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Yorodumi- PDB-7vhp: Structural insights into the membrane microdomain organization by... -
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-Basic information
Entry | Database: PDB / ID: 7vhp | ||||||
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Title | Structural insights into the membrane microdomain organization by SPFH family proteins | ||||||
Components |
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Keywords | MEMBRANE PROTEIN / membrane microdomain organization | ||||||
Function / homology | Function and homology information regulation of peptidase activity / Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / ATP-dependent peptidase activity / protein catabolic process / metalloendopeptidase activity / peptidase activity / membrane => GO:0016020 / cell division / ATP hydrolysis activity / zinc ion binding ...regulation of peptidase activity / Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / ATP-dependent peptidase activity / protein catabolic process / metalloendopeptidase activity / peptidase activity / membrane => GO:0016020 / cell division / ATP hydrolysis activity / zinc ion binding / ATP binding / plasma membrane Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.27 Å | ||||||
Authors | Ma, C.Y. / Wang, C.K. / Luo, D.Y. / Yan, L. / Yang, W.X. / Li, N.N. / Gao, N. | ||||||
Funding support | 1items
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Citation | Journal: Cell Res / Year: 2022 Title: Structural insights into the membrane microdomain organization by SPFH family proteins. Authors: Chengying Ma / Chengkun Wang / Dingyi Luo / Lu Yan / Wenxian Yang / Ningning Li / Ning Gao / Abstract: The lateral segregation of membrane constituents into functional microdomains, conceptually known as lipid raft, is a universal organization principle for cellular membranes in both prokaryotes and ...The lateral segregation of membrane constituents into functional microdomains, conceptually known as lipid raft, is a universal organization principle for cellular membranes in both prokaryotes and eukaryotes. The widespread Stomatin, Prohibitin, Flotillin, and HflK/C (SPFH) family proteins are enriched in functional membrane microdomains at various subcellular locations, and therefore were hypothesized to play a scaffolding role in microdomain formation. In addition, many SPFH proteins are also implicated in highly specific processes occurring on the membrane. However, none of these functions is understood at the molecular level. Here we report the structure of a supramolecular complex that is isolated from bacterial membrane microdomains and contains two SPFH proteins (HflK and HflC) and a membrane-anchored AAA+ protease FtsH. HflK and HflC form a circular 24-mer assembly, featuring a laterally segregated membrane microdomain (20 nm in diameter) bordered by transmembrane domains of HflK/C and a completely sealed periplasmic vault. Four FtsH hexamers are embedded inside this microdomain through interactions with the inner surface of the vault. These observations provide a mechanistic explanation for the role of HflK/C and their mitochondrial homologs prohibitins in regulating membrane-bound AAA+ proteases, and suggest a general model for the organization and functionalization of membrane microdomains by SPFH proteins. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7vhp.cif.gz | 1.6 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7vhp.ent.gz | 1.2 MB | Display | PDB format |
PDBx/mmJSON format | 7vhp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7vhp_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 7vhp_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 7vhp_validation.xml.gz | 174.9 KB | Display | |
Data in CIF | 7vhp_validation.cif.gz | 277.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vh/7vhp ftp://data.pdbj.org/pub/pdb/validation_reports/vh/7vhp | HTTPS FTP |
-Related structure data
Related structure data | 32002MC 7vhqC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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-Components
#1: Protein | Mass: 70797.031 Da / Num. of mol.: 24 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) Gene: ftsH, ftsH_1, ftsH_2, ftsH_3, BANRA_01798, BANRA_03817, BANRA_04194, BANRA_04343, BvCms2454_04835, BvCmsC61A_01490, BvCmsHHP019_05301, BvCmsHHP056_02497, BvCmsKKP005_04143, BvCmsKKP036_00257, ...Gene: ftsH, ftsH_1, ftsH_2, ftsH_3, BANRA_01798, BANRA_03817, BANRA_04194, BANRA_04343, BvCms2454_04835, BvCmsC61A_01490, BvCmsHHP019_05301, BvCmsHHP056_02497, BvCmsKKP005_04143, BvCmsKKP036_00257, BvCmsKKP057_00928, BvCmsKKP061_00875, BvCmsKSNP073_02150, BvCmsKSP011_02063, BvCmsKSP067_01451, BvCmsKSP076_01617, BvCmsNSNP036_02138, BvCmsSIP024_04392, BvCmsSIP082_00789, CV83915_02920, EC3234A_53c00570, EC95NR1_02561, ERS085358_02102, ERS085366_00565, ERS085386_00500, ERS085406_02919, ERS139208_02225, Esc0902E_34410, ETECE1373_00582, ETECE36_01186, ETECE925_00608, HmCms169_01189, HmCms184_00222, HmCmsJML074_04865, JE86ST02C_36600, JE86ST05C_36640, MS7163_03476, NCTC10082_02960, NCTC10089_00619, NCTC10090_03652, NCTC10764_03997, NCTC10865_00800, NCTC11022_03344, NCTC11112_00879, NCTC11126_02919, NCTC11181_02861, NCTC12950_00611, NCTC13148_03277, NCTC13216_01230, NCTC4450_02597, NCTC7922_03737, NCTC7927_00682, NCTC7928_02353, NCTC8008_05220, NCTC8179_06085, NCTC8500_00501, NCTC8621_00639, NCTC8959_03144, NCTC8960_03202, NCTC9036_00669, NCTC9044_01223, NCTC9045_00707, NCTC9048_00646, NCTC9050_03735, NCTC9075_00889, NCTC9077_00753, NCTC9081_01067, NCTC9111_00988, NCTC9434_00556, NCTC9702_00663, NCTC9703_05090, NCTC9706_02858, NCTC9775_04136, NCTC9777_02143, PGD_03938, SAMEA3472043_01811, SAMEA3472044_03322, SAMEA3472056_03082, SAMEA3472064_00676, SAMEA3472080_00955, SAMEA3472112_01517, SAMEA3472117_01725, SAMEA3472120_02456, SAMEA3472147_01888, SAMEA3484427_00598, SAMEA3484429_00744, SAMEA3485101_01720, SAMEA3485110_00623, SAMEA3751407_00536, SAMEA3752312_02461, SAMEA3752386_00450, SAMEA3753064_02946, SAMEA3753290_00138, SAMEA3753300_02121, SM09_03453, THOESC010_05460, TUM18780_05440, WP2S18E08_05220, WP4S18E07_05560, WP4S18E08_05420 Production host: Escherichia coli (E. coli) References: UniProt: A0A024LAA6, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases #2: Protein | Mass: 45598.793 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) Gene: hflK, hflK_1, hflK_2, A6519_001745, A6592_09725, A8C65_01745, A8W81_003029, A8X68_000832, A9819_23885, A9X72_22800, AAG43_001305, AAS29_001394, ABE90_022860, ABT96_001979, ACN002_4400, ACN68_ ...Gene: hflK, hflK_1, hflK_2, A6519_001745, A6592_09725, A8C65_01745, A8W81_003029, A8X68_000832, A9819_23885, A9X72_22800, AAG43_001305, AAS29_001394, ABE90_022860, ABT96_001979, ACN002_4400, ACN68_17960, ACN81_01545, ACU57_19135, ACW72_001442, AM270_14655, AM464_15610, AMK64_000388, AO169_001107, AT335_001051, AUQ29_20590, AW059_20300, AW086_09965, B2D52_002145, B5N24_002885, B6L15_001818, B6R12_001213, B6R15_002000, B6R17_000435, B6R27_001127, B6R48_001127, B6R87_001128, B7C15_002844, BANRA_02754, BANRA_02863, BE963_12385, BF481_004151, BFL24_28330, BG821_000571, BHF52_13010, BHS81_24975, BHS87_23380, BIZ41_02865, BJI68_16630, BJJ90_23295, BK292_24855, BK375_06700, BKD45_001714, BMC79_002199, BMR21_08485, BMT50_06160, BMT91_05645, BN17_41511, BO068_002517, BOB65_001220, BOH76_10870, BON63_12720, BON65_22450, BON70_11075, BON72_19745, BON73_07535, BON76_04120, BON83_17400, BON92_18435, BON93_15510, BON94_18225, BON96_04085, BON98_15490, BRV34_000762, BRV41_002747, BTQ06_07290, BUE81_24150, BUE82_22495, BvCms2454_04355, BvCmsC61A_01680, BvCmsHHP019_00839, BvCmsHHP056_01641, BvCmsKKP005_02259, BvCmsKKP036_00104, BvCmsKKP057_02394, BvCmsKKP061_03355, BvCmsKSNP073_03478, BvCmsKSP011_04670, BvCmsKSP067_03844, BvCmsKSP076_04394, BvCmsNSNP036_02335, BvCmsSIP082_00672, BVL39_04255, BXT93_16385, BZL69_06755, C2U48_11640, C3F40_14180, C5542_000569, C5715_23370, C5F72_23640, C5N07_07180, C5Y87_09380, C6B22_03255, C6N50_003506, C7B02_22710, C9114_00835, C9E67_27580, C9Z62_19540, CA593_04940, CBT22_001965, CCS08_01775, CCZ91_002203, CDC27_22675, CF32_000405, CG692_00215, CG831_001929, CIG67_23195, CLG78_004222, COD50_25005, CQB02_20420, CR539_02820, CS116_002254, CV83915_01855, CWS33_03550, CXJ73_002149, CY655_26335, D0X26_12950, D3822_10590, D3O91_01570, D3Y67_00715, D4V09_14425, D5H22_23970, D9D31_07890, D9D43_14560, D9D77_08735, D9E34_14855, D9H13_15300, D9H94_06295, D9J03_08445, D9J11_13475, DAH18_07400, DAH23_05540, DAH34_17745, DAH37_06200, DAH50_08360, DB282_10350, DD762_20800, DEN95_17280, DEO15_07875, DIV22_15560, DL654_20975, DLX40_22285, DM968_08655, DN627_22580, DNQ45_06710, DP258_23175, DRW19_23360, DS732_02655, DTL43_02345, DTL90_17250, DTM45_20950, DU321_10415, DXT69_21915, DXT71_04260, DXT73_07390, E0I42_01060, E0N24_15540, E2112_14640, E2119_06465, E2127_06860, E2128_01910, E2129_03990, E2135_09640, E4K51_09085, E4K54_09665, E5P52_11720, E5S34_00845, E5S38_10455, E5S47_20580, E5S52_05155, E5S61_21835, E5S62_12240, EAI46_08375, EAN77_04025, EBP16_20780, EC1094V2_4081, EC3234A_108c00160, EC95NR1_03794, ECs5150, ED648_13765, EGC08_07270, EH88_000588, EHD79_20020, EHH55_18930, EI021_09690, EI041_05010, EIZ93_17475, EKI52_12650, EL79_4169, EL80_4084, ELT17_13910, ELT21_00845, ELT29_19175, ELU85_14525, ELV08_11370, ELV15_00975, ELV28_07675, ELX69_13470, ELX96_07270, ELY05_00525, ELY32_09020, ELY41_00540, ELY48_02815, EO241_14855, ERS085366_02335, ERS139208_00850, ETECE1373_04258, ETECE925_04168, EXX13_20220, EYX47_03520, EYX55_02905, EYY34_13925, F2N27_07320, F2N28_06810, F3N40_08340, F9400_18305, F9407_16545, F9B07_05995, F9S76_18130, F9S83_12630, F9V07_13695, F9V24_16410, F9X20_007165, F9X20_07235, FA849_10885, FA868_05460, FC554_05795, FEL34_15225, FFF58_08240, FGY90_11850, FHD44_08690, FHR00_07400, FJQ51_04640, FKO60_18290, FMP09_08525, FOI11_014740, FOI11_20940, FPS82_03975, FQE77_15260, FQF29_05195, FV293_00865, FVB16_06380, FWK02_13090, FY127_03730, G3813_002774, G4A38_03090, G5696_13885, G6Z99_19860, G7635_003092, GAJ26_12530, GBE29_17460, GF646_10360, GFY34_21205, GIB53_02425, GKF86_05500, GKF89_03455, GKG12_11675, GKZ24_24990, GNO40_09845, GOP20_15705, GP650_21115, GP662_06525, GP979_12080, GQA06_06275, GQE42_10425, GQE64_09105, GQE87_16240, GQF58_15680, GQF59_13895, GQM04_15800, GQM06_01935, GQM09_08025, GQM10_00835, GQW07_15995, GQW68_01985, GQW76_14640, GRO95_15840, GRQ19_15895, GRW05_08865, GRW80_01335, GRW81_08410, GSY44_04535, GUC01_09055, GW978_03300, GXV26_004242, H0O53_13460, H0O72_04915, H4P50_23020, H4P51_22860, HHG09_002879, HHH44_002336, HIE44_001312, HIF90_000433, HIR12_000250, HJ940_001563, HJ942_000803, HJN04_003334, HJO75_003272, HJQ60_002514, HJS37_003331, HJS41_003150, HJU54_000802, HL563_08480, HLU56_08180, HLZ50_23395, HmCmsJML074_01365, HMT08_17905, HMV95_06705, HNC36_09185, HNC52_04490, HNC59_12550, HNC66_09365, HNC99_21075, HNV65_03230, HPE39_02365, HV109_21490, HVW11_07920, HVW43_13980, HVX16_23365, HVX31_18205, HVX32_02295, HVZ30_18915, HVZ33_22260, HVZ71_22535, HX136_22685, HZ71_003229, HZ72_003440, I6H00_16150, I6H01_15315, I6H02_16705, IA00_000506, JE86ST02C_47500, JE86ST05C_48560, NCTC10082_01824, NCTC10090_02573, NCTC10429_04710, NCTC10974_05098, NCTC11022_04511, NCTC11181_01756, NCTC11341_03057, NCTC12950_04913, NCTC13127_05909, NCTC13216_02308, NCTC4450_01452, NCTC7922_05246, NCTC8008_04078, NCTC8500_05052, NCTC8959_04284, NCTC8960_02016, NCTC9036_04401, NCTC9044_02658, NCTC9045_05319, NCTC9048_04880, NCTC9077_05652, NCTC9117_05600, NCTC9702_05278, NCTC9706_01788, NCTC9777_00916, NCTC9969_04623, ND22_003119, PGD_03356, PU06_09640, RG28_05870, SAMEA3472043_02154, SAMEA3472044_01523, SAMEA3472056_01694, SAMEA3472064_04041, SAMEA3472080_00094, SAMEA3472112_03401, SAMEA3472117_03579, SAMEA3472120_02725, SAMEA3484427_02085, SAMEA3484429_03125, SAMEA3485101_04737, SAMEA3485110_03176, SAMEA3751407_02266, SAMEA3752386_02711, SAMEA3752557_01673, SAMEA3753064_01612, SAMEA3753290_02101, SAMEA3753300_00648, THOESC010_40300, TUM18780_39570, UN91_24800, WP2S18E08_42680, WP4S18E07_40780, WP4S18E08_41270, WQ89_21930, WR15_07020 Production host: Escherichia coli (E. coli) / References: UniProt: C3SG32 #3: Protein | Mass: 37703.887 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: HMPREF1611_02636 / Production host: Escherichia coli (E. coli) / References: UniProt: V0YWD5 |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: KCF complex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 60 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
CTF correction | Type: NONE |
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3D reconstruction | Resolution: 3.27 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 84693 / Symmetry type: POINT |