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

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Basic information

Entry
Database: PDB / ID: 9gtu
TitleCollagen VI alpha 1, 2, 3 heterotrimer recombinant C terminal region. Local refinement.
Components(Collagen alpha- ...) x 3
KeywordsSTRUCTURAL PROTEIN / extracellular / matrix / collagen / co6A1 / co6A2 / co6A3 / von willebrand / von-willebrand / coiled-coil / ECM / double-bead / structural / microfibril / Bethlem myopathy / Ullrich congenital muscular dystrophy
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.14 Å
AuthorsGodwin, A. / Snee, M. / Dajani, R. / Becker, M. / Roseman, A. / Baldock, C.
Funding support United Kingdom, 1items
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, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 20, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Collagen alpha-3(VI) chain
B: Collagen alpha-2(VI) chain
A: Collagen alpha-1(VI) chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,6947
Polymers158,1103
Non-polymers1,5844
Water77543
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, The heterotrimer is a fragment of a larger fibrillar assembly that forms when the full N terminal and collagenous regions are present.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Collagen alpha- ... , 3 types, 3 molecules CBA

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


Mass: 53947.332 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: COL6A3 / Cell line (production host): Expi293 F / Production host: Homo sapiens (human) / References: UniProt: P12111
#2: Protein Collagen alpha-2(VI) chain


Mass: 52290.398 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: COL6A2 / Cell line (production host): Expi293F / Production host: Homo sapiens (human) / References: UniProt: P12110
#3: Protein Collagen alpha-1(VI) chain


Mass: 51872.395 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: COL6A1 / Cell line (production host): Expi293F / Production host: Homo sapiens (human) / References: UniProt: P12109

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Sugars , 2 types, 4 molecules

#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#5: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 1 types, 43 molecules

#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: 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
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.
Entity ID: #1-#3 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human) / Strain: EXPI-293 F / Plasmid: pHL-SEC
Buffer solutionpH: 7.4
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: This sample was prepared via affinity chromatography with three tags and was monodisperse and biologically pure prior to vitrification
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 98 % / Chamber temperature: 277.15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 130000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 750 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 1.09 sec. / Electron dose: 28.11 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 35706

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Processing

EM software
IDNameVersionCategoryDetails
1cryoSPARCparticle selection
2Topazparticle selection
3EPU3.5.1image acquisition
5cryoSPARCCTF correctionPatch CTF estimation
8UCSF Chimeramodel fitting
9UCSF ChimeraXmodel fitting
10Cootmodel fitting
12cryoSPARCinitial Euler assignment
13cryoSPARCfinal Euler assignment
14cryoSPARCclassification
15cryoSPARC3D reconstruction
16PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 10665534
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.14 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 246984 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL / Target criteria: RSC
Atomic model buildingSource name: AlphaFold / Type: in silico model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0035671
ELECTRON MICROSCOPYf_angle_d0.5267694
ELECTRON MICROSCOPYf_dihedral_angle_d4.767818
ELECTRON MICROSCOPYf_chiral_restr0.041911
ELECTRON MICROSCOPYf_plane_restr0.0041004

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