6v05: Difference between revisions

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 <StructureSection load='6v05' size='340' side='right'caption='[[6v05]], [[Resolution|resolution]] 4.10&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6v05]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6V05 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6V05 FirstGlance]. <br>
+<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6V05 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6V05 FirstGlance]. <br>
-</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">bamA, yaeT, yzzN, yzzY, b0177, JW0172 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI]), bamB, yfgL, b2512, JW2496 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI]), bamC, nlpB, A6581_02455, A6592_19755, A8C65_04235, A8G17_10975, AC067_02730, AC789_1c28090, ACN002_2512, ACN68_11560, ACN81_26800, ACU57_04515, ACU90_01100, AKG99_13055, AM270_06735, AM446_08445, AM464_03885, AML07_10810, AML35_21815, APT94_12605, APZ14_05885, AUQ13_12835, AUS26_08895, AW106_01925, AWP75_05795, B1K96_18050, B9M99_18180, B9T59_21405, BANRA_01021, BANRA_03170, BANRA_04601, BB545_17690, BE963_28130, BEN53_15545, BER14_02350, BHF46_00865, BHS81_15170, BIQ87_14450, BIU72_15910, BIZ41_13405, BK248_16985, BK292_09100, BK373_06140, BK375_00595, BK383_22560, BK400_08740, BMT91_12040, BOH76_02570, BON66_22990, BON69_13590, BON71_05810, BON75_17940, BON76_02345, BON81_08015, BON83_11105, BON86_12870, BON92_23095, BON94_05640, BON95_12010, BON96_16290, BTQ06_24710, BUE81_00175, BvCms2454_00576, BvCms28BK_03651, BvCmsA75A_03498, BvCmsC61A_03920, BvCmsHHP001_02989, BvCmsHHP019_02257, BvCmsHHP056_03727, BvCmsKKP061_00365, BvCmsKSNP019_02678, BvCmsKSNP073_01370, BvCmsKSNP081_01804, BvCmsKSNP120_01449, BvCmsKSP011_03652, BvCmsKSP024_03770, BvCmsKSP026_00127, BvCmsKSP045_01057, BvCmsKSP058_05104, BvCmsKSP067_01143, BvCmsNSNP036_03233, BvCmsNSP007_05045, BvCmsNSP047_01191, BvCmsNSP072_03470, BvCmsSINP011_00589, BvCmsSINP012_02461, BvCmsSINP022_03246, BVL39_14450, BW690_08400, BXT93_09065, BZL31_19830, BZL69_23975, C3449_00575, C4J69_10905, C5N07_10515, C5P01_06205, C5P43_23745, C5P44_22155, C6669_16365, C6986_16055, C7235_07205, C9025_02075, C9083_01895, C9212_02290, C9299_09010, C9E25_13305, C9Y80_06105, C9Y95_21475, C9Z12_16640, CA593_14465, CDL37_24220, CEG98_13220, CG692_24660, CI641_005275, CI694_19990, CIJ94_07570, COD30_00650, COD46_27330, CQP61_08535, CR538_07295, CRM83_27895, CRT46_14950, CWM24_12580, CWS33_10415, CY655_15855, D2184_13985, D2188_18170, D3821_11830, D3822_05395, D3O91_03970, D3Y67_12985, D9D31_00585, D9D43_09275, D9E34_00585, D9E35_17030, D9F17_05285, D9G42_10275, D9G48_19890, D9H68_00610, D9H70_20745, D9H94_18900, D9I11_00510, D9I18_08285, D9I87_03080, D9I88_00655, D9J11_04670, D9J44_00445, D9J60_12530, D9K48_26220, D9K54_08830, DAH27_02200, DAH30_02900, DAH34_02675, DAH37_19960, DBQ99_07990, DD762_13530, DEN86_22815, DEN89_10395, DEN97_02085, DEO19_00630, DIV22_31745, DL545_07645, DL800_18795, DM102_07120, DM129_09435, DNQ41_17525, DNQ45_02690, DP258_07610, DQE83_18935, DQF57_11025, DQO13_11190, DS732_18480, DTL43_01510, DTL90_08635, DTM10_01015, DTM25_19255, DTM45_09650, DU321_10720, DWB25_07365, DXT71_21935, E2112_00485, E2115_16230, E2119_05135, E2126_07380, E2127_04515, E2129_06730, E2132_10070, E2134_09470, E2135_00555, E2855_03225, E2863_03132, E5S46_08270, E5S47_00585, E5S58_10625, E5S61_11100, EAI42_12280, EAI52_02570, EC1094V2_1211, EC3234A_44c00830, EC382_03360, EC95NR1_01696, ECTO6_01409, ED600_00620, ED648_19505, EEP23_23015, EHH55_03705, EIA21_06830, EJC75_11395, EKI52_22355, EL75_1174, EL79_1185, EL80_1190, ELT58_05595, ELU85_09985, ELV08_03665, ELV26_03145, ELV28_11920, EO240_05615, EO241_29005, EPS71_00265, EPS97_10555, EPT01_15160, EQ820_10645, EQ823_08955, EQ825_24025, EQ830_05480, ERL57_11390, ERS085365_02853, ERS085366_00345, ERS085374_00117, ERS085379_00986, ERS085383_02107, ERS085386_00039, ERS085404_01131, ERS085416_01322, ERS139211_02639, ERS150876_00778, ExPECSC038_04470, EXX06_10435, EXX13_08605, EXX23_06350, EXX40_08105, EXX53_08115, EXX55_10135, EXX71_05165, EXX73_17945, EXX78_07240, EXX87_17745, EYD11_06585, EYY78_21115, FAX15_16530, FE198_07360, FNJ69_10855, FNJ79_09165, FNJ83_16390, FORC28_1482, FQR64_06705, FV293_04230, HmCms184_03495, HmCmsJML072_03247, HmCmsJML074_00064, HmCmsJML204_03962, HMPREF3040_02807, HW43_16770, JD73_18025, MJ49_18500, NCTC10090_04434, NCTC10764_00647, NCTC10865_01743, NCTC11022_02534, NCTC11126_06126, NCTC11181_03634, NCTC11341_00816, NCTC12950_01648, NCTC13148_02274, NCTC13462_05111, NCTC13846_01494, NCTC7927_01568, NCTC8621_01448, NCTC8960_04114, NCTC9036_01478, NCTC9044_00198, NCTC9045_01669, NCTC9050_04702, NCTC9055_03350, NCTC9062_01737, NCTC9077_01815, NCTC9111_01883, NCTC9117_01960, NCTC9119_01583, NCTC9702_01656, NCTC9703_01031, NCTC9706_04674, NCTC9969_01610, PGD_00767, RG28_09510, RK56_024525, RX35_01364, SAMEA3472033_00601, SAMEA3472043_00977, SAMEA3472044_02057, SAMEA3472047_03903, SAMEA3472055_00995, SAMEA3472056_00816, SAMEA3472070_00123, SAMEA3472080_01551, SAMEA3472090_01290, SAMEA3472108_03434, SAMEA3472147_00102, SAMEA3484427_00337, SAMEA3484429_00446, SAMEA3484434_00350, SAMEA3485101_04932, SAMEA3485113_01786, SAMEA3752557_01026, SAMEA3752559_00799, SAMEA3752620_00108, SAMEA3753097_02061, SAMEA3753164_00674, SAMEA3753300_00970, SK85_02726, UC41_17115, UN86_00295, UN91_14105, WQ89_05460, WR15_19465, YDC107_1000 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI]), yfiO, bamD, ECIAI39_2800 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI]), smpA, bamE, NCTC8196_03449 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 4.1&#8491;</td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6v05 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6v05 OCA], [http://pdbe.org/6v05 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6v05 RCSB], [http://www.ebi.ac.uk/pdbsum/6v05 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6v05 ProSAT]</span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=6v05 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6v05 OCA], [https://pdbe.org/6v05 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6v05 RCSB], [https://www.ebi.ac.uk/pdbsum/6v05 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6v05 ProSAT]</span></td></tr>
 </table>
-== Function ==
-[[http://www.uniprot.org/uniprot/BAMA_ECOLI BAMA_ECOLI]] Part of the outer membrane protein assembly complex, which is involved in assembly and insertion of beta-barrel proteins into the outer membrane. Constitutes, with BamD, the core component of the assembly machinery.<ref>PMID:15951436</ref> <ref>PMID:16102012</ref> <ref>PMID:16824102</ref> <ref>PMID:20378773</ref> <ref>PMID:21823654</ref>  [[http://www.uniprot.org/uniprot/W8SZY2_ECOLX W8SZY2_ECOLX]] Part of the outer membrane protein assembly complex, which is involved in assembly and insertion of beta-barrel proteins into the outer membrane.[HAMAP-Rule:MF_00924] [[http://www.uniprot.org/uniprot/BAMB_ECOLI BAMB_ECOLI]] Part of the outer membrane protein assembly complex, which is involved in assembly and insertion of beta-barrel proteins into the outer membrane. Nonessential member of the complex, which may orient the flexible periplasmic domain of BamA for interaction with other Bam components, chaperones and nascent outer membrane proteins.<ref>PMID:20378773</ref> <ref>PMID:21823654</ref> <ref>PMID:21586578</ref> <ref>PMID:21277859</ref>  [[http://www.uniprot.org/uniprot/A0A0H3MJ38_ECO7I A0A0H3MJ38_ECO7I]] Part of the outer membrane protein assembly complex, which is involved in assembly and insertion of beta-barrel proteins into the outer membrane. Constitutes, with BamA, the core component of the assembly machinery.[HAMAP-Rule:MF_00922]
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-Mitochondria, chloroplasts and Gram-negative bacteria are encased in a double layer of membranes. The outer membrane contains proteins with a beta-barrel structure(1,2). beta-Barrels are sheets of beta-strands wrapped into a cylinder, in which the first strand is hydrogen-bonded to the final strand. Conserved multi-subunit molecular machines fold and insert these proteins into the outer membrane(3-5). One subunit of the machines is itself a beta-barrel protein that has a central role in folding other beta-barrels. In Gram-negative bacteria, the beta-barrel assembly machine (BAM) consists of the beta-barrel protein BamA, and four lipoproteins(5-8). To understand how the BAM complex accelerates folding without using exogenous energy (for example, ATP)(9), we trapped folding intermediates on this machine. Here we report the structure of the BAM complex of Escherichia coli folding BamA itself. The BamA catalyst forms an asymmetric hybrid beta-barrel with the BamA substrate. The N-terminal edge of the BamA catalyst has an antiparallel hydrogen-bonded interface with the C-terminal edge of the BamA substrate, consistent with previous crosslinking studies(10-12); the other edges of the BamA catalyst and substrate are close to each other, but curl inward and do not pair. Six hydrogen bonds in a membrane environment make the interface between the two proteins very stable. This stability allows folding, but creates a high kinetic barrier to substrate release after folding has finished. Features at each end of the substrate overcome this barrier and promote release by stepwise exchange of hydrogen bonds. This mechanism of substrate-assisted product release explains how the BAM complex can stably associate with the substrate during folding and then turn over rapidly when folding is complete.
-Structure of a nascent membrane protein as it folds on the BAM complex.,Tomasek D, Rawson S, Lee J, Wzorek JS, Harrison SC, Li Z, Kahne D Nature. 2020 Jun 11. pii: 10.1038/s41586-020-2370-1. doi:, 10.1038/s41586-020-2370-1. PMID:32528179<ref>PMID:32528179</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 6v05" style="background-color:#fffaf0;"></div>
 ==See Also==
 *[[Bam complex 3D structures|Bam complex 3D structures]]
-== References ==
-<references/>
 __TOC__
 </StructureSection>
-[[Category: Ecoli]]
 [[Category: Large Structures]]
-[[Category: Harrison, S C]]
+[[Category: Harrison SC]]
-[[Category: Kahne, D]]
+[[Category: Kahne D]]
-[[Category: Lee, J]]
+[[Category: Lee J]]
-[[Category: Li, Z]]
+[[Category: Li Z]]
-[[Category: Rawson, S]]
+[[Category: Rawson S]]
-[[Category: Tomasek, D]]
+[[Category: Tomasek D]]
-[[Category: Wzorek, J S]]
+[[Category: Wzorek JS]]
-[[Category: Beta-barrel]]
-[[Category: Insertase]]
-[[Category: Membrane protein]]