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- EMDB-49474: Honeybee silk hetereotetramer coiled coil -

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Basic information

Entry
Database: EMDB / ID: EMD-49474
TitleHoneybee silk hetereotetramer coiled coil
Map dataMap of honeybee silk heterotetrametric coiled coil
Sample
  • Complex: Honeybee silk heterotetrametric coiled coil
    • Other: Honeybee silk heterotetrametric coiled coil
KeywordsSilk / Coiled-coil / STRUCTURAL PROTEIN
Biological speciesApis melifera (honey bee) / Apis mellifera (honey bee)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsJohnston CL / Jobichen C
Funding support Australia, 1 items
OrganizationGrant numberCountry
Commonwealth Scientific and Industrial Research Organisation (CSIRO) Australia
CitationJournal: Protein Sci / Year: 2025
Title: Resolving the structure and assembly of the honeybee silk heterotetrameric coiled coil.
Authors: Caitlin L Johnston / Chacko Jobichen / Lyndall J Briggs / Michelle Michie / Jian-Wei Liu / Craig J Morton / Andrew C Warden / Tara D Sutherland /
Abstract: Coiled coil structures, first proposed by Crick in the 1950s, are protein structural motifs found across diverse biological systems. Honeybee silk was among the earliest identified coiled coils, with ...Coiled coil structures, first proposed by Crick in the 1950s, are protein structural motifs found across diverse biological systems. Honeybee silk was among the earliest identified coiled coils, with X-ray diffraction studies in the 1960s revealing its characteristic helical packing. Decades of research have provided insights into silk composition and formation, yet the molecular details of its coiled coil assembly and final structure remained unresolved. In this study, we generated a structural model of the tetrameric coiled coil using AlphaFold and validated it with crosslinking mass spectrometry and medium-resolution cryo-electron microscopy. The model reveals that the four proteins (F1-F4) adopt an antiparallel configuration in a defined clockwise arrangement (F1-F3-F2-F4). Furthermore, we experimentally investigated the formation of this coiled coil complex using biochemical techniques, including blue-native PAGE and circular dichroism spectroscopy. The sum of these experimental results and the structural predictions has allowed for the elucidation of key transitional steps in the assembly pathway, suggesting molecular interactions that may drive tetramer formation. These findings support a stepwise assembly model in which F2 and F4 form a stable core, F3 binds to the complex, and F1 initiates formation of the final, highly ordered structure. These structural insights establish a framework for understanding and directing coiled coil assembly, the fundamental building block of honeybee silk. By resolving this structure and its assembly process, this work lays the foundation for future rational design of functional sequences and materials with tailored properties.
History
DepositionFeb 26, 2025-
Header (metadata) releaseJan 28, 2026-
Map releaseJan 28, 2026-
UpdateJan 28, 2026-
Current statusJan 28, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49474.png

Downloads & links

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Map

FileDownload / File: emd_49474.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMap of honeybee silk heterotetrametric coiled coil
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1 Å/pix.
x 256 pix.
= 254.976 Å		1 Å/pix.
x 256 pix.
= 254.976 Å		1 Å/pix.
x 256 pix.
= 254.976 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.996 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0327
Minimum - Maximum-0.39697343 - 1.3023292
Average (Standard dev.)0.0006917356 (±0.010495229)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 254.976 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map of honeybee silk heterotetrametric coiled coil

Fileemd_49474_half_map_1.map
AnnotationHalf map of honeybee silk heterotetrametric coiled coil
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map of honeybee silk heterotetrametric coiled coil

Fileemd_49474_half_map_2.map
AnnotationHalf map of honeybee silk heterotetrametric coiled coil
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Honeybee silk heterotetrametric coiled coil

EntireName: Honeybee silk heterotetrametric coiled coil
Components
  • Complex: Honeybee silk heterotetrametric coiled coil
    • Other: Honeybee silk heterotetrametric coiled coil

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Supramolecule #1: Honeybee silk heterotetrametric coiled coil

SupramoleculeName: Honeybee silk heterotetrametric coiled coil / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Apis melifera (honey bee)

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Macromolecule #1: Honeybee silk heterotetrametric coiled coil

MacromoleculeName: Honeybee silk heterotetrametric coiled coil / type: other / ID: 1 / Classification: other
Source (natural)Organism: Apis mellifera (honey bee)
SequenceString: MGLEGSGNSL PELVKGSASA TASTAVTARS GLRAGQVALA SQKDAVLQAE AAASAASEAR AAADLTAKLS QESASVQSQA AAKGKETEEA AVGQARAGLE SVSIAASATS AAKEASTAAK TAASALSTAT VQAKIAERAA KAEAVASEEA KVKAIAAANL AAAASAAAEA ...String:
MGLEGSGNSL PELVKGSASA TASTAVTARS GLRAGQVALA SQKDAVLQAE AAASAASEAR AAADLTAKLS QESASVQSQA AAKGKETEEA AVGQARAGLE SVSIAASATS AAKEASTAAK TAASALSTAT VQAKIAERAA KAEAVASEEA KVKAIAAANL AAAASAAAEA ALKAEKVAEE AIARAASAKA AARAAAAALA SSKEAATASA RNAAESEARN EVAVLIAEID KKSREIDAAT SLNARAAAKA SSRNVETATI GANIDSSKQV VSIPVEIKKF PEPELSTSWR EDEEVTKGKK EDINLNGF R VINHESLKTS EDIQGGYSAG IVGDGSDALG SSIENAQKVA RAAENVGLNL ELGAGARAAS VAAAAQAKNT EAAEAGANAA LAAAIAKREE AIKASEIANQ LLTNAAKAAE ATVSATKRAA QLTAAAKEAT RASAAAAEAA TEAQVKANAD SIITKRAAIA EAQAAAEAQV KAAIARKSAA NFLAKAQIAA AAESEATKLA AEAVVALTNA EVAVNQARNA QANASTQASM AVRVDSQAAN AEAAAVAQAE TLLVTAEAVA AAEAEVANKA ATFAKQIVNE KKIHVAKLE GVEEFKSSAT EEVISKNLEV DLLKNVDTSA KRRENGAPVL GKNTLQSLEK IKTSASVNAK AAAVVKASAL ALAEAYLRAS ALSAAASAKA AAALKNAQQA QLNAQEKSLA ALKAQSEEEA ASARANAATA ATQSALERAQ ASSRLATVAQ NVASDLQKRT STKAAAEAAA TLRQLQDAER TKWSANAALE VSAAAAAAET KTTASSEAAN AAAKKAAAIA SDADGAERSA STEAQSAAKI ESVAAAEGSA NSASEDSRAA QLEASTAARA NVAAAVGDGA IIGLGEEAGA AAQLLAQAKA LAEVSSKSEN IEDKKF ARE EVETRDKTKT STVVKSEKVE VVAPAKDELK LTSEPIFGRR VGTGASEVAS SSGEAIAISL GAGQSAAESQ ALAASQSKTA ANAAIGASEL TNKVAALVAG ATGAQARATA ASSSALKASL ATEEAAEEAE AAVADAKAAA EKAESLAKNL ASASARAALS SERANELAQA ESAAAAEAQA KTAAAAKAAE IALKVAEIAV KAEADAAAAA VAAAKARAVA DAAAARAAAV NAIAKAEEEA SAQAENAAGV LQAAASAAAE SRAAAAAAAA TSEAAAEAGP LAGEMKPPHW KWERIPVKKE EWKTSTKEEW KTTNEEWEVK
Recombinant expressionOrganism: Escherichia coli (E. coli)

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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
GridModel: UltrAuFoil R1.2/1.3 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeJEOL CRYO ARM 200
Image recordingFilm or detector model: DIRECT ELECTRON DE-64 (8k x 8k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm

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Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. 4.5.3) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.5.3) / Number images used: 38205
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC (ver. 4.5.3)
Final angle assignmentType: PROJECTION MATCHING

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