7VHP

Structural insights into the membrane microdomain organization by SPFH family proteins

• PDB DOI: https://doi.org/10.2210/pdb7VHP/pdb
• EM Map EMD-32002: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 
• Membrane Protein: Yes  OPMPDBTMmpstruc


• Deposited: 2021-09-22 Released: 2022-03-23 
• Deposition Author(s): Ma, C.Y., Wang, C.K., Luo, D.Y., Yan, L., Yang, W.X., Li, N.N., Gao, N.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.27 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural insights into the membrane microdomain organization by SPFH family proteins.

Ma, C., Wang, C., Luo, D., Yan, L., Yang, W., Li, N., Gao, N.

(2022) Cell Res 32: 176-189

• PubMed: 34975153 
• DOI: https://doi.org/10.1038/s41422-021-00598-3
• Primary Citation of Related Structures:  
  7VHP, 7VHQ


• PubMed 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 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.

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Organizational Affiliation: 

State Key Laboratory of Membrane Biology, Peking-Tsinghua Joint Centre for Life Sciences, School of Life Sciences, Peking University, Beijing, China.

Biological Assembly 1  

Global Symmetry: Cyclic - C4  (Explore in 3D)
Global Stoichiometry: Hetero 48-mer - A24B12C12 Pseudo Symmetry: Cyclic - C4  (Explore in 3D)
Pseudo Stoichiometry: Hetero 48-mer - A24B24 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 2,698.76 kDa 
• Atom Count: 66,600 
• Modelled Residue Count: 8,304 
• Deposited Residue Count: 24,492 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP-dependent zinc metalloprotease FtsH	A, AA [auth b], B, BA [auth d], C, D, IA [auth t], JA [auth v], K [auth e], KA [auth J], L [auth f], LA [auth K], M [auth W], MA [auth L], N [auth Y], NA [auth M], O [auth a], P [auth c], UA [auth T], VA [auth V], W [auth s], X [auth u], Y [auth X], Z	644	Escherichia coli	Mutation(s): 0  Gene Names:  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 EC: 3.4.24 Membrane Entity: Yes
UniProt
Find proteins for P0AAI3 (Escherichia coli (strain K12)) Explore P0AAI3  Go to UniProtKB:  P0AAI3

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein HflK	CA [auth h], DA [auth j], E, F, HA [auth r], J [auth U], OA [auth N], PA [auth O], Q [auth g], R [auth i], TA [auth S], V [auth q]	419	Escherichia coli	Mutation(s): 0  Gene Names:  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 Membrane Entity: Yes
UniProt
Find proteins for P0ABC7 (Escherichia coli (strain K12)) Explore P0ABC7  Go to UniProtKB:  P0ABC7

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Modulator of FtsH protease HflC	EA [auth l], FA [auth n], G, GA [auth p], H, I, QA [auth P], RA [auth Q], S [auth k], SA [auth R], T [auth m], U [auth o]	334	Escherichia coli	Mutation(s): 0  Gene Names: HMPREF1611_02636 Membrane Entity: Yes
UniProt
Find proteins for P0ABC3 (Escherichia coli (strain K12)) Explore P0ABC3  Go to UniProtKB:  P0ABC3

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.27 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-03-23 
Deposition Author(s): Ma, C.Y., Wang, C.K., Luo, D.Y., Yan, L., Yang, W.X., Li, N.N., Gao, N.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2022-03-23
  Type: Initial release
  
• Version 1.1: 2024-06-19
  Changes: Data collection