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- EMDB-76173: In situ subtomogram average of the transition zone linker in huma... -

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Basic information

Entry
Database: EMDB / ID: EMD-76173
TitleIn situ subtomogram average of the transition zone linker in human airway cilia (composite map)
Map dataA composite map of TZ linker from human airway cilia
Sample
  • Organelle or cellular component: Human airway ciliary transition zone (TZ) linker
    • Protein or peptide: S-phase kinase-associated protein 1
    • Protein or peptide: Dynein light chain 1, cytoplasmic
    • Protein or peptide: Double zinc ribbon and ankyrin repeat-containing protein 1
    • Protein or peptide: Epithelial cell-transforming sequence 2 oncogene-like
KeywordsCilia / Transition Zone / TZ linker / Subtomogram Averaging / STRUCTURAL PROTEIN
Function / homology
Function and homology information


nitric-oxide synthase inhibitor activity / negative regulation of DNA strand resection involved in replication fork processing / eye photoreceptor cell development / negative regulation of phosphorylation / Activation of BIM and translocation to mitochondria / intraciliary retrograde transport / motile cilium assembly / synaptic assembly at neuromuscular junction / F-box domain binding / Intraflagellar transport ...nitric-oxide synthase inhibitor activity / negative regulation of DNA strand resection involved in replication fork processing / eye photoreceptor cell development / negative regulation of phosphorylation / Activation of BIM and translocation to mitochondria / intraciliary retrograde transport / motile cilium assembly / synaptic assembly at neuromuscular junction / F-box domain binding / Intraflagellar transport / positive regulation of intracellular transport / PcG protein complex / regulation of xenophagy / maintenance of protein location in nucleus / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / Cul7-RING ubiquitin ligase complex / positive regulation of mitotic cell cycle spindle assembly checkpoint / regulation of cell cycle process / neural crest cell differentiation / COPI-independent Golgi-to-ER retrograde traffic / ubiquitin ligase activator activity / regulation of BMP signaling pathway / regulation of mitophagy / cytoplasmic dynein complex / regulation of centrosome duplication / spermatid development / regulation of TOR signaling / SCF ubiquitin ligase complex / male germ cell nucleus / regulation of DNA damage checkpoint / Macroautophagy / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / Prolactin receptor signaling / dynein intermediate chain binding / ubiquitin ligase complex scaffold activity / tertiary granule membrane / ciliary tip / limb development / ficolin-1-rich granule membrane / cullin family protein binding / centrosome duplication / cilium assembly / COPI-mediated anterograde transport / ubiquitin-like ligase-substrate adaptor activity / Nuclear events stimulated by ALK signaling in cancer / axon cytoplasm / protein K48-linked ubiquitination / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / MHC class II antigen presentation / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / substantia nigra development / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / guanyl-nucleotide exchange factor activity / AURKA Activation by TPX2 / Resolution of Sister Chromatid Cohesion / molecular function activator activity / enzyme inhibitor activity / positive regulation of insulin secretion involved in cellular response to glucose stimulus / regulation of mitotic cell cycle / Regulation of BACH1 activity / MAP3K8 (TPL2)-dependent MAPK1/3 activation / G1/S transition of mitotic cell cycle / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / Vpu mediated degradation of CD4 / RHO GTPases Activate Formins / Dectin-1 mediated noncanonical NF-kB signaling / Degradation of CRY and PER proteins / Iron uptake and transport / Activation of NF-kappaB in B cells / Degradation of GLI1 by the proteasome / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Negative regulation of NOTCH4 signaling / mitotic spindle / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / beta-catenin binding / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / GSK3B-mediated proteasomal degradation of PD-L1(CD274) / NOTCH1 Intracellular Domain Regulates Transcription / regulation of circadian rhythm / Degradation of beta-catenin by the destruction complex / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / CLEC7A (Dectin-1) signaling / SCF(Skp2)-mediated degradation of p27/p21 / FCERI mediated NF-kB activation / kinetochore / protein polyubiquitination / HCMV Early Events / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / Interleukin-1 signaling / Orc1 removal from chromatin / Aggrephagy
Similarity search - Function
Domain of unknown function DUF4347 / Double zinc ribbon / : / : / Double zinc ribbon / Domain of unknown function (DUF4347) / Fn3 associated repeat / Fn3 associated / Dynein light chain, type 1/2, conserved site / Dynein light chain type 1 signature. ...Domain of unknown function DUF4347 / Double zinc ribbon / : / : / Double zinc ribbon / Domain of unknown function (DUF4347) / Fn3 associated repeat / Fn3 associated / Dynein light chain, type 1/2, conserved site / Dynein light chain type 1 signature. / Dynein light chain, type 1/2 / Dynein light chain type 1 / Dynein light chain type 1 / Dynein light chain superfamily / F-box-like / F-box-like domain superfamily / SKP1 component, dimerisation / S-phase kinase-associated protein 1 / SKP1-like, dimerisation domain superfamily / Skp1 family, dimerisation domain / F-box domain / Dbl homology (DH) domain superfamily / RhoGEF domain / Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases / Dbl homology (DH) domain / Dbl homology (DH) domain profile. / S-phase kinase-associated protein 1-like / SKP1 component, POZ domain / Skp1 family, tetramerisation domain / Found in Skp1 protein family / SKP1/BTB/POZ domain superfamily / Ankyrin repeats (3 copies) / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / PH-like domain superfamily
Similarity search - Domain/homology
Dynein light chain 1, cytoplasmic / S-phase kinase-associated protein 1 / Epithelial cell-transforming sequence 2 oncogene-like / Double zinc ribbon and ankyrin repeat-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsubtomogram averaging / cryo EM / Resolution: 9.6 Å
AuthorsZhou H / Brown A
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
The Giovanni Armenise-Harvard Foundation United States
Richard and Susan Smith Family Foundation United States
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionMar 17, 2026-
Header (metadata) releaseSep 9, 2026-
Map releaseSep 9, 2026-
UpdateSep 9, 2026-
Current statusSep 9, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_76173.png

Downloads & links

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Map

FileDownload / File: emd_76173.map.gz / Format: CCP4 / Size: 43.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationA composite map of TZ linker from human airway cilia
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.92 Å/pix.
x 187 pix.
= 359.788 Å		1.92 Å/pix.
x 263 pix.
= 506.012 Å		1.92 Å/pix.
x 234 pix.
= 450.216 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 1.924 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0005
Minimum - Maximum0.0 - 0.024856986
Average (Standard dev.)0.0005679599 (±0.0019069515)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin76242137
Dimensions263234187
Spacing234263187
CellA: 450.216 Å / B: 506.012 Å / C: 359.788 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Human airway ciliary transition zone (TZ) linker

EntireName: Human airway ciliary transition zone (TZ) linker
Components
  • Organelle or cellular component: Human airway ciliary transition zone (TZ) linker
    • Protein or peptide: S-phase kinase-associated protein 1
    • Protein or peptide: Dynein light chain 1, cytoplasmic
    • Protein or peptide: Double zinc ribbon and ankyrin repeat-containing protein 1
    • Protein or peptide: Epithelial cell-transforming sequence 2 oncogene-like

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Supramolecule #1: Human airway ciliary transition zone (TZ) linker

SupramoleculeName: Human airway ciliary transition zone (TZ) linker / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #2-#4, #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Epithelial cell-transforming sequence 2 oncogene-like

MacromoleculeName: Epithelial cell-transforming sequence 2 oncogene-like / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 105.0175 KDa
SequenceString: MESFHTRFSA WTPFSNKSLN RQLFQERVAL ISHWFDLWTN KQRQEFLFAI FLRCTKSQLR FVQDWFSERM QVAKVDFSTV LPRFISLYI FSFLSPKDLC AAAQVSWPWK FLTEQDCLWM PKCVKFGWFL PYTPTDNEYG AWKRHYIACV SHLDWLTPRE A AATYGTLN ...String:
MESFHTRFSA WTPFSNKSLN RQLFQERVAL ISHWFDLWTN KQRQEFLFAI FLRCTKSQLR FVQDWFSERM QVAKVDFSTV LPRFISLYI FSFLSPKDLC AAAQVSWPWK FLTEQDCLWM PKCVKFGWFL PYTPTDNEYG AWKRHYIACV SHLDWLTPRE A AATYGTLN EPKTEDEELL ERQREKCLRK RIWEKIALRK KELFKVRPPW VSGTCCSSVL KPRCQPRLSQ TVRERVGLHE AL EKQLVLT SLETLPKRSN ISGSHSYPLL SKKNWHGVHK NDDRSSYALR PHFMLISSRI PAYEMVMESV KAGVVSVVYE HSV TLESLL YLIEKALDGQ KAQSIGIFSD GDSREINLLQ GYKIGVKNLL RPEVRDFWEK LGSYVATEEE GGHVDFFVPL GASE AGIEV LSQLSQLTGT FFTAPTGIAT GSYQHILSDW LGSQWGKAPS SIYFCESKLQ TWSSFTDFLE ETLKTVRKQL YPFFK ELQK SISGRMIGQF MFDTMGMTNI LNNQDTAQAL ADGLMELSKE DSERNVVEDN SWDTKSRLSK NDLNFEALIN LERILQ KDS AEKRARVVRE LLQSERKYVQ ILEIVRDVYV APLKAALSSN RAILSAANIQ IIFCDILQIL SLNRQFLDNL RDRLQEW GP AHCVGEIVTK FGSQLNTYTN FFNNYPVILK TIEKCREMIP AFRTFLKRHD KTIVTKMLSL PELLLYPSRR FEEYLNLL Y AVRLHTPAEH VDRGDLTTAI DQIKKYKGYI DQMKQNITMK DHLSDIQRII WGCPTLSEVN RYLIRVQDVA QLHCCDEEI SFSLRLYEHI HDLSLFLFND ALLVSSRGTS HTPFERTSKT TYQFIASVAL HRLLIENIPD SKYVKNAFIL QGPKYKWICA TEIEDDKFL WLSVLRNAIK SSMEK

UniProtKB: Epithelial cell-transforming sequence 2 oncogene-like

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Macromolecule #2: S-phase kinase-associated protein 1

MacromoleculeName: S-phase kinase-associated protein 1 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 18.679965 KDa
SequenceString:
MPSIKLQSSD GEIFEVDVEI AKQSVTIKTM LEDLGMDDEG DDDPVPLPNV NAAILKKVIQ WCTHHKDDPP PPEDDENKEK RTDDIPVWD QEFLKVDQGT LFELILAANY LDIKGLLDVT CKTVANMIKG KTPEEIRKTF NIKNDFTEEE EAQVRKENQW C EEK

UniProtKB: S-phase kinase-associated protein 1

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Macromolecule #3: Dynein light chain 1, cytoplasmic

MacromoleculeName: Dynein light chain 1, cytoplasmic / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 10.381899 KDa
SequenceString:
MCDRKAVIKN ADMSEEMQQD SVECATQALE KYNIEKDIAA HIKKEFDKKY NPTWHCIVGR NFGSYVTHET KHFIYFYLGQ VAILLFKSG

UniProtKB: Dynein light chain 1, cytoplasmic

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Macromolecule #4: Double zinc ribbon and ankyrin repeat-containing protein 1

MacromoleculeName: Double zinc ribbon and ankyrin repeat-containing protein 1
type: protein_or_peptide / ID: 4 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 82.295812 KDa
SequenceString: MTAGSVCVPQ IIPLRVPQPG KANHEIDNNT LLEMKSDTPD VNIYYTLDGS KPEFLKRIGY GENNTFKYIK PITLPDGKIQ VKAIAVSKD CRQSGIVTKV FHVDYEPPNI VSPEDNVENV LKDSSRQEFK NGFVGSKLKK KYKNSENQRS WNVNLRKFPE S PLEIPAYG ...String:
MTAGSVCVPQ IIPLRVPQPG KANHEIDNNT LLEMKSDTPD VNIYYTLDGS KPEFLKRIGY GENNTFKYIK PITLPDGKIQ VKAIAVSKD CRQSGIVTKV FHVDYEPPNI VSPEDNVENV LKDSSRQEFK NGFVGSKLKK KYKNSENQRS WNVNLRKFPE S PLEIPAYG GGSGSRPPTR QSQSPGFAHV SGQKCLTSTE IMRIQRETDF LKCAHCLAPR PSDPFARFCQ ECGSPVPPIF GC RLPPPEG AQMGLCAECR SLVPMNTPIC VVCEAPLALQ LQPQASLHLK EKVICRACGT GNPAHLRYCV TCEGALPSSQ ESM CSGDKA PPPPTQKGGT ISCYRCGRWN LWEASFCGWC GAMLGIPAGC SVCPKCGASN HLSARFCGSC GICVKSLVKL SLDR SLALA AEEPRPFSES LNIPLPRSDV GTKRDIGTQT VGLFYPSGKL LAKKEQELAS QKQRQEKMSD HKPLLTAISP GRGYW RRQL DHISAHLRCY AQNNPEFRAL IAEPRMGKLI SATVHEDGCE VSIRLNYSQV SNKNLYLNKA VNFSDHLLSS AAEGDG GLC GSRSSWVSDY SQSTSDTIEK IKRIKNFKTK TFQEKKEQLI PENRLLLKEV GPTGEGRVSV IEQLLDEGAD PNCCDED NR PVITVAVMNK HHEAIPVLVQ RGADIDQQWG PLRNTALHEA TLLGLAGRES TATLLGCNAS IQKKNAGGQT AYDLALNT G DDLVTSLFAA KFGQGLEDQL AQTRSLSLDD C

UniProtKB: Double zinc ribbon and ankyrin repeat-containing protein 1

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

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Sample preparation

BufferpH: 7.2
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: 4.68 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.0 µm / Nominal defocus min: 2.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 9.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5)
Details: The deposited volume is a composite map. The general TZ linker was refined to 9.6 using 12,237 subtomograms. The main part of TZ linker was refined to 8.1 using 6,373 subtomograms. The ...Details: The deposited volume is a composite map. The general TZ linker was refined to 9.6 using 12,237 subtomograms. The main part of TZ linker was refined to 8.1 using 6,373 subtomograms. The region of TZ linker interacting with A tubule was refined to 6.9 using 10,395 subtomograms. The region of TZ linker interacting with B tubule was refined to 7.0 using 12,780 subtomograms.
Number subtomograms used: 12237
ExtractionNumber tomograms: 209 / Number images used: 66385 / Software - Name: Warp (ver. 2)
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Final angle assignmentType: MAXIMUM LIKELIHOOD

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