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- PDB-7v75: Thermostabilized human prestin in complex with salicylate -

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Basic information

Entry
Database: PDB / ID: 7v75
TitleThermostabilized human prestin in complex with salicylate
Componentsprestin
KeywordsMEMBRANE PROTEIN / motor protein / prestin / SLC26A5 / electromotility
Function / homologyCHOLESTEROL / 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine / 2-HYDROXYBENZOIC ACID
Function and homology information
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.57 Å
AuthorsFutamata, H. / Fukuda, M. / Yamashita, K. / Nishizawa, T. / Nureki, O.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: Nat Commun / Year: 2022
Title: Cryo-EM structures of thermostabilized prestin provide mechanistic insights underlying outer hair cell electromotility.
Authors: Haon Futamata / Masahiro Fukuda / Rie Umeda / Keitaro Yamashita / Atsuhiro Tomita / Satoe Takahashi / Takafumi Shikakura / Shigehiko Hayashi / Tsukasa Kusakizako / Tomohiro Nishizawa / ...Authors: Haon Futamata / Masahiro Fukuda / Rie Umeda / Keitaro Yamashita / Atsuhiro Tomita / Satoe Takahashi / Takafumi Shikakura / Shigehiko Hayashi / Tsukasa Kusakizako / Tomohiro Nishizawa / Kazuaki Homma / Osamu Nureki /
Abstract: Outer hair cell elecromotility, driven by prestin, is essential for mammalian cochlear amplification. Here, we report the cryo-EM structures of thermostabilized prestin (Pres), complexed with ...Outer hair cell elecromotility, driven by prestin, is essential for mammalian cochlear amplification. Here, we report the cryo-EM structures of thermostabilized prestin (Pres), complexed with chloride, sulfate, or salicylate at 3.52-3.63 Å resolutions. The central positively-charged cavity allows flexible binding of various anion species, which likely accounts for the known distinct modulations of nonlinear capacitance (NLC) by different anions. Comparisons of these Pres structures with recent prestin structures suggest rigid-body movement between the core and gate domains, and provide mechanistic insights into prestin inhibition by salicylate. Mutations at the dimeric interface severely diminished NLC, suggesting that stabilization of the gate domain facilitates core domain movement, thereby contributing to the expression of NLC. These findings advance our understanding of the molecular mechanism underlying mammalian cochlear amplification.
History
DepositionAug 21, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 31, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 15, 2023Group: Database references / Refinement description
Category: citation / citation_author / pdbx_initial_refinement_model
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jun 12, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_3d_fitting_list / refine
Item: _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id ..._em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _refine.ls_d_res_high / _refine.ls_d_res_low

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: prestin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,49512
Polymers82,5031
Non-polymers6,99211
Water0
1
A: prestin
hetero molecules

A: prestin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)178,99124
Polymers165,0072
Non-polymers13,98422
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation1
2


  • Idetical with deposited unit
  • point asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit in distinct coordinate
  • point asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Schoenflies symbol: C2 (2 fold cyclic))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(-1), (-1), (1)188.133336, 188.133336

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Components

#1: Protein prestin /


Mass: 82503.375 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293SGNTI- / Production host: Homo sapiens (human)
#2: Chemical ChemComp-SAL / 2-HYDROXYBENZOIC ACID / SALICYLIC ACID / Salicylic acid


Mass: 138.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H6O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CLR / CHOLESTEROL / Cholesterol


Mass: 386.654 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H46O
#4: Chemical
ChemComp-LBN / 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine / (2R)-2-[(9Z)-9-Octadecenoyloxy]-3-(palmitoyloxy)propyl 2-(trimethylammonio)ethyl phosphate / POPC


Mass: 760.076 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C42H82NO8P / Comment: phospholipid*YM
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: prestin in complex with chloride ion / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER/RHODIUM / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 54 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

SoftwareName: REFMAC / Version: 5.8.0272 / Classification: refinement
EM software
IDNameVersionCategory
2SerialEMimage acquisition
4CTFFINDCTF correction
7Cootmodel fitting
9REFMACmodel refinement
10RELION3.1initial Euler assignment
11RELION3.1final Euler assignment
12RELION3.1classification
13RELION3.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 3.57 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 113410 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: RECIPROCAL
Atomic model buildingPDB-ID: 5DA0

5da0


Accession code: 5DA0 / Source name: PDB / Type: experimental model
RefinementResolution: 3.57→3.57 Å / Cor.coef. Fo:Fc: 0.911 / WRfactor Rwork: 0.337 / SU B: 11.072 / SU ML: 0.178 / Average fsc overall: 0.7614 / Average fsc work: 0.7614 / ESU R: 0.223
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rwork0.337 122783 -
all0.337 --
Rfree--0 %
obs--100 %
Solvent computationSolvent model: BABINET MODEL
Displacement parametersBiso mean: 169.57 Å2
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0120.0135091
ELECTRON MICROSCOPYr_bond_other_d0.0280.0175382
ELECTRON MICROSCOPYr_ext_dist_refined_d0.2170.177665
ELECTRON MICROSCOPYr_angle_refined_deg1.7161.6356867
ELECTRON MICROSCOPYr_angle_other_deg1.3481.56212423
ELECTRON MICROSCOPYr_dihedral_angle_1_deg5.5085602
ELECTRON MICROSCOPYr_dihedral_angle_2_deg33.74921.518191
ELECTRON MICROSCOPYr_dihedral_angle_3_deg18.82315824
ELECTRON MICROSCOPYr_dihedral_angle_4_deg18.7971520
ELECTRON MICROSCOPYr_chiral_restr0.0910.2652
ELECTRON MICROSCOPYr_gen_planes_refined0.0090.025293
ELECTRON MICROSCOPYr_gen_planes_other0.0020.021055
ELECTRON MICROSCOPYr_nbd_refined0.2020.22132
ELECTRON MICROSCOPYr_symmetry_nbd_other0.1870.29864
ELECTRON MICROSCOPYr_nbtor_refined0.1750.25022
ELECTRON MICROSCOPYr_symmetry_nbtor_other0.080.25574
ELECTRON MICROSCOPYr_xyhbond_nbd_refined0.1640.290
ELECTRON MICROSCOPYr_symmetry_nbd_refined0.2130.234
ELECTRON MICROSCOPYr_nbd_other0.240.2164
ELECTRON MICROSCOPYr_mcbond_it22.89115.4912417
ELECTRON MICROSCOPYr_mcbond_other22.87915.4882416
ELECTRON MICROSCOPYr_mcangle_it31.70523.323016
ELECTRON MICROSCOPYr_mcangle_other31.70523.3263017
ELECTRON MICROSCOPYr_scbond_it27.00419.4722674
ELECTRON MICROSCOPYr_scbond_other2719.4752675
ELECTRON MICROSCOPYr_scangle_it41.46127.9043851
ELECTRON MICROSCOPYr_scangle_other41.45527.9063852
ELECTRON MICROSCOPYr_lrange_it59.18580.22778581
ELECTRON MICROSCOPYr_lrange_other59.18580.22478582
LS refinement shell

Refine-ID: ELECTRON MICROSCOPY / Num. reflection Rfree: 0 / Total num. of bins used: 20 / % reflection obs: 100 %

Resolution (Å)Rfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc workWRfactor Rwork
3-3.0781.83291291.83291290.2951.832
3.078-3.1621.31588251.31588250.3921.315
3.162-3.2541.31186451.31186450.4641.311
3.254-3.3541.27782801.27782800.561.277
3.354-3.4641.20581231.20581230.6531.205
3.464-3.5851.0177971.0177970.761.01
3.585-3.720.776250.776250.8470.7
3.72-3.8720.46273100.46273100.8970.462
3.872-4.0440.29369460.29369460.9380.293
4.044-4.2410.19366160.19366160.960.193
4.241-4.4710.21663760.21663760.9720.216
4.471-4.7410.2659650.2659650.9740.26
4.741-5.0680.26456720.26456720.9750.264
5.068-5.4730.23852440.23852440.9670.238
5.473-5.9940.21148420.21148420.9530.211
5.994-6.70.23443960.23443960.930.234
6.7-7.7320.25438240.25438240.9230.254
7.732-9.460.26732430.26732430.9320.267
9.46-13.3370.2425390.2425390.9320.24
13.337-119.520.60313860.60313860.9630.603

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