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- EMDB-51984: Bovine collagen VI local refinement of C-terminal region -

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Basic information

Entry
Database: EMDB / ID: EMD-51984
TitleBovine collagen VI local refinement of C-terminal region
Map datamain map from cryoSPARC local refinement of the C terminal region of bovine collagen VI sharpened to the GSFSC
Sample
  • Complex: Collagen VI microfibrils isolated from bovine cornea
    • Protein or peptide: Collagen type VI alpha 1 chain
    • Protein or peptide: Collagen type VI alpha 2 chain
  • Protein or peptide: Collagen type VI alpha 3 chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsCollagen / Col6A1 / Col6A2 / Col6A3 / triple-helix / bovine / microfibril / ECM / extracellular / matrix / fibril / STRUCTURAL PROTEIN
Function / homology
Function and homology information


Collagen chain trimerization / Collagen biosynthesis and modifying enzymes / Signaling by PDGF / Assembly of collagen fibrils and other multimeric structures / Integrin cell surface interactions / ECM proteoglycans / Collagen degradation / collagen trimer / response to UV / collagen binding ...Collagen chain trimerization / Collagen biosynthesis and modifying enzymes / Signaling by PDGF / Assembly of collagen fibrils and other multimeric structures / Integrin cell surface interactions / ECM proteoglycans / Collagen degradation / collagen trimer / response to UV / collagen binding / extracellular matrix / phosphatidylinositol 3-kinase/protein kinase B signal transduction / serine-type endopeptidase inhibitor activity / sarcolemma / : / neuron apoptotic process / cell adhesion / protein-containing complex / extracellular region
Similarity search - Function
: / Collagen alpha-3(VI) chain, vWA domain / : / Collagen triple helix repeat / Collagen triple helix repeat (20 copies) / von Willebrand factor type A domain / Proteinase inhibitor I2, Kunitz, conserved site / Pancreatic trypsin inhibitor (Kunitz) family signature. / BPTI/Kunitz family of serine protease inhibitors. / Pancreatic trypsin inhibitor Kunitz domain ...: / Collagen alpha-3(VI) chain, vWA domain / : / Collagen triple helix repeat / Collagen triple helix repeat (20 copies) / von Willebrand factor type A domain / Proteinase inhibitor I2, Kunitz, conserved site / Pancreatic trypsin inhibitor (Kunitz) family signature. / BPTI/Kunitz family of serine protease inhibitors. / Pancreatic trypsin inhibitor Kunitz domain / Kunitz/Bovine pancreatic trypsin inhibitor domain / Pancreatic trypsin inhibitor (Kunitz) family profile. / Pancreatic trypsin inhibitor Kunitz domain superfamily / VWFA domain profile. / von Willebrand factor (vWF) type A domain / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily / Fibronectin type III domain / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Collagen type VI alpha 3 chain / Collagen alpha-2(VI) chain / Collagen alpha-1(VI) chain
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.33 Å
AuthorsGodwin A / Snee M / Roseman A / Baldock C
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC) United Kingdom
CitationJournal: Nat Commun / Year: 2025
Title: Collagen VI microfibril structure reveals mechanism for molecular assembly and clustering of inherited pathogenic mutations
Authors: Godwin A / Snee M / Becker M / Dajani R / Collins R / Roseman A / Baldock C
History
DepositionNov 4, 2024-
Header (metadata) releaseAug 20, 2025-
Map releaseAug 20, 2025-
UpdateAug 20, 2025-
Current statusAug 20, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51984.png

Downloads & links

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Map

FileDownload / File: emd_51984.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmain map from cryoSPARC local refinement of the C terminal region of bovine collagen VI sharpened to the GSFSC
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.66 Å/pix.
x 256 pix.
= 424.448 Å		1.66 Å/pix.
x 256 pix.
= 424.448 Å		1.66 Å/pix.
x 256 pix.
= 424.448 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.658 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.686
Minimum - Maximum-3.157608 - 4.063454
Average (Standard dev.)0.0017126048 (±0.08189459)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 424.448 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_51984_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B from cryoSPARC local refinement of...

Fileemd_51984_half_map_1.map
AnnotationHalf map B from cryoSPARC local refinement of the C terminal region of bovine collagen VI
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A from cryoSPARC local refinement of...

Fileemd_51984_half_map_2.map
AnnotationHalf map A from cryoSPARC local refinement of the C terminal region of bovine collagen VI
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Collagen VI microfibrils isolated from bovine cornea

EntireName: Collagen VI microfibrils isolated from bovine cornea
Components
  • Complex: Collagen VI microfibrils isolated from bovine cornea
    • Protein or peptide: Collagen type VI alpha 1 chain
    • Protein or peptide: Collagen type VI alpha 2 chain
  • Protein or peptide: Collagen type VI alpha 3 chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Collagen VI microfibrils isolated from bovine cornea

SupramoleculeName: Collagen VI microfibrils isolated from bovine cornea / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #2-#3
Details: This structure is a local refinement of the C terminal region of the bead structure from bovine collagen VI
Source (natural)Organism: Bos taurus (domestic cattle)

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Macromolecule #1: Collagen type VI alpha 3 chain

MacromoleculeName: Collagen type VI alpha 3 chain / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (domestic cattle)
Molecular weightTheoretical: 330.562562 KDa
SequenceString: MRKHRHLPLV AILCLFFSGF SFTRGQQQPE NYTSLHDIVG NLVACVRSSM APERAGGTEI PKDITAQDSA DIIFLIDGSN NTGSVNFAV ILDFLVNLLE RLSIGTQQIR VGVVQYSDEP RTMFSLNSYS TKAQVLDAVK ALGFIGGELA NVGLALDFVV E NHFTRAGG ...String:
MRKHRHLPLV AILCLFFSGF SFTRGQQQPE NYTSLHDIVG NLVACVRSSM APERAGGTEI PKDITAQDSA DIIFLIDGSN NTGSVNFAV ILDFLVNLLE RLSIGTQQIR VGVVQYSDEP RTMFSLNSYS TKAQVLDAVK ALGFIGGELA NVGLALDFVV E NHFTRAGG SRAEEGVPQV LVLISAGPSS DEIRDGVVAL KQASVFSFGL GAQAASKAEL QHIATNDNLV FTVPEFRSLG DV QEQLLPY IVGVAQRHIV LQPPTIVTQV IEVNKRDIVF LVDGSSKLGL TNFNAIRDFI AKVIQRLEIR QDLIQVAVAQ YAD TVRPEF YFNTYPSKRE VINAVRKMKA LDGSALYTGS ALDFVRNNLF TEAAGYRAAE GVPKLLVLVT GGKSLDAVSQ PAQE LKRSG ILAFAVGNKV ADQAELEEIA FDSSLVFTAT EFRPAPLQGV LPGLLGPLRT LTGTTEVRVN KRDIIFLLDG SSNVG ETNF PYVRDFVMNL VNSLDVGSDH IRVGLVQFSD TPVTEFSLNT YPTKSELLAH LRQMQLQGGS VLNTGAALSY VHANHF TEA GGSRIQDHVP QLLLLLTAGQ SEDSYLQAAN ALARAGILTF CVGTSQADRA ELEEIAFNPG LVYLMDDFSS LPALPQQ LI QPLTTYVSGG VEEVPLAQPE SKRDILFLFD GSANLMGQFT AARDFLYKVI DELDVKPEGT RVAVAQFSDD VKVESRFD Q HQNKPEILNL VKRMKLKTGK ALNLGYALDY AQRYIFVKSA GSRIEDGVLQ FLVLLVAGKS SDRVDTPALN LKQSGVVPF ILQAKNADPA ELELIVPSPA FILVAESLPK IGDLQPQIVN LLKSVQNGAP APVSVEKDVV FLIDGSEGVR SGFPLLKEFV QRVVESLDV GPDRVRVAVV QYSDRTRPEF YLNSYMDQQS VVGAIRGLTL LGGPAPNTGA ALEFVLRNIL VGSAGSRIAE G VPQLLIVL TADRSGDDVR GPSVVLRRGG AVPIGIGIGN ADITEMQTLS FVPDFAVVIP TFRQLGTIQQ VISERVTQLS RE ELSRLQA SVTPLTTPVV SSKRDVVFLI DGSQSAGPEF QYIRTLIERL VDYLDVGFDT TRVAVIQFSD DPRVEFLLNV HSS KDEVQN AVRRLRPKGG RQVNVGGALE YVARNIFKRP LGSRIEEGVP QFLVLISSGK SDDEVEDSAI ELKQFGVAPL TIAR NVDQE ELVKISLSPE YVFSVNTFRE LPSLEQKLLT PLTTLTAGQI QQLLASTRYP PPAVESDAAD IVFLIDSSDG VKPDG IAHI RDFVIRIVRR LNVGPNKVRI GVLQFSNDVF PEFQLKTYKS QASVLDAIRR LRFKGGSPLN TGKALEFVAR NYFVKS AGS RIEDGVPQHL VLFLGGKSQD DISRYSQVIK SAGIASLGVG DRNIDRTELQ TITSDPRLVF TVREFRDLPS IEERMVN SF GSSGVTPAPP GVDTPSPSRP EKKKADIVFL LDGSINFRRD SFQEVLRFVS EIVDTVYEGG DSIQVGLVQY NSDPTDEF F LKDFPTKQQI IDAINKVVYK GGRHANTKVG LEHLRRNHFV PEAGSRLDQR VPQIAFVITG GKSVEDAQEA SMALTQRGV KVFAVGVRNI DSEEVGKIAS NSATAFRVGN VQELSELSEQ VLETLHDAMH ETLCPGVTDV SKACNLDVIL GFDGSGDQNV FVAQKGLEP KVDTILRRIS QMQKISCSGS QLPTVRVSVV ALTPSGPVEA FDFAEYQPEL FEKFQNMRAQ HPYVLTADTL K LYQNKFRQ ASMDNVKVVI HFTDGVDGDL ADLQRASEEL RQEGVRALIL VGLERVANLE QLMQLEFGRG FTYNRPLRLN LL DLDYELA EQLDNIAEKA CCGIPCKCSG QRGDRGPIGS IGPKGIPGED GYRGYPGDEG GPGERGPPGV NGTQGFQGCP GQR GVKGSR GFPGEKGELG EIGLDGLDGE DGDKGLPGTS GEKGSPGRRG DKGPKGDKGE RGDVGIRGDP GNSGQDSQQR GAKG ETGDI GPVGLPGRDG VSGGPGEPGK SGGFGRRGPA GAKGNQGGPG QQGPVGEQGT RGAQGPPGPT GPPGLIGEQG IPGPR GGGG TAGAPGERGR TGPLGRKGEP GDPGPKGSIG NRGPRGETGD DGRDGVGSEG RIGKKGERGF PGYPGPKGNP GEPGTD GPP GPKGIRGRRG NSGPPGIAGQ KGDPGYPGPS GYKGSRGDSM DQCALVQSIK DKCPCCYGPL ECPVFPTELA FALDTSE GV TQDRFSQMRE VVLKILDDLT IAESNCPRGA RVAVVTYNNE VTTEIRFADS KKKSVLLDKI KNLQVSLTSK QQSLETAM S FVARNTFKRV RSGFLMRKVA VFFSNKPTRA TPQLREAVLK LSDAGITPLF LTSQEDRQLI NALQINNTAV GHALVLPAG GDLTDFLKNV LTCHVCLDIC NIDPSCGFGS WRPSFRDRRA AGSDVDIDMA FILDSSESTT PFQFNEMRKY IEYLVRQLDV SPDPKASQH FARVAVVQHA PYEAVDNASV PPVKVEFSLT DYGSKEKLLA FLGSRMTQLQ GTRALGRAID YTIENIFESA P NPRDLKIV VLMLTGEVQK QQLEEAQRAI LQAKCKGYFF VILGIGRKVN VKELYSSASE PNDVFFKLVD KSTELNEEPL MR FGRLLPS FVSSKDAFYL SPDIRKQCDW FQADQPAKNL VQFGYKQINV PNNVTSSPTS KLVTTTKPVI TTTKPITVVN LPA SKPAAT RPVDERPAAG RSVATKMDSA RPVATKTEAT KPVATKTEAT KTEAAKPVVT KAEAAKPTAT KTEATKTEAA KLMA TKTEA TKPVAARPEA AKTATARPAA AAKPAAAKPA PARPPTAARS MATRSEAPRP QAVKLAASRP GAAKPVVKAP REIHV SEVT ENSAKLHWER PEPPSPYLYN LTVTSAHDQA VVLKQNLTVT DRVIGGLLPG QTYHVTVTCS LRSQVRAIYQ GSFSTK KIQ PPPPQTERSA SSATINLVVS ADRLAGSKAD ICKLPKDGGT CREFVLKWYY DSVTENCARF WYGGCGGNEN RFNSQDE CE KVCPPVPIKQ PGVIAAMGT

UniProtKB: Collagen type VI alpha 3 chain

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Macromolecule #2: Collagen type VI alpha 1 chain

MacromoleculeName: Collagen type VI alpha 1 chain / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (domestic cattle)
Molecular weightTheoretical: 108.800656 KDa
SequenceString: MRLPRALLPL LLQACWASAQ DDPVASRAIA FQDCPVDLFF VLDTSESVAL RLKPYGALVD KVKSFTKRFI DNLNDRYYRC DRNLVWNAG ALHYSDEVEI IRGLTRMPSG RDELKSSVDA VKYFGKGTYT DCAIKKGLEE LLVGGSHLKE NKYLVVVTDG H PLEGYKEP ...String:
MRLPRALLPL LLQACWASAQ DDPVASRAIA FQDCPVDLFF VLDTSESVAL RLKPYGALVD KVKSFTKRFI DNLNDRYYRC DRNLVWNAG ALHYSDEVEI IRGLTRMPSG RDELKSSVDA VKYFGKGTYT DCAIKKGLEE LLVGGSHLKE NKYLVVVTDG H PLEGYKEP CGGLEDAVNE AKHLGIKVFS VAITPDHLEP RLSIIATDHT YRRNFTAADW GQSRDAEEVI SQTIDTITDM IK NNVEQVC CSFECQPARG PPGPRGDPGY EGERGKPGLP GEKGEAGDPG RPGDLGPVGY QGMKGEKGSR GEKGSRGPKG YKG EKGKRG MDGVDGMKGE TGFPGLPGCK GSPGFDGIQG PPGPKGDPGA FGLKGQKGEP GADGEPGRPG STGPPGDEGE PGEP GPPGE KGEAGDEGNA GPDGAPGERG GPGERGPRGT PGARGPRGDP GEAGPQGDQG REGPVGVPGD PGEAGPIGPK GYRGD EGPP GTEGPKGAPG PAGPPGDPGL MGERGEDGPP GNGTEGFPGF PGYPGSRGPP GINGTKGYPG LKGDEGEAGD PGEDNN DIA ARGAKGAKGY RGPEGPQGPP GHVGPPGPDE CEILDIIMKM CSCCECKCGP IDILFVLDSS ESIGLQNFEI AKDFIVK VI DRLSKDELVK FEPGQSHAGV VQYSHNQMQE HVDLRDPNIR NAQDLKEAIK KLQWMGGGTF TGEALQYTRS RLLPPTPN N RIALVITDGR SDTQRDTTPL SVLCGPDIQV VSVGIKDVFG LAAGSDQLNV ISCQGLAPQG RPGISLVKEN YAELLDDGF LKNITAQICI DKKCPDYSCP ITFSSPADIT ILLDGSASVG SHNFDITKRF AKRLAERFLT ASRTDPGQDV RVAVVQYSGT GQQRPERAA LQFLQNYTVL ANTVDSMDFF NDATDVMDAL GYVTRFYREA SSNAAKKRLL LFSDGNSQGA TPAAIEKAVQ E AQRAGVEI FAVVVGRQVN EPHVRVLVTG KAAEYDVVFG ERHLFRVPSY QALLRGVFYQ TVSRKVALD

UniProtKB: Collagen alpha-1(VI) chain

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Macromolecule #3: Collagen type VI alpha 2 chain

MacromoleculeName: Collagen type VI alpha 2 chain / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (domestic cattle)
Molecular weightTheoretical: 109.477688 KDa
SequenceString: MLRRKGAAKM LRSPCSALLL WGLLGAVHAQ QQEVISPGPS DRNSCPEKAD CPVHVYFVLD TSESITMQSP TDSLLYHMQQ FVLQFISQL QDELYLDQVA LSWRYGGLHF SDLVEVFSPP GSDRASFTKS LQSISSFRRG TFTDCMLANM TQEVRRHVGK G VVNFAVVI ...String:
MLRRKGAAKM LRSPCSALLL WGLLGAVHAQ QQEVISPGPS DRNSCPEKAD CPVHVYFVLD TSESITMQSP TDSLLYHMQQ FVLQFISQL QDELYLDQVA LSWRYGGLHF SDLVEVFSPP GSDRASFTKS LQSISSFRRG TFTDCMLANM TQEVRRHVGK G VVNFAVVI TDGHVTGSPC GGIKLQAERA REEGIRLFAV PPNLKLNEQG LRDIANTPHE LYRNNYATMR PDSTEIDQDT IN RIIKVMK HEAYGECYKV SCLEIPGPPG PKGYRGQKGA KGNMGEPGEP GQKGRQGDPG IEGPIGFPGP KGVPGFKGEK GEF GADGRK GAPGLAGKNG TDGQKGKLGR IGPPGCKGDT GDRGPDGYVG EAGSPGERGD QGSKGDPGRP GRRGPPGENG AKGS KGYQG NNGAPGSPGL KGAKGGPGPR GPKGEPGRRG DPGTKGGPGS DGPKGEKGDP GPEGPRGLAG EVGNKGAKAN RGLPG PRGP QGTVGEPGKQ GSRGDPGDAG PRGDSGQPGP KGDPGRPGFS YPGPRGAPGD KGEPGPPGPE GGRGDFGSKG EPGRKG QKG EPADPGPPGE PGPRGQRGAP GPEGEPGPPG DPGLTECDVM TYVRETCGCC DCEKRCGALD VVFVIDSSES IGYTNFT LE KNFVINVVNR LGAIAKDPKS ETGTRVGVVQ YSHEGTFEAI QLDDERIDSL SSFKEAVKNL EWIAGGTWTP SALKFAYN K LIKESRRQKT RVFAVVITDG RHDPRDDDLN LRALCNHEVT VTAIGIGDMF HEKHESENLY SIACDKPQQV RNMTLFSDL VAEKFIDDME DVLCPDPQIV CPDLPCQTEL YVAQCTQRPV DIVFLLDGSE RLGEQNFHKV RRFVEEVSRR LTLARKDDDP LNARVALLQ FGGPREQQVA FPLTSNLTVI QEALASARYL NSFSHVGTGI VQAINQVVQG ARAGARRHAE LSFVFLTDGV T GNDSLDEA VHSMRKQNVV PTVVAVGSDV DTDVLSKISL GDPAAVFREK DYDSLAQPGF FDRFIRWIC

UniProtKB: Collagen alpha-2(VI) chain

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Macromolecule #7: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 7 / Number of copies: 2 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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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 / Details: 20 mM Tris-HCL, 400 mM NaCl, 2.5 mM CaCl2
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 29595 / Average exposure time: 2.3 sec. / Average electron dose: 22.165 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.75 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1011458
CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL / In silico model: cryoSPARC ab initio model
Final reconstructionNumber classes used: 1 / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 4.33 Å / Resolution method: FSC 0.143 CUT-OFF / Details: Symmetry expanded particles / Number images used: 175682
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC / Details: cryoSPARC refinement
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC / Details: cryoSPARC local refinement
FSC plot (resolution estimation)

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