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- PDB-8j4i: Unveiling the Role of Human Prohibitin 2 as a Mitochondrial Calci... -

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Basic information

Entry
Database: PDB / ID: 8j4i
TitleUnveiling the Role of Human Prohibitin 2 as a Mitochondrial Calcium Channel in Parkinson's Disease
ComponentsProhibitin-2
KeywordsTRANSPORT PROTEIN / Mitochondria calcium uptake / Calcium channel / Prohibitin 2 / Ion-conducting pore
Function / homology
Function and homology information


mitochondrial prohibitin complex / regulation of cardiolipin metabolic process / regulation of cytochrome-c oxidase activity / amide binding / regulation of branching involved in mammary gland duct morphogenesis / negative regulation of mammary gland epithelial cell proliferation / sphingolipid binding / Processing of SMDT1 / Cellular response to mitochondrial stress / positive regulation of exit from mitosis ...mitochondrial prohibitin complex / regulation of cardiolipin metabolic process / regulation of cytochrome-c oxidase activity / amide binding / regulation of branching involved in mammary gland duct morphogenesis / negative regulation of mammary gland epithelial cell proliferation / sphingolipid binding / Processing of SMDT1 / Cellular response to mitochondrial stress / positive regulation of exit from mitosis / RIG-I signaling pathway / negative regulation of intracellular estrogen receptor signaling pathway / mammary gland branching involved in thelarche / positive regulation of cell cycle G1/S phase transition / sister chromatid cohesion / mammary gland epithelial cell proliferation / positive regulation of immunoglobulin production / B cell activation / presynaptic active zone / mammary gland alveolus development / mitophagy / cellular response to retinoic acid / estrogen receptor signaling pathway / antiviral innate immune response / positive regulation of DNA-binding transcription factor activity / cell periphery / GABA-ergic synapse / nuclear estrogen receptor binding / mitochondrion organization / negative regulation of DNA-binding transcription factor activity / positive regulation of non-canonical NF-kappaB signal transduction / nuclear matrix / protein import into nucleus / cell migration / cellular response to hypoxia / mitochondrial outer membrane / mitochondrial inner membrane / positive regulation of ERK1 and ERK2 cascade / postsynaptic density / protein stabilization / protein heterodimerization activity / axon / negative regulation of DNA-templated transcription / negative regulation of apoptotic process / glutamatergic synapse / cell surface / protein homodimerization activity / protein-containing complex / mitochondrion / identical protein binding / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Prohibitin / Band 7 domain / SPFH domain / Band 7 family / prohibitin homologues / Band 7/SPFH domain superfamily
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsLi, Y.Y. / Fang, Y. / Gao, Y.X. / Ding, W. / Yang, J. / Liu, Y. / Shen, B. / Wang, J.F. / Zhou, S.
Funding support China, 1items
OrganizationGrant numberCountry
Chinese Academy of Sciences China
CitationJournal: To Be Published
Title: Human Prohibitin 2 is a Mitochondrial Ca2+-Selective Channel
Authors: Li, Y.Y. / Fang, Y. / Gao, Y.X. / Ding, W. / Yang, J. / Liu, Y. / Shen, B. / Wang, J.F. / Zhou, S.
History
DepositionApr 20, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 5, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Prohibitin-2
B: Prohibitin-2
C: Prohibitin-2
D: Prohibitin-2
E: Prohibitin-2
F: Prohibitin-2


Theoretical massNumber of molelcules
Total (without water)127,0656
Polymers127,0656
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: cross-linking, light scattering, static light scattering, gel filtration, size exclusion chromatography, electron microscopy, 300 kV cryo-EM, assay for oligomerization, in cell crosslinking
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14250 Å2
ΔGint-69 kcal/mol
Surface area69330 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 100structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein
Prohibitin-2 / B-cell receptor-associated protein BAP37 / D-prohibitin / Repressor of estrogen receptor activity


Mass: 21177.529 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PHB2, BAP, REA / Production host: Escherichia coli (E. coli) / References: UniProt: Q99623

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic22D 1H-15N HSQC
828isotropic22D 1H-15N HSQC
232isotropic22D 1H-13C HSQC
545isotropic22D 1H-13C HSQC
253isotropic13D HN(CA)CB
363isotropic13D HN(COCA)CB
373isotropic13D HN(CO)CA
383isotropic13D HNCA
393isotropic13D HNCO
3103isotropic13D HN(CA)CO
2112isotropic23D (H)CCH-TOCSY
2122isotropic23D CC(CO)NH
2132isotropic23D H(CCO)NH
8148isotropic23D 1H-15N NOESY
4154isotropic23D 1H-15N NOESY
7167isotropic33D 1H-15N NOESY
2172isotropic33D 1H-15N NOESY
6186isotropic33D 1H-15N NOESY
2192isotropic33D 1H-13C NOESY
4204isotropic33D 1H-13C NOESY
6216isotropic33D 1H-13C NOESY
7227isotropic33D 1H-13C NOESY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.35 mM [U-15N] [15N]-hPHB2, 90% H2O/10% D2O[15N]90% H2O/10% D2O
solution80.35 mM [U-15N] [15N]-hPHB2, 90% H2O/10% D2O[2H, 15N]90% H2O/10% D2O
solution20.35 mM [U-15N, U-13C] [15N, 13C]-hPHB2, 90% H2O/10% D2O[15N, 13C]90% H2O/10% D2O
solution30.35 mM [2H, 15N, 13C] [2H, 15N, 13C]-hPHB2, 90% H2O/10% D2O[2H, 15N, 13C]90% H2O/10% D2O
solution40.35 mM [50%-2H, 15N, 13C] [50%-2H, 15N, 13C]-hPHB2, 90% H2O/10% D2O[50%-2H, 15N, 13C]90% H2O/10% D2O
solution50.35 mM [2H, 15N, IVL-13C] [2H, 15N, IVL-13C]-hPHB2, 90% H2O/10% D2O[2H, 15N, IVL-13C]90% H2O/10% D2O
solution60.5 mM 50%[15N, 13C]-50%[14N, 12C] 50%[15N, 13C]-50%[14N, 12C]-hPHB2, 90% H2O/10% D2O50%[15N, 13C]-50%[14N, 12C]90% H2O/10% D2O
solution70.5 mM 50%[15N, 2H]-50%[15%C13] 50%[15N, 2H]-50%[15%C13]-hPHB2, 90% H2O/10% D2O50%[15N, 2H]-50%[15%C13]90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.35 mM[15N]-hPHB2[U-15N]1
0.35 mM[15N]-hPHB2[U-15N]8
0.35 mM[15N, 13C]-hPHB2[U-15N, U-13C]2
0.35 mM[2H, 15N, 13C]-hPHB2[2H, 15N, 13C]3
0.35 mM[50%-2H, 15N, 13C]-hPHB2[50%-2H, 15N, 13C]4
0.35 mM[2H, 15N, IVL-13C]-hPHB2[2H, 15N, IVL-13C]5
0.5 mM50%[15N, 13C]-50%[14N, 12C]-hPHB250%[15N, 13C]-50%[14N, 12C]6
0.5 mM50%[15N, 2H]-50%[15%C13]-hPHB250%[15N, 2H]-50%[15%C13]7
Sample conditions
Conditions-IDIonic strengthLabelpHPressure (kPa)Temperature (K)
150 mMcondition_sample_15.61 atm308 K
250 mMcondition_sample_25.61 atm308 K
350 mMcondition_sample_35.61 atm308 K
450 mMcondition_sample_45.61 atm308 K
550 mMcondition_sample_55.61 atm308 K
650 mMcondition_sample_65.61 atm308 K
750 mMcondition_sample_75.61 atm308 K
850 mMcondition_sample_85.61 atm308 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III6001
Bruker AVANCE IIIBrukerAVANCE III8502
Bruker AVANCE IIIBrukerAVANCE III9503

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Processing

NMR software
NameDeveloperClassification
CcpNmr AnalysisCCPNchemical shift assignment
X-PLOR NIHX-PLOR NIHstructure calculation
X-PLOR NIHX-PLOR NIHrefinement
CcpNmr AnalysisCCPNpeak picking
RefinementMethod: simulated annealing / Software ordinal: 3
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 15

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