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- EMDB-48568: PTCH1 in complex with Fab6H3 -

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Basic information

Entry
Database: EMDB / ID: EMD-48568
TitlePTCH1 in complex with Fab6H3
Map data
Sample
  • Complex: PTCH1 in complex with Fab6H3
    • Protein or peptide: Protein patched homolog 1
    • Protein or peptide: 6H3 Fab light chain
    • Protein or peptide: 6H3 Fab heavy chain
KeywordsPTCH1 / Antibody / hedgehog signaling / cryo-EM / membrane protein. / MEMBRANE PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


neural plate axis specification / response to chlorate / cell differentiation involved in kidney development / hedgehog receptor activity / neural tube patterning / cell proliferation involved in metanephros development / smoothened binding / hedgehog family protein binding / Ligand-receptor interactions / hindlimb morphogenesis ...neural plate axis specification / response to chlorate / cell differentiation involved in kidney development / hedgehog receptor activity / neural tube patterning / cell proliferation involved in metanephros development / smoothened binding / hedgehog family protein binding / Ligand-receptor interactions / hindlimb morphogenesis / epidermal cell fate specification / spinal cord motor neuron differentiation / prostate gland development / limb morphogenesis / Activation of SMO / patched binding / negative regulation of cell division / somite development / smooth muscle tissue development / dorsal/ventral neural tube patterning / pharyngeal system development / cellular response to cholesterol / mammary gland duct morphogenesis / mammary gland epithelial cell differentiation / cell fate determination / commissural neuron axon guidance / metanephric collecting duct development / regulation of smoothened signaling pathway / dorsal/ventral pattern formation / Class B/2 (Secretin family receptors) / embryonic limb morphogenesis / negative regulation of multicellular organism growth / ciliary membrane / branching involved in ureteric bud morphogenesis / cholesterol binding / positive regulation of epidermal cell differentiation / dendritic growth cone / keratinocyte proliferation / spermatid development / positive regulation of cholesterol efflux / negative regulation of keratinocyte proliferation / embryonic organ development / response to retinoic acid / negative regulation of osteoblast differentiation / response to mechanical stimulus / axonal growth cone / heart morphogenesis / negative regulation of stem cell proliferation / Hedgehog 'off' state / liver regeneration / cyclin binding / regulation of mitotic cell cycle / animal organ morphogenesis / stem cell proliferation / protein localization to plasma membrane / negative regulation of smoothened signaling pathway / neural tube closure / Hedgehog 'on' state / brain development / caveola / protein processing / apical part of cell / endocytic vesicle membrane / response to estradiol / glucose homeostasis / heparin binding / regulation of protein localization / midbody / in utero embryonic development / postsynaptic membrane / response to xenobiotic stimulus / intracellular membrane-bounded organelle / positive regulation of DNA-templated transcription / protein-containing complex binding / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / signal transduction / plasma membrane
Similarity search - Function
Transmembrane receptor, patched / : / Sterol-sensing domain of SREBP cleavage-activation / Sterol-sensing domain (SSD) profile. / Sterol-sensing domain
Similarity search - Domain/homology
Protein patched homolog 1
Similarity search - Component
Biological speciesHomo sapiens (human) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.73 Å
AuthorsHu Q / Qi X / Li X
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM149533 United States
CitationJournal: Cell Discov / Year: 2025
Title: Inhibiting hedgehog signal by a patched-1 antibody.
Authors: Qinli Hu / Xiaofeng Qi / Linda Donnelly / Xiaochun Li /
History
DepositionJan 9, 2025-
Header (metadata) releaseApr 2, 2025-
Map releaseApr 2, 2025-
UpdateApr 16, 2025-
Current statusApr 16, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48568.png

Downloads & links

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Map

FileDownload / File: emd_48568.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 300 pix.
= 249.9 Å		0.83 Å/pix.
x 300 pix.
= 249.9 Å		0.83 Å/pix.
x 300 pix.
= 249.9 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.833 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.287
Minimum - Maximum-1.106707 - 1.7919387
Average (Standard dev.)0.0038261702 (±0.044401746)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 249.9 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_48568_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_48568_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 : PTCH1 in complex with Fab6H3

EntireName: PTCH1 in complex with Fab6H3
Components
  • Complex: PTCH1 in complex with Fab6H3
    • Protein or peptide: Protein patched homolog 1
    • Protein or peptide: 6H3 Fab light chain
    • Protein or peptide: 6H3 Fab heavy chain

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Supramolecule #1: PTCH1 in complex with Fab6H3

SupramoleculeName: PTCH1 in complex with Fab6H3 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

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Macromolecule #1: Protein patched homolog 1

MacromoleculeName: Protein patched homolog 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 122.175109 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MASAGNAAEP QDRGGGGSGC IGAPGRPAGG GRRRRTGGLR RAAAPDRDYL HRPSYCDAAF ALEQISKGKA TGRKAPLWLR AKFQRLLFK LGCYIQKNCG KFLVVGLLIF GAFAVGLKAA NLETNVEELW VEVGGRVSRE LNYTRQKIGE EAMFNPQLMI Q TPKEEGAN ...String:
MASAGNAAEP QDRGGGGSGC IGAPGRPAGG GRRRRTGGLR RAAAPDRDYL HRPSYCDAAF ALEQISKGKA TGRKAPLWLR AKFQRLLFK LGCYIQKNCG KFLVVGLLIF GAFAVGLKAA NLETNVEELW VEVGGRVSRE LNYTRQKIGE EAMFNPQLMI Q TPKEEGAN VLTTEALLQH LDSALQASRV HVYMYNRQWK LEHLCYKSGE LITETGYMDQ IIEYLYPCLI ITPLDCFWEG AK LQSGTAY LLGKPPLRWT NFDPLEFLEE LKKINYQVDS WEEMLNKAEV GHGYMDRPCL NPADPDCPAT APNKNSTKPL DMA LVLNGG CHGLSRKYMH WQEELIVGGT VKNSTGKLVS AHALQTMFQL MTPKQMYEHF KGYEYVSHIN WNEDKAAAIL EAWQ RTYVE VVHQSVAQNS TQKVLSFTTT TLDDILKSFS DVSVIRVASG YLLMLAYACL TMLRWDCSKS QGAVGLAGVL LVALS VAAG LGLCSLIGIS FNAATTQVLP FLALGVGVDD VFLLAHAFSE TGQNKRIPFE DRTGECLKRT GASVALTSIS NVTAFF MAA LIPIPALRAF SLQAAVVVVF NFAMVLLIFP AILSMDLYRR EDRRLDIFCC FTSPCHCLEP PCTKWTLSSF AEKHYAP FL LKPKAKVVVI FLFLGLLGVS LYGTTRVRDG LDLTDIVPRE TREYDFIAAQ FKYFSFYNMY IVTQKADYPN IQHLLYDL H RSFSNVKYVM LEENKQLPKM WLHYFRDWLQ GLQDAFDSDW ETGKIMPNNY KNGSDDGVLA YKLLVQTGSR DKPIDISQL TKQRLVDADG IINPSAFYIY LTAWVSNDPV AYAASQANIR PHRPEWVHDK ADYMPETRLR IPAAEPIEYA QFPFYLNGLR DTSDFVEAI EKVRTICSNY TSLGLSSYPN GYPFLFWEQY IGLRHWLLLF ISVVLACTFL VCAVFLLNPW TAGIIVMVLA L MTVELFGM MGLIGIKLSA VPVVILIASV GIGVEFTVHV ALAFLTAIGD KNRRAVLALE HMFAPVLDGA VSTLLGVLML AG SEFDFIV RYFFAVLAIL TILGVLNGLV LLPVLLSFFG PYPEVSPAND YKDDDDK

UniProtKB: Protein patched homolog 1, Protein patched homolog 1

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Macromolecule #2: 6H3 Fab light chain

MacromoleculeName: 6H3 Fab light chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 10.96813 KDa
Recombinant expressionOrganism: Mus musculus (house mouse)
SequenceString:
VLTQSPAIMS ASLGERVTLT CTASSSVTSS YLHWYQQKPG SSPKLWIYST SNLPFGVSPR FSGSGSGTSF SLTISSMEAE DAATYYCHQ FHRSPYTFGG GTK

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Macromolecule #3: 6H3 Fab heavy chain

MacromoleculeName: 6H3 Fab heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 12.267724 KDa
Recombinant expressionOrganism: Mus musculus (house mouse)
SequenceString:
EVQLVESGGG LVKPGGSRKL SCVASGFTLS DYGMHWVRQA PEKGLEWVAY IGSDSYTIYH ADTMKGRFTI SRDNAKNTLF LQMTSLRSE DTAMYYCGRN YGMDYWGQGT S

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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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 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: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.73 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 258693
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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