7VHP

Structural insights into the membrane microdomain organization by SPFH family proteins


Experimental Data Snapshot

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

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


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

  • 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.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ATP-dependent zinc metalloprotease FtsH644Escherichia coliMutation(s): 0 
Gene Names: 
ftsHftsH_1ftsH_2ftsH_3BANRA_01798BANRA_03817BANRA_04194BANRA_04343BvCms2454_04835BvCmsC61A_01490BvCmsHHP019_05301BvCmsHHP056_02497BvCmsKKP005_04143BvCmsKKP036_00257BvCmsKKP057_00928BvCmsKKP061_00875BvCmsKSNP073_02150BvCmsKSP011_02063BvCmsKSP067_01451BvCmsKSP076_01617BvCmsNSNP036_02138BvCmsSIP024_04392BvCmsSIP082_00789CV83915_02920EC3234A_53c00570EC95NR1_02561ERS085358_02102ERS085366_00565ERS085386_00500ERS085406_02919ERS139208_02225Esc0902E_34410ETECE1373_00582ETECE36_01186ETECE925_00608HmCms169_01189HmCms184_00222HmCmsJML074_04865JE86ST02C_36600JE86ST05C_36640MS7163_03476NCTC10082_02960NCTC10089_00619NCTC10090_03652NCTC10764_03997NCTC10865_00800NCTC11022_03344NCTC11112_00879NCTC11126_02919NCTC11181_02861NCTC12950_00611NCTC13148_03277NCTC13216_01230NCTC4450_02597NCTC7922_03737NCTC7927_00682NCTC7928_02353NCTC8008_05220NCTC8179_06085NCTC8500_00501NCTC8621_00639NCTC8959_03144NCTC8960_03202NCTC9036_00669NCTC9044_01223NCTC9045_00707NCTC9048_00646NCTC9050_03735NCTC9075_00889NCTC9077_00753NCTC9081_01067NCTC9111_00988NCTC9434_00556NCTC9702_00663NCTC9703_05090NCTC9706_02858NCTC9775_04136NCTC9777_02143PGD_03938SAMEA3472043_01811SAMEA3472044_03322SAMEA3472056_03082SAMEA3472064_00676SAMEA3472080_00955SAMEA3472112_01517SAMEA3472117_01725SAMEA3472120_02456SAMEA3472147_01888SAMEA3484427_00598SAMEA3484429_00744SAMEA3485101_01720SAMEA3485110_00623SAMEA3751407_00536SAMEA3752312_02461SAMEA3752386_00450SAMEA3753064_02946SAMEA3753290_00138SAMEA3753300_02121SM09_03453THOESC010_05460TUM18780_05440WP2S18E08_05220WP4S18E07_05560WP4S18E08_05420

EC: 3.4.24
Membrane Entity: Yes 
UniProt
Find proteins for P0AAI3 (Escherichia coli (strain K12))
Explore P0AAI3 
Go to UniProtKB:  P0AAI3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0AAI3
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Protein HflK419Escherichia coliMutation(s): 0 
Gene Names: 
hflKhflK_1hflK_2A6519_001745A6592_09725A8C65_01745A8W81_003029A8X68_000832A9819_23885A9X72_22800AAG43_001305AAS29_001394ABE90_022860ABT96_001979ACN002_4400ACN68_17960ACN81_01545ACU57_19135ACW72_001442AM270_14655AM464_15610AMK64_000388AO169_001107AT335_001051AUQ29_20590AW059_20300AW086_09965B2D52_002145B5N24_002885B6L15_001818B6R12_001213B6R15_002000B6R17_000435B6R27_001127B6R48_001127B6R87_001128B7C15_002844BANRA_02754BANRA_02863BE963_12385BF481_004151BFL24_28330BG821_000571BHF52_13010BHS81_24975BHS87_23380BIZ41_02865BJI68_16630BJJ90_23295BK292_24855BK375_06700BKD45_001714BMC79_002199BMR21_08485BMT50_06160BMT91_05645BN17_41511BO068_002517BOB65_001220BOH76_10870BON63_12720BON65_22450BON70_11075BON72_19745BON73_07535BON76_04120BON83_17400BON92_18435BON93_15510BON94_18225BON96_04085BON98_15490BRV34_000762BRV41_002747BTQ06_07290BUE81_24150BUE82_22495BvCms2454_04355BvCmsC61A_01680BvCmsHHP019_00839BvCmsHHP056_01641BvCmsKKP005_02259BvCmsKKP036_00104BvCmsKKP057_02394BvCmsKKP061_03355BvCmsKSNP073_03478BvCmsKSP011_04670BvCmsKSP067_03844BvCmsKSP076_04394BvCmsNSNP036_02335BvCmsSIP082_00672BVL39_04255BXT93_16385BZL69_06755C2U48_11640C3F40_14180C5542_000569C5715_23370C5F72_23640C5N07_07180C5Y87_09380C6B22_03255C6N50_003506C7B02_22710C9114_00835C9E67_27580C9Z62_19540CA593_04940CBT22_001965CCS08_01775CCZ91_002203CDC27_22675CF32_000405CG692_00215CG831_001929CIG67_23195CLG78_004222COD50_25005CQB02_20420CR539_02820CS116_002254CV83915_01855CWS33_03550CXJ73_002149CY655_26335D0X26_12950D3822_10590D3O91_01570D3Y67_00715D4V09_14425D5H22_23970D9D31_07890D9D43_14560D9D77_08735D9E34_14855D9H13_15300D9H94_06295D9J03_08445D9J11_13475DAH18_07400DAH23_05540DAH34_17745DAH37_06200DAH50_08360DB282_10350DD762_20800DEN95_17280DEO15_07875DIV22_15560DL654_20975DLX40_22285DM968_08655DN627_22580DNQ45_06710DP258_23175DRW19_23360DS732_02655DTL43_02345DTL90_17250DTM45_20950DU321_10415DXT69_21915DXT71_04260DXT73_07390E0I42_01060E0N24_15540E2112_14640E2119_06465E2127_06860E2128_01910E2129_03990E2135_09640E4K51_09085E4K54_09665E5P52_11720E5S34_00845E5S38_10455E5S47_20580E5S52_05155E5S61_21835E5S62_12240EAI46_08375EAN77_04025EBP16_20780EC1094V2_4081EC3234A_108c00160EC95NR1_03794ECs5150ED648_13765EGC08_07270EH88_000588EHD79_20020EHH55_18930EI021_09690EI041_05010EIZ93_17475EKI52_12650EL79_4169EL80_4084ELT17_13910ELT21_00845ELT29_19175ELU85_14525ELV08_11370ELV15_00975ELV28_07675ELX69_13470ELX96_07270ELY05_00525ELY32_09020ELY41_00540ELY48_02815EO241_14855ERS085366_02335ERS139208_00850ETECE1373_04258ETECE925_04168EXX13_20220EYX47_03520EYX55_02905EYY34_13925F2N27_07320F2N28_06810F3N40_08340F9400_18305F9407_16545F9B07_05995F9S76_18130F9S83_12630F9V07_13695F9V24_16410F9X20_007165F9X20_07235FA849_10885FA868_05460FC554_05795FEL34_15225FFF58_08240FGY90_11850FHD44_08690FHR00_07400FJQ51_04640FKO60_18290FMP09_08525FOI11_014740FOI11_20940FPS82_03975FQE77_15260FQF29_05195FV293_00865FVB16_06380FWK02_13090FY127_03730G3813_002774G4A38_03090G5696_13885G6Z99_19860G7635_003092GAJ26_12530GBE29_17460GF646_10360GFY34_21205GIB53_02425GKF86_05500GKF89_03455GKG12_11675GKZ24_24990GNO40_09845GOP20_15705GP650_21115GP662_06525GP979_12080GQA06_06275GQE42_10425GQE64_09105GQE87_16240GQF58_15680GQF59_13895GQM04_15800GQM06_01935GQM09_08025GQM10_00835GQW07_15995GQW68_01985GQW76_14640GRO95_15840GRQ19_15895GRW05_08865GRW80_01335GRW81_08410GSY44_04535GUC01_09055GW978_03300GXV26_004242H0O53_13460H0O72_04915H4P50_23020H4P51_22860HHG09_002879HHH44_002336HIE44_001312HIF90_000433HIR12_000250HJ940_001563HJ942_000803HJN04_003334HJO75_003272HJQ60_002514HJS37_003331HJS41_003150HJU54_000802HL563_08480HLU56_08180HLZ50_23395HmCmsJML074_01365HMT08_17905HMV95_06705HNC36_09185HNC52_04490HNC59_12550HNC66_09365HNC99_21075HNV65_03230HPE39_02365HV109_21490HVW11_07920HVW43_13980HVX16_23365HVX31_18205HVX32_02295HVZ30_18915HVZ33_22260HVZ71_22535HX136_22685HZ71_003229HZ72_003440I6H00_16150I6H01_15315I6H02_16705IA00_000506JE86ST02C_47500JE86ST05C_48560NCTC10082_01824NCTC10090_02573NCTC10429_04710NCTC10974_05098NCTC11022_04511NCTC11181_01756NCTC11341_03057NCTC12950_04913NCTC13127_05909NCTC13216_02308NCTC4450_01452NCTC7922_05246NCTC8008_04078NCTC8500_05052NCTC8959_04284NCTC8960_02016NCTC9036_04401NCTC9044_02658NCTC9045_05319NCTC9048_04880NCTC9077_05652NCTC9117_05600NCTC9702_05278NCTC9706_01788NCTC9777_00916NCTC9969_04623ND22_003119PGD_03356PU06_09640RG28_05870SAMEA3472043_02154SAMEA3472044_01523SAMEA3472056_01694SAMEA3472064_04041SAMEA3472080_00094SAMEA3472112_03401SAMEA3472117_03579SAMEA3472120_02725SAMEA3484427_02085SAMEA3484429_03125SAMEA3485101_04737SAMEA3485110_03176SAMEA3751407_02266SAMEA3752386_02711SAMEA3752557_01673SAMEA3753064_01612SAMEA3753290_02101SAMEA3753300_00648THOESC010_40300TUM18780_39570UN91_24800WP2S18E08_42680WP4S18E07_40780WP4S18E08_41270WQ89_21930WR15_07020

Membrane Entity: Yes 
UniProt
Find proteins for P0ABC7 (Escherichia coli (strain K12))
Explore P0ABC7 
Go to UniProtKB:  P0ABC7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0ABC7
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Modulator of FtsH protease HflC334Escherichia coliMutation(s): 0 
Gene Names: HMPREF1611_02636
Membrane Entity: Yes 
UniProt
Find proteins for P0ABC3 (Escherichia coli (strain K12))
Explore P0ABC3 
Go to UniProtKB:  P0ABC3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0ABC3
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

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

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

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