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- EMDB-70268: The human PHB1/2 complex (open) -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-70268
TitleThe human PHB1/2 complex (open)
Map data
Sample
  • Complex: Human PHB1/2 complex
    • Protein or peptide: Prohibitin 1
    • Protein or peptide: Prohibitin-2
KeywordsSPFH / Mitochondria / PHB1 / PHB2 / MEMBRANE PROTEIN
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsGao J / Shao S / Sherpa D / Kupko N
Funding support United States, 3 items
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, 2025-
Header (metadata) releaseOct 22, 2025-
Map releaseOct 22, 2025-
UpdateOct 22, 2025-
Current statusOct 22, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_70268.png

Downloads & links

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Map

FileDownload / File: emd_70268.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 512 pix.
= 373.76 Å		0.73 Å/pix.
x 512 pix.
= 373.76 Å		0.73 Å/pix.
x 512 pix.
= 373.76 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.73 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05
Minimum - Maximum-0.27695397 - 0.45553932
Average (Standard dev.)0.0013805102 (±0.013205855)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 373.76 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_70268_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram

Histogram (log scale)

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Additional map: #2

Fileemd_70268_additional_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_70268_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_70268_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Human PHB1/2 complex

EntireName: Human PHB1/2 complex
Components
  • Complex: Human PHB1/2 complex
    • Protein or peptide: Prohibitin 1
    • Protein or peptide: Prohibitin-2

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Supramolecule #1: Human PHB1/2 complex

SupramoleculeName: Human PHB1/2 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Prohibitin 1

MacromoleculeName: Prohibitin 1 / type: protein_or_peptide / ID: 1 / Number of copies: 11 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 33.288652 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSAWSHPQFE KGGGSGGGSG GSAWSHPQFE KGSGSMAAKV FESIGKFGLA LAVAGGVVNS ALYNVDAGHR AVIFDRFRGV QDIVVGEGT HFLIPWVQKP IIFDCRSRPR NVPVITGSKD LQNVNITLRI LFRPVASQLP RIFTSIGEDY DERVLPSITT E ILKSVVAR ...String:
MSAWSHPQFE KGGGSGGGSG GSAWSHPQFE KGSGSMAAKV FESIGKFGLA LAVAGGVVNS ALYNVDAGHR AVIFDRFRGV QDIVVGEGT HFLIPWVQKP IIFDCRSRPR NVPVITGSKD LQNVNITLRI LFRPVASQLP RIFTSIGEDY DERVLPSITT E ILKSVVAR FDAGELITQR ELVSRQVSDD LTERAATFGL ILDDVSLTHL TFGKEFTEAV EAKQVAQQEA ERARFVVEKA EQ QKKAAII SAEGDSKAAE LIANSLATAG DGLIELRKLE AAEDIAYQLS RSRNITYLPA GQSVLLQLPQ

UniProtKB: Prohibitin 1

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Macromolecule #2: Prohibitin-2

MacromoleculeName: Prohibitin-2 / type: protein_or_peptide / ID: 2 / Number of copies: 11 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 33.341355 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAQNLKDLAG RLPAGPRGMG TALKLLLGAG AVAYGVRESV FTVEGGHRAI FFNRIGGVQQ DTILAEGLHF RIPWFQYPII YDIRARPRK ISSPTGSKDL QMVNISLRVL SRPNAQELPS MYQRLGLDYE ERVLPSIVNE VLKSVVAKFN ASQLITQRAQ V SLLIRREL ...String:
MAQNLKDLAG RLPAGPRGMG TALKLLLGAG AVAYGVRESV FTVEGGHRAI FFNRIGGVQQ DTILAEGLHF RIPWFQYPII YDIRARPRK ISSPTGSKDL QMVNISLRVL SRPNAQELPS MYQRLGLDYE ERVLPSIVNE VLKSVVAKFN ASQLITQRAQ V SLLIRREL TERAKDFSLI LDDVAITELS FSREYTAAVE AKQVAQQEAQ RAQFLVEKAK QEQRQKIVQA EGEAEAAKML GE ALSKNPG YIKLRKIRAA QNISKTIATS QNRIYLTADN LVLNLQDESF TRGSDSLIKG KK

UniProtKB: Prohibitin-2

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: C11 (11 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 7010
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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