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- PDB-9oa0: The human PHB1/2 complex (open) -

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Basic information

Entry
Database: PDB / ID: 9oa0
TitleThe human PHB1/2 complex (open)
Components
  • Prohibitin 1
  • Prohibitin-2
KeywordsMEMBRANE PROTEIN / SPFH / Mitochondria / PHB1 / PHB2
Function / homology
Function and homology information


complement component C3a binding / mitochondrial prohibitin complex / regulation of cardiolipin metabolic process / regulation of cytochrome-c oxidase activity / amide binding / host-mediated perturbation of viral RNA genome replication / proteinase activated receptor binding / regulation of branching involved in mammary gland duct morphogenesis / negative regulation of nuclear receptor-mediated glucocorticoid signaling pathway / negative regulation of mammary gland epithelial cell proliferation ...complement component C3a binding / mitochondrial prohibitin complex / regulation of cardiolipin metabolic process / regulation of cytochrome-c oxidase activity / amide binding / host-mediated perturbation of viral RNA genome replication / proteinase activated receptor binding / regulation of branching involved in mammary gland duct morphogenesis / negative regulation of nuclear receptor-mediated glucocorticoid signaling pathway / negative regulation of mammary gland epithelial cell proliferation / sphingolipid binding / Processing of SMDT1 / Cellular response to mitochondrial stress / T-helper 17 type immune response / RIG-I signaling pathway / positive regulation of complement activation / complement component C3b binding / mammary gland branching involved in thelarche / negative regulation of intracellular estrogen receptor signaling pathway / negative regulation of androgen receptor signaling pathway / negative regulation of transcription by competitive promoter binding / positive regulation of G protein-coupled receptor signaling pathway / cellular response to interleukin-6 / sister chromatid cohesion / mammary gland epithelial cell proliferation / DNA biosynthetic process / positive regulation of immunoglobulin production / positive regulation of interleukin-17 production / B cell activation / progesterone receptor signaling pathway / mammary gland alveolus development / negative regulation of DNA-binding transcription factor activity / positive regulation of DNA-binding transcription factor activity / mitophagy / estrogen receptor signaling pathway / antiviral innate immune response / positive regulation of smooth muscle cell proliferation / epigenetic regulation of gene expression / nuclear estrogen receptor binding / cell periphery / mitochondrion organization / RAF activation / positive regulation of non-canonical NF-kappaB signal transduction / negative regulation of cell growth / negative regulation of protein catabolic process / negative regulation of ERK1 and ERK2 cascade / histone deacetylase binding / nuclear matrix / protein import into nucleus / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / osteoblast differentiation / transcription corepressor activity / cell migration / positive regulation of neuron apoptotic process / regulation of apoptotic process / mitochondrial outer membrane / early endosome / positive regulation of ERK1 and ERK2 cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / mitochondrial inner membrane / protein stabilization / protein heterodimerization activity / negative regulation of cell population proliferation / negative regulation of DNA-templated transcription / positive regulation of gene expression / regulation of DNA-templated transcription / symbiont entry into host cell / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / enzyme binding / cell surface / negative regulation of transcription by RNA polymerase II / signal transduction / protein homodimerization activity / protein-containing complex / mitochondrion / extracellular exosome / nucleoplasm / identical protein binding / nucleus / membrane / 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
Prohibitin 1 / Prohibitin-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsGao, J. / Shao, S. / Sherpa, D. / Kupko, N.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Aging (NIH/NIA)AG073277 United States
David and Lucile Packard Foundation United States
Richard and Susan Smith Family Foundation United States
CitationJournal: To Be Published
Title: The human PHB1/2 complex (open)
Authors: Gao, J. / Shao, S. / Sherpa, D. / Kupko, N.
History
DepositionApr 18, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 22, 2025Provider: repository / Type: Initial release
Revision 1.0Oct 22, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Oct 22, 2025Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Oct 22, 2025Data content type: Additional map / Part number: 2 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Oct 22, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Oct 22, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Oct 22, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Oct 22, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Oct 22, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Prohibitin 1
B: Prohibitin 1
C: Prohibitin 1
D: Prohibitin 1
E: Prohibitin 1
F: Prohibitin 1
G: Prohibitin 1
H: Prohibitin 1
I: Prohibitin 1
J: Prohibitin 1
K: Prohibitin 1
a: Prohibitin-2
b: Prohibitin-2
c: Prohibitin-2
d: Prohibitin-2
e: Prohibitin-2
f: Prohibitin-2
g: Prohibitin-2
h: Prohibitin-2
i: Prohibitin-2
j: Prohibitin-2
k: Prohibitin-2


Theoretical massNumber of molelcules
Total (without water)732,93022
Polymers732,93022
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Prohibitin 1


Mass: 33288.652 Da / Num. of mol.: 11
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PHB1, PHB / Production host: Homo sapiens (human) / References: UniProt: P35232
#2: Protein
Prohibitin-2 / B-cell receptor-associated protein BAP37 / D-prohibitin / Repressor of estrogen receptor activity


Mass: 33341.355 Da / Num. of mol.: 11
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PHB2, BAP, REA / Production host: Homo sapiens (human) / References: UniProt: Q99623
Has protein modificationN

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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: Human PHB1/2 complex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C11 (11 fold cyclic)
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 7010 / Symmetry type: POINT

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