1.8 0.89 149 132 1.31 43 6 Isocitrate lyase ( 1f61 ; Sharma et al. , 2000 ▶ ) 1.8 0.65 836 754 1.59 42 81 MBP ( 1ytt ; Burling et al. , 1996 ▶ ) 1.8 0.89 227 194 1.41 69 9 P9 ( 1bkb ; Peat et al. , 1998 ▶ ) 1.8 0.81 136 128 1.61 76 9 Penicillopepsin ( 3app ; James & Sielecki, 1983 ▶ ) 1.8 0.84 323 279 1.58 41 10 Myoglobin (Ana Gonzales, personal communication) 1.9 0.73 154 139 1.96 5 10 ROP ( 1f4n ; Willis et al. , 2000 ▶ ) 1.9 0.84 108 107 2.07 60 4 1167B ( 1s12 ; Shin et al. , 2005 ▶ ) 2.0 0.72 370 254 1.77 42 10 CobD ( 1kus ; Cheong et al. , 2002 ▶ ) 2.0 0.80 355 331 1.73 32 18 NSF-N ( 1qcs ; Yu et al. , 1999 ▶ ) 2.0 0.80 195 162 1.57 40 8 Synapsin ( 1auv ; Esser et al. , 1998 ▶ ) 2.0 0.78 585 421 1.71 60 24 Tryparedoxin ( 1qk8 ; Alphey et al. , 1999 ▶ ) 2.0 0.79 143 142 1.67 47 6 PDZ ( 1kwa ; Daniels et al. , 1998 ▶ ) 2.1 0.67 174 130 1.65 50 7 Fusion complex ( 1sfc ; Sutton et al. , 1998 ▶ ) 2.3 0.73 867 643 1.98 14 141 GPATase ( 1ecf ; Muchmore et al. , 1998 ▶ ) 2.3 0.82 992 901 1.49 71 50 Granulocyte ( 2gmf ; Rozwarski et al. , 1996 ▶ ) 2.3 0.62 241 141 1.80 16 8 VMP ( 1l8w ; Eicken et al. , 2002 ▶ ) 2.3 0.76 1141 833 1.42 41 37 Armadillo ( 3bct ; Huber et al. , 1997 ▶ ) 2.4 0.86 457 369 1.21 59 23 Cyanase ( 1dw9 ; Walsh et al. , 2000 ▶ ) 2.4 0.82 1560 1506 1.71 55 62 Mev kinase ( 1kkh ; Yang et al. , 2002 ▶ ) 2.4 0.83 317 302 1.38 66 9 NSF D2 ( 1nsf ; Yu et al. , 1998 ▶ ) 2.4 0.84 247 243 1.59 49 11 1102B ( 1l2f ; Shin, Nguyen et al. , 2003 ▶ ) 2.5 0.78 344 308 1.45 56 22 AEP transaminase ( 1m32 ; Chen et al. , 2002 ▶ ) 2.5 0.81 2169 2045 1.32 71 95 FLR ( 1bkj ; Tanner et al. , 1996 ▶ ) 2.5 0.77 460 401 2.01 39 13 P32 ( 1p32 ; Jiang et al. , 1999 ▶ ) 2.5 0.86 529 475 1.38 71 13 PSD-95 ( 1jxm ; Tavares et al. , 2001 ▶ ) 2.5 0.76 264 231 1.46 53 13 QAPRTase ( 1qpo ; Sharma et al. , 1998 ▶ ) 2.5 0.71 1704 1209 1.53 35 69 RNase S ( 1rge ; Sevcik et al. , 1996 ▶ ) 2.5 0.65 192 133 2.06 42 7 Gene V ( 1vqb ; Skinner et al. , 1994 ▶ ) 2.6 0.74 86 74 1.52 65 4 Rab3A ( 1zbd ; Ostermeier & Brünger, 1999 ▶ ) 2.6 0.82 301 262 1.55 41 19 GerE ( 1fse ; Ducros et al. , 2001 ▶ ) 2.7 0.70 384 317 1.41 27 14 CP synthase ( 1l1e ; Huang et al. , 2002 ▶ ) 2.8 0.75 534 253 1.53 40 18 Rh dehalogenase ( 1bn7 ; Newman et al. , 1999 ▶ ) 2.8 0.78 291 270 1.42 56 9 S-hydrolase ( 1a7a ; Turner et al. , 1998 ▶ ) 2.8 0.81 861 813 1.62 41 43 UT synthase ( 1e8c ; Gordon et al. , 2001 ▶ ) 2.8 0.78 990 867 1.53 60 48 1029B ( 1n0e ; Chen et al. , 2004 ▶ ) 3.0 0.73 1130 1016 1.57 61 37 1038B ( 1lql ; Choi et al. , 2003 ▶ ) 3.0 0.71 1432 1308 1.39 70 114 1071B ( 1nf2 ; Shin, Roberts et al. , 2003 ▶ ) 3.0 0.65 801 760 1.63 67 62 Synaptotagmin ( 1dqv ; Sutton et al. , 1999 ▶ ) 3.2 0.67 275 199 2.55 19 29 GroEL ( 1oel ; Braig et al. , 1995 ▶ ) 3.8 0.55 3668 1960 1.98 14 247 Table 2 Comparison of model-building procedures Method Residues built (of 26651 possible residues in 42 experimental density-modified maps) R.m.s.d. (Å) Time (s) Residues per second trace_chain † 21428 1.61 1441 14.9 Helices–strands ‡ 12322 1.24 5331 2.3 RESOLVE § 19037 1.16 16933 1.1 phenix.autobuild ¶ 20601 0.95 155767 0.1 † trace_chain is the method in this paper (without optional assembly steps) with phenix.find_helices_strands and trace_chain=True.

Publication Year: 2010


MOTIF-EM: an automated computational tool for identifying conserved regions in CryoEM structures.

(2010) Bioinformatics 26

PubMed: 20529921 | PubMedCentral: PMC2881380 | DOI: 10.1093/bioinformatics/btq195

We create two synthetic cryoEM maps A and B. Map A is simulated from an ‘open’ conformation GroEL atomic coordinates (PDB id: 1oel) containing a domain called ‘equatorial ... 9;.

Publication Year: 2010


Robust probabilistic superposition and comparison of protein structures.

(2010) BMC Bioinformatics 11

PubMed: 20594332 | PubMedCentral: PMC2912885 | DOI: 10.1186/1471-2105-11-363

Cartoon representation of the superposition of the bound and unbound state of GroEL (1AON (grey) and 1OEL (colored)) using a Gaussian model (A, D), a Student t (B, E) model and a K distribution (C, F)...

Pooled distribution of local structural differences in all three spatial directions between the bound and unbound state of GroEL (1AON and 1OEL) is shown as grey histogram.

Table 1 Marginal likelihood of different models Protein PDB IDs Student t K Laplace Gauss GroEL 1AON - 1OEL -4328.57 -4307.22 -5132.84 -5722.35 DNA Pol 1IH7 - 1IG9 -5574.80 -5750.12 -6340.01 -8011.05 RAN 1RRP - 1BYU -1124.86 -1176.53 -1795.92 -2286.10 Topo II 1BGW - 1BJT -4496.17 -4553.50 -7210.74 -8042.00 Pneumolysin 2BK2 - 2BK1 -2692.73 -2465.09 -5195.85 -5491.90 ER 3ERD - 3ERT -538.11 -622.69 -1290.81 -1980.96 RNA Pol 1QLN - 1MSW -5296.61 -5455.79 -8471.69 -10168.07 Adenylate Kinase 1AKE - 4AKE -1499.73 -1502.75 -1685.11 -2000.35 Myosin 1B7T - 1DFK -4819.91 -5046.02 -6380.11 -7701.83 Synthetic data Student t -9179.46 -9253.48 -12465.97 -13951.94 Synthetic data Gauss -5108.73 -5112.43 -5077.97 -5115.98 Logarithm of the marginal likelihood P ( M | D ) of the different displacement models obtained for nine structure pairs undergoing domain movements.

Publication Year: 2010


Conformational sampling and nucleotide-dependent transitions of the GroEL subunit probed by unbiased molecular dynamics simulations.

(2011) PLoS Comput Biol 7

PubMed: 21423709 | PubMedCentral: PMC3053311 | DOI: 10.1371/journal.pcbi.1002004

A total of 21 crystal structures (287 GroEL subunits) were kept for further analysis (PDB-codes: 1PCQ, 1PF9, 1SVT, 3C9V, 1AON, 1GRU, 1MNF, 1XCK, 2C7D, 2NWC, 3E76, 2EU1, 1SS8, 1SX3, 1J4Z, 1KPO, 2C7E, 1... P8, 1OEL, 1WE3, 1WF4).

Contact matrices were calculated for 28 closed (T) apo subunits (PDB code: 1XCK, 1SS8, 1OEL), 28 closed (T) ATP bound subunits (PDB code: 1KP8, 1SX3) and 28 open (R″) ADP bound subunits (PDB codes: 1AON, 1SVT, 1SX4, and 1PF9), and 6000 snapshots obtained from the last 50 ns of the 12 independent MD simulations on the closed GroEL subunit (6 apo and 6 holo).

Publication Year: 2011


MultiFit: a web server for fitting multiple protein structures into their electron microscopy density map.

(2011) Nucleic Acids Res 39

PubMed: 21715383 | PubMedCentral: PMC3125811 | DOI: 10.1093/nar/gkr490

Seven copies of the GroEL chaperon monomer [PDB entry 1oel ( 33 )] are simultaneously fitted to its ring density map at 11.5-Å resolution [EMDB entry 1080 ( 34 )] using cyclic symmetry mode.

Publication Year: 2011


ATP-triggered conformational changes delineate substrate-binding and -folding mechanics of the GroEL chaperonin.

(2012) Cell 149

PubMed: 22445172 | PubMedCentral: PMC3326522 | DOI: 10.1016/j.cell.2012.02.047

Figure S3 Flow Chart of Steps in the Flexible Fitting, Related to Figures 2 and 3 Lateral sheet superimposition in the equatorial domain contact was done by manual rigid fitting of the four st... ands from the 1OEL structure.

Extended Experimental Procedures Steps in Atomic Structure Fitting (1) Rs1: A single subunit of 1OEL was flexibly fitted, first as two rigid bodies (the equatorial domain and the combined intermediate and apical domains) for ten iterations.

The images were filtered, normalized, and aligned to a filtered side-view projection of the apo GroEL crystal structure (Protein Data Bank [PDB] ID 1OEL; Braig et al., 1995 ).

Atomic Structure Fitting and Refinement Starting from the apo rings of the GroEL-ATP 7 maps (the three T rings), the crystal structure of the full heptameric ring of apo GroEL (PDB ID 1OEL; Braig et al., 1995 ) was rigidly docked using Chimera ( Pettersen et al., 2004 ), showing a good fit (cross-correlation coefficients: Rs1 = 0.616, Rs2 = 0.620, Rs-open = 0.633).

Two crystal structures were used as starting points—apo GroEL 14 (PDB ID 1OEL) and GroEL 14 -GroES 7 (PDB ID 1SVT; Chaudhry et al., 2004 ).

Publication Year: 2012


ATP-driven molecular chaperone machines.

(2013) Biopolymers 99

PubMed: 23877967 | PubMedCentral: PMC3814418 | DOI: 10.1002/bip.22361

Two subunits, viewed from inside the folding chamber, of apo-GroEL, GroEL–Rs1, GroEL–Rs2, GroEL–Rs-open, and GroEL–GroES–ADP.AlF 3 complexes (EM Databank and PD... ID: EMD-1997/1OEL, EMD-1998/4AAQ, EMD-1999/4AAR, EMD-2000/4AAS, and 1SVT.

Side (a,d) and top views (b,e) of unliganded GroEL and GroEL–GroES–ADP.AlF 3 complexes (PDB ID: 1OEL and 1SVT).

Publication Year: 2013


Modeling protein conformational transitions by a combination of coarse-grained normal mode analysis and robotics-inspired methods.

(2013) BMC Struct Biol 13 Suppl 1

PubMed: 24564964 | PubMedCentral: PMC3953241 | DOI: 10.1186/1472-6807-13-S1-S2

Table 3 Proteins used in the experiments Protein Residues PDB ID init PDB ID goal C α RMSD ADK 214 4ake 1ake 6.51 LAO 238 2lao 1laf 3.73 DAP 320 1dap 3dap 3.78 NS3 436 3kqk 3kql 2.75 DDT 535 1... dt 1mdt 10.96 GroEL 547 1aon 1oel 10.49 ATP 573 1m8p 1i2d 3.78 LTF 691 1cb6 1bka 4.75 IBS 876 1ukl 1qgk 6.17 HKC 917 1hkc 1hkb 3.00 Figure 4 The ten proteins used in the experiment .

Publication Year: 2013


PubMed ID is not available.

Published in 2015

PubMedCentral: PMC4520291

The 20 top-scoring fits of a single GroEL subunit (PDB code 1oel ; Braig et al. , 1995 ▸ ) within the 11.5 Å resolution density map of GroEL (EMD code 1080; Ludtke et al. , 200... ▸ ) (in grey) are shown based on four different scores: CCC ( a ), MI ( b ), NV ( c ) and NV with Sobel filter (NV-S) ( d ).

Experimental benchmark: assessment of a local search ensemble and score performance   We applied the ensemble clustering approach to an experimental case using the X-ray structure of the bacterial chaperonin apo-GroEL (PDB code 1oel ; Braig et al. , 1995 ▸ ) and a cryo EM density map of apo-GroEL at 11.5 Å resolution (EMD code 1080; Ludtke et al. , 2001 ▸ ).

Publication Year: 2015