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- EMDB-51567: Collagen VI alpha 1, 2, 3 heterotrimer recombinant C terminal reg... -

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Basic information

Entry
Database: EMDB / ID: EMD-51567
TitleCollagen VI alpha 1, 2, 3 heterotrimer recombinant C terminal region. Local refinement.
Map dataMap produced from Cryosparc local refinement filtered at the gold-standard FSC
Sample
  • Complex: Subcomplex of Collagen 6 alpha 2 C2 domain with Collagen 6 alpha 3 C1 and C2 domains, and the coiled coil formed from ALpha 1,2,3
    • Protein or peptide: Collagen alpha-3(VI) chain
    • Protein or peptide: Collagen alpha-2(VI) chain
    • Protein or peptide: Collagen alpha-1(VI) chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: water
Keywordsextracellular / matrix / collagen / co6A1 / co6A2 / co6A3 / von willebrand / von-willebrand / coiled-coil / ECM / double-bead / structural / microfibril / Bethlem myopathy / Ullrich congenital muscular dystrophy / STRUCTURAL PROTEIN
Function / homology
Function and homology information


response to polyamine macromolecule / response to bleomycin / regulation of collagen fibril organization / muscle cell apoptotic process / collagen type VI trimer / multicellular organismal locomotion / muscle system process / apoptotic nuclear changes / caveola assembly / limb joint morphogenesis ...response to polyamine macromolecule / response to bleomycin / regulation of collagen fibril organization / muscle cell apoptotic process / collagen type VI trimer / multicellular organismal locomotion / muscle system process / apoptotic nuclear changes / caveola assembly / limb joint morphogenesis / reduction of food intake in response to dietary excess / mitochondrial transmembrane transport / skeletal muscle tissue growth / fat cell proliferation / extracellular matrix assembly / Collagen chain trimerization / response to decreased oxygen levels / extracellular matrix structural constituent conferring tensile strength / platelet-derived growth factor binding / response to peptide / tissue remodeling / skeletal muscle fiber differentiation / lung epithelial cell differentiation / Collagen biosynthesis and modifying enzymes / basement membrane organization / sensory perception of mechanical stimulus / collagen metabolic process / Signaling by PDGF / mitochondrial depolarization / energy reserve metabolic process / skeletal muscle tissue regeneration / myelination in peripheral nervous system / 2-oxoglutarate metabolic process / respiratory system process / NCAM1 interactions / cartilage development / collagen fibril organization / Assembly of collagen fibrils and other multimeric structures / response to pain / lung alveolus development / muscle organ development / regulation of cell size / bone mineralization / response to muscle activity / intracellular vesicle / endodermal cell differentiation / myofibril / lung morphogenesis / transmission of nerve impulse / uterus development / Collagen degradation / basement membrane / homeostasis of number of cells / hair follicle development / ECM proteoglycans / Integrin cell surface interactions / canonical Wnt signaling pathway / adipose tissue development / response to mechanical stimulus / single fertilization / response to glucose / response to UV / skeletal muscle fiber development / collagen binding / tricarboxylic acid cycle / extracellular matrix / insulin-like growth factor receptor signaling pathway / reactive oxygen species metabolic process / sarcoplasmic reticulum / response to reactive oxygen species / glycolytic process / mitochondrion organization / protein tetramerization / cellular response to amino acid stimulus / phosphatidylinositol 3-kinase/protein kinase B signal transduction / serine-type endopeptidase inhibitor activity / sarcolemma / circadian rhythm / bone development / response to toxic substance / autophagy / response to wounding / cell morphogenesis / osteoblast differentiation / insulin receptor signaling pathway / extracellular vesicle / : / heart development / neuron apoptotic process / response to lipopolysaccharide / gene expression / cell adhesion / inflammatory response / response to xenobiotic stimulus / endoplasmic reticulum lumen / lysosomal membrane / protein-containing complex / mitochondrion / extracellular space / extracellular exosome
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 profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Collagen alpha-1(VI) chain / Collagen alpha-2(VI) chain / Collagen alpha-3(VI) chain
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.14 Å
AuthorsGodwin A / Snee M / Dajani R / Becker 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
DepositionSep 18, 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_51567.png

Downloads & links

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Map

FileDownload / File: emd_51567.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMap produced from Cryosparc local refinement filtered at the gold-standard FSC
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.3 Å/pix.
x 200 pix.
= 260.4 Å		1.3 Å/pix.
x 200 pix.
= 260.4 Å		1.3 Å/pix.
x 200 pix.
= 260.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.302 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.242
Minimum - Maximum-1.0967467 - 1.9394765
Average (Standard dev.)-0.001373866 (±0.030879164)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 260.40002 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_51567_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Locally filtered map from cryosparc local filtering FSC=0.143

Fileemd_51567_additional_1.map
AnnotationLocally filtered map from cryosparc local filtering FSC=0.143
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map (B) produced from Cryosparc local refinement

Fileemd_51567_half_map_1.map
AnnotationHalf map (B) produced from Cryosparc local refinement
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map (A) produced from Cryosparc local refinement

Fileemd_51567_half_map_2.map
AnnotationHalf map (A) produced from Cryosparc local refinement
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram

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Sample components

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Entire : Subcomplex of Collagen 6 alpha 2 C2 domain with Collagen 6 alpha ...

EntireName: Subcomplex of Collagen 6 alpha 2 C2 domain with Collagen 6 alpha 3 C1 and C2 domains, and the coiled coil formed from ALpha 1,2,3
Components
  • Complex: Subcomplex of Collagen 6 alpha 2 C2 domain with Collagen 6 alpha 3 C1 and C2 domains, and the coiled coil formed from ALpha 1,2,3
    • Protein or peptide: Collagen alpha-3(VI) chain
    • Protein or peptide: Collagen alpha-2(VI) chain
    • Protein or peptide: Collagen alpha-1(VI) chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: water

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Supramolecule #1: Subcomplex of Collagen 6 alpha 2 C2 domain with Collagen 6 alpha ...

SupramoleculeName: Subcomplex of Collagen 6 alpha 2 C2 domain with Collagen 6 alpha 3 C1 and C2 domains, and the coiled coil formed from ALpha 1,2,3
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Details: C terminal regions of collagen 6 alpha 1,2,3 were expressed including some collagenous region, the coiled-coil region and the C1 and C2 von willebrand domains. Alpha 2 C2, alpha 3 C1,C2 and ...Details: C terminal regions of collagen 6 alpha 1,2,3 were expressed including some collagenous region, the coiled-coil region and the C1 and C2 von willebrand domains. Alpha 2 C2, alpha 3 C1,C2 and the coiled coil are resolved as a globular subcomplex with the other domains observed as flexible without the constraining effect of the full microfibril.
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Collagen alpha-3(VI) chain

MacromoleculeName: Collagen alpha-3(VI) chain / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 53.947332 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DYKDDDDKGG GGSGGGGSGP PGIVGQKGRP GYPGPAGPRG NRGDSIDQCA LIQSIKDKCP CCYGPLECPV FPTELAFALD TSEGVNQDT FGRMRDVVLS IVNVLTIAES NCPTGARVAV VTYNNEVTTE IRFADSKRKS VLLDKIKNLQ VALTSKQQSL E TAMSFVAR ...String:
DYKDDDDKGG GGSGGGGSGP PGIVGQKGRP GYPGPAGPRG NRGDSIDQCA LIQSIKDKCP CCYGPLECPV FPTELAFALD TSEGVNQDT FGRMRDVVLS IVNVLTIAES NCPTGARVAV VTYNNEVTTE IRFADSKRKS VLLDKIKNLQ VALTSKQQSL E TAMSFVAR NTFKRVRNGF LMRKVAVFFS NTPTRASPQL REAVLKLSDA GITPLFLTRQ EDRQLINALQ INNTAVGHAL VL PAGRDLT DFLENVLTCH VCLDICNIDP SCGFGSWRPS FRDAAAAGSD VDIDMAFILD SAETTTLFQF NEMKKYIAYL VRQ LDMSPD PKASQHFARV AVVQHAPSES VDNASMPPVK VEFSLTDYGS KEKLVDFLSR GMTQLQGTRA LGSAIEYTIE NVFE SAPNP RDLKIVVLML TGEVPEQQLE EAQRVILQAK CKGYFFVVLG IGRKVNIKEV YTFASEPNDV FFKLVDKSTE LNEEP LMRF GRLLPSFV

UniProtKB: Collagen alpha-3(VI) chain

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Macromolecule #2: Collagen alpha-2(VI) chain

MacromoleculeName: Collagen alpha-2(VI) chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 52.290398 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: SAWSHPQFEK GGGGSGGGGS GEPGPRGPRG VPGPEGEPGP PGDPGLTECD VMTYVRETCG CCDCEKRCGA LDVVFVIDSS ESIGYTNFT LEKNFVINVV NRLGAIAKDP KSETGTRVGV VQYSHEGTFE AIQLDDEHID SLSSFKEAVK NLEWIAGGTW T PSALKFAY ...String:
SAWSHPQFEK GGGGSGGGGS GEPGPRGPRG VPGPEGEPGP PGDPGLTECD VMTYVRETCG CCDCEKRCGA LDVVFVIDSS ESIGYTNFT LEKNFVINVV NRLGAIAKDP KSETGTRVGV VQYSHEGTFE AIQLDDEHID SLSSFKEAVK NLEWIAGGTW T PSALKFAY DRLIKESRRQ KTRVFAVVIT DGRHDPRDDD LNLRALCDRD VTVTAIGIGD MFHEKHESEN LYSIACDKPQ QV RNMTLFS DLVAEKFIDD MEDVLCPDPQ IVCPDLPCQT ELSVAQCTQR PVDIVFLLDG SERLGEQNFH KARRFVEQVA RRL TLARRD DDPLNARVAL LQFGGPGEQQ VAFPLSHNLT AIHEALETTQ YLNSFSHVGA GVVHAINAIV RSPRGGARRH AELS FVFLT DGVTGNDSLH ESAHSMRNEN VVPTVLALGS DVDMDVLTTL SLGDRAAVFH EKDYDSLAQP GFFDRFIRWI C

UniProtKB: Collagen alpha-2(VI) chain

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Macromolecule #3: Collagen alpha-1(VI) chain

MacromoleculeName: Collagen alpha-1(VI) chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 51.872395 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: HHHHHHGGGG SGGGGSGVKG AKGYRGPEGP QGPPGHQGPP GPDECEILDI IMKMCSCCEC KCGPIDLLFV LDSSESIGLQ NFEIAKDFV VKVIDRLSRD ELVKFEPGQS YAGVVQYSHS QMQEHVSLRS PSIRNVQELK EAIKSLQWMA GGTFTGEALQ Y TRDQLLPP ...String:
HHHHHHGGGG SGGGGSGVKG AKGYRGPEGP QGPPGHQGPP GPDECEILDI IMKMCSCCEC KCGPIDLLFV LDSSESIGLQ NFEIAKDFV VKVIDRLSRD ELVKFEPGQS YAGVVQYSHS QMQEHVSLRS PSIRNVQELK EAIKSLQWMA GGTFTGEALQ Y TRDQLLPP SPNNRIALVI TDGRSDTQRD TTPLNVLCSP GIQVVSVGIK DVFDFIPGSD QLNVISCQGL APSQGRPGLS LV KENYAEL LEDAFLKNVT AQICIDKKCP DYTCPITFSS PADITILLDG SASVGSHNFD TTKRFAKRLA ERFLTAGRTD PAH DVRVAV VQYSGTGQQR PERASLQFLQ NYTALASAVD AMDFINDATD VNDALGYVTR FYREASSGAA KKRLLLFSDG NSQG ATPAA IEKAVQEAQR AGIEIFVVVV GRQVNEPHIR VLVTGKTAEY DVAYGESHLF RVPSYQALLR GVFHQTVSRK VALG

UniProtKB: Collagen alpha-1(VI) chain

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Macromolecule #5: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / 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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Macromolecule #6: water

MacromoleculeName: water / type: ligand / ID: 6 / Number of copies: 43 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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

Concentration1 mg/mL
BufferpH: 7.4
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 98 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV
DetailsThis sample was prepared via affinity chromatography with three tags and was monodisperse and biologically pure prior to vitrification

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 35706 / Average exposure time: 1.09 sec. / Average electron dose: 28.11 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: 130000
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: 10665534
CTF correctionSoftware - Name: cryoSPARC / Software - details: Patch CTF estimation / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL / In silico model: cryoSPARC Ab initio model
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.14 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 246984
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC / Details: cryoSPARC non-uniform refinement
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC / Details: cryosparc Local refinement
Final 3D classificationNumber classes: 2 / Avg.num./class: 189243 / Software - Name: cryoSPARC
Details: cryoSPARC heterogenous refinement (combined classification and angle re-assignment)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Target criteria: RSC
Output model

PDB-9gtu:
Collagen VI alpha 1, 2, 3 heterotrimer recombinant C terminal region. Local refinement.

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