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- EMDB-66353: cryo-EM structure of a mammalian collagen fibril -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-66353
Titlecryo-EM structure of a mammalian collagen fibril
Map data
Sample
  • Complex: collagen
    • Protein or peptide: x 30 types
  • Ligand: x 2 types
Keywordscollagen / glycan / PROTEIN FIBRIL
Function / homology
Function and homology information


collagen type IX trimer / extracellular matrix structural constituent / animal organ morphogenesis / carbohydrate binding / protein homodimerization activity / extracellular region / metal ion binding
Similarity search - Function
Mimecan/Epiphycan / : / Fibrillar collagen, C-terminal / Fibrillar collagen C-terminal domain / Fibrillar collagen C-terminal non-collagenous (NC1) domain profile. / Fibrillar collagens C-terminal domain / : / Thrombospondin N-terminal -like domains. / : / Laminin G domain ...Mimecan/Epiphycan / : / Fibrillar collagen, C-terminal / Fibrillar collagen C-terminal domain / Fibrillar collagen C-terminal non-collagenous (NC1) domain profile. / Fibrillar collagens C-terminal domain / : / Thrombospondin N-terminal -like domains. / : / Laminin G domain / von Willebrand factor type C domain / VWFC domain signature. / Laminin G domain / VWFC domain profile. / Laminin G domain / von Willebrand factor (vWF) type C domain / VWFC domain / Collagen triple helix repeat / Collagen triple helix repeat (20 copies) / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
Collagen alpha-1(V) chain / Chromaffin granule amine transporter isoform X1 / Collagen alpha-3(IX) chain / Collagen type XI alpha 1 chain / Collagen type V alpha 2 chain / Collagen type IX alpha 2 chain / Collagen type XI alpha 1 chain / Opticin / Collagen type IX alpha 2 chain / Collagen type V alpha 2 chain ...Collagen alpha-1(V) chain / Chromaffin granule amine transporter isoform X1 / Collagen alpha-3(IX) chain / Collagen type XI alpha 1 chain / Collagen type V alpha 2 chain / Collagen type IX alpha 2 chain / Collagen type XI alpha 1 chain / Opticin / Collagen type IX alpha 2 chain / Collagen type V alpha 2 chain / Collagen alpha-1(IX) chain / Fibrillar collagen NC1 domain-containing protein / Fibrillar collagen NC1 domain-containing protein / Collagen type XI alpha 1 chain / Collagen type IX alpha 3 chain / Collagen alpha-1(IX) chain / Collagen type II alpha 1 chain / Collagen type II alpha 1 chain / Collagen type IX alpha 1 chain / Collagen type V alpha 2 chain
Similarity search - Component
Biological speciesSus scrofa (pig)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsLou X / Cong Y / Xu Y / Yan C
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32341016 China
CitationJournal: To Be Published
Title: The molecular architecture of a mammalian collagen fibril
Authors: Lou X / Cong Y / Xu Y / Yan C
History
DepositionSep 25, 2025-
Header (metadata) releaseAug 5, 2026-
Map releaseAug 5, 2026-
UpdateAug 5, 2026-
Current statusAug 5, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_66353.png

Downloads & links

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Map

FileDownload / File: emd_66353.map.gz / Format: CCP4 / Size: 732.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 1200 pix.
= 1317.48 Å		1.1 Å/pix.
x 400 pix.
= 439.16 Å		1.1 Å/pix.
x 400 pix.
= 439.16 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: 1.0979 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03
Minimum - Maximum0.0 - 0.6419977
Average (Standard dev.)0.0029897727 (±0.012565937)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin4004000
Dimensions4004001200
Spacing4004001200
CellA: 439.16 Å / B: 439.16 Å / C: 1317.48 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : collagen

EntireName: collagen
Components
  • Complex: collagen
    • Protein or peptide: Collagen alpha-1(V) chain
    • Protein or peptide: Fibrillar collagen NC1 domain-containing protein
    • Protein or peptide: Fibrillar collagen NC1 domain-containing protein
    • Protein or peptide: Fibrillar collagen NC1 domain-containing protein
    • Protein or peptide: Fibrillar collagen NC1 domain-containing protein
    • Protein or peptide: Collagen type XI alpha 1 chain
    • Protein or peptide: Collagen type XI alpha 1 chain
    • Protein or peptide: Collagen type XI alpha 1 chain
    • Protein or peptide: Fibrillar collagen NC1 domain-containing protein
    • Protein or peptide: Fibrillar collagen NC1 domain-containing protein
    • Protein or peptide: Chromaffin granule amine transporter isoform X1
    • Protein or peptide: Collagen type V alpha 2 chain
    • Protein or peptide: Collagen type V alpha 2 chain
    • Protein or peptide: Collagen alpha-2(V) chain preproprotein
    • Protein or peptide: Collagen alpha-2(V) chain preproprotein
    • Protein or peptide: Collagen type II alpha 1 chain
    • Protein or peptide: Collagen type II alpha 1 chain
    • Protein or peptide: Collagen type II alpha 1 chain
    • Protein or peptide: Collagen type II alpha 1 chain
    • Protein or peptide: Collagen type II alpha 1 chain
    • Protein or peptide: Collagen type IX alpha 1 chain
    • Protein or peptide: Collagen alpha-1(IX) chain
    • Protein or peptide: Collagen alpha-1(IX) chain
    • Protein or peptide: Collagen type IX alpha 2 chain
    • Protein or peptide: Collagen type IX alpha 2 chain
    • Protein or peptide: Collagen type IX alpha 2 chain
    • Protein or peptide: Collagen alpha-3(IX) chain
    • Protein or peptide: Collagen alpha-3(IX) chain
    • Protein or peptide: Collagen alpha-3(IX) chain
    • Protein or peptide: Opticin
  • Ligand: alpha-D-glucopyranose
  • Ligand: beta-D-galactopyranose

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Supramolecule #1: collagen

SupramoleculeName: collagen / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#30
Source (natural)Organism: Sus scrofa (pig)

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Macromolecule #1: Collagen alpha-1(V) chain

MacromoleculeName: Collagen alpha-1(V) chain / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 23.201516 KDa
SequenceString: SQAQAILQQA RLALRGPAGP MGLTGRPGPM GPPGSGGL(LYZ)G EPGDMGPQGP RGVQGPPGPA GKPGRRGRAG SDGARG MPG QTGP(LYZ)GDRGF DGLAGLPGE(LYZ) GHRGDPGPSG PPGPPGDDGE RGDDGEVGPR GLPGEPGPRG LLGPKGPPG PPGPPGVTGT ...String:
SQAQAILQQA RLALRGPAGP MGLTGRPGPM GPPGSGGL(LYZ)G EPGDMGPQGP RGVQGPPGPA GKPGRRGRAG SDGARG MPG QTGP(LYZ)GDRGF DGLAGLPGE(LYZ) GHRGDPGPSG PPGPPGDDGE RGDDGEVGPR GLPGEPGPRG LLGPKGPPG PPGPPGVTGT DGQPGP(LYZ)GNV GPQGEPGPPG QQGNPGAQGL PGPQGAIGPP GEKGPLGKPG LPGMPGADGP PGHPGK EGP PGE(LYZ)GGQGPP GPQGPIGYP

UniProtKB: Collagen alpha-1(V) chain

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Macromolecule #2: Fibrillar collagen NC1 domain-containing protein

MacromoleculeName: Fibrillar collagen NC1 domain-containing protein / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 22.416535 KDa
SequenceString: GPRGV(LYZ)GADG IRGL(LYZ)GT(LYZ)GE (LYZ)GEDGFPGF(LYZ) GDMGI(LYZ)GDRG EIGPPGPRGE DGPEGP (LYZ)GR GGPNGDPGPL GPPGE(LYZ)GKLG VPGLPGYPGR QGP(LYZ)GSIGFP GFPGANGE(LYZ)G GRGTPGKPGP R GQRGPTGP ...String:
GPRGV(LYZ)GADG IRGL(LYZ)GT(LYZ)GE (LYZ)GEDGFPGF(LYZ) GDMGI(LYZ)GDRG EIGPPGPRGE DGPEGP (LYZ)GR GGPNGDPGPL GPPGE(LYZ)GKLG VPGLPGYPGR QGP(LYZ)GSIGFP GFPGANGE(LYZ)G GRGTPGKPGP R GQRGPTGP RGERGPRGIT GKPGP(LYZ)GNSG GDGPAGPPGE RGPNGPQGPT GFPGPKGPPG PPGKDGLPGH PGQRGETG F QGKTGPPGPP GVVGPQGPTG ETGPMGERGH PGPPGP

UniProtKB: Fibrillar collagen NC1 domain-containing protein

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Macromolecule #3: Fibrillar collagen NC1 domain-containing protein

MacromoleculeName: Fibrillar collagen NC1 domain-containing protein / type: protein_or_peptide / ID: 3 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 21.669555 KDa
SequenceString: PGEQGLPGLA GKEGT(LYZ)GDPG PAGLPGKDGP PGLRGFPGDR GLPGPVGALG L(LYZ)GSEGPPGP PGPAGSPGER GP AGAAGPI GIPGRPGPQG PPGPAGE(LYZ)GA PGEKGPQGPA GRDGLQGPVG LPGPAGPVGP PGEDGDKGEI GEPGQ (LYZ)GS(LYZ) GD(LYZ) ...String:
PGEQGLPGLA GKEGT(LYZ)GDPG PAGLPGKDGP PGLRGFPGDR GLPGPVGALG L(LYZ)GSEGPPGP PGPAGSPGER GP AGAAGPI GIPGRPGPQG PPGPAGE(LYZ)GA PGEKGPQGPA GRDGLQGPVG LPGPAGPVGP PGEDGDKGEI GEPGQ (LYZ)GS(LYZ) GD(LYZ)GEQGPPG PTGPQGPIGQ PGPSGADGEP GPRGQQGLFG QKGDEGPRGF PGPPGPVGLQ GLPG PPGE(LYZ) GETGDVGQMG PPGPPGP

UniProtKB: Fibrillar collagen NC1 domain-containing protein

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Macromolecule #4: Fibrillar collagen NC1 domain-containing protein

MacromoleculeName: Fibrillar collagen NC1 domain-containing protein / type: protein_or_peptide / ID: 4 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 21.58717 KDa
SequenceString: RGPSGAPGAD GPQGPPGGIG NPGAVGE(LYZ)GE PGEAGEPGLP GEGGPPGP(LYZ)G ERGE(LYZ)GESGP SGAAGPPG P KGPPGDDGP(LYZ) GSPGPVGFPG DPGPPGEPGP AGQDGPPGDK GDDGEPGQTG SPGPTGEPGP SGPPGKRGPP GPAGP EGRQ GE(LYZ) ...String:
RGPSGAPGAD GPQGPPGGIG NPGAVGE(LYZ)GE PGEAGEPGLP GEGGPPGP(LYZ)G ERGE(LYZ)GESGP SGAAGPPG P KGPPGDDGP(LYZ) GSPGPVGFPG DPGPPGEPGP AGQDGPPGDK GDDGEPGQTG SPGPTGEPGP SGPPGKRGPP GPAGP EGRQ GE(LYZ)GA(LYZ)GEAG LEGPPGKTGP IGPQGAPGKP GPDGLRGIPG PVGEQGLPGA PGPDGPPGPM GPPGLPGL (LYZ) GDSGP(LYZ)GE(LYZ)G HPGLIGLIGP

UniProtKB: Fibrillar collagen NC1 domain-containing protein

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Macromolecule #5: Fibrillar collagen NC1 domain-containing protein

MacromoleculeName: Fibrillar collagen NC1 domain-containing protein / type: protein_or_peptide / ID: 5 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 6.999511 KDa
SequenceString:
PGEQGE(LYZ)GDR GLPGPQGSSG P(LYZ)GEQGITGP SGPIGPPGPP GLPGPPGP(LYZ)G A(LYZ)GSSGPTGP (LYZ)GEAGHPGP PGPPGPPG

UniProtKB: Fibrillar collagen NC1 domain-containing protein

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Macromolecule #6: Collagen type XI alpha 1 chain

MacromoleculeName: Collagen type XI alpha 1 chain / type: protein_or_peptide / ID: 6 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 23.352639 KDa
SequenceString: EAQAQAILQQ ARIALRGPPG PMGLTGRPGP VGGPGSSGA(LYZ) GESGEPGPQG PRGVQGPPGP TGKPGKRGRP GADGGR GMP GEPGA(LYZ)GDRG FDGLPGLPGD (LYZ)GHRGERGPQ GPPGPPGEDG MRGEDGEIGP RGLPGEAGPR GLLGPRGTP GPTGQPGIAG ...String:
EAQAQAILQQ ARIALRGPPG PMGLTGRPGP VGGPGSSGA(LYZ) GESGEPGPQG PRGVQGPPGP TGKPGKRGRP GADGGR GMP GEPGA(LYZ)GDRG FDGLPGLPGD (LYZ)GHRGERGPQ GPPGPPGEDG MRGEDGEIGP RGLPGEAGPR GLLGPRGTP GPTGQPGIAG VDGPPGP(LYZ)GN MGPQGEPGPP GQQGNPGPQG LPGPQGPIGP PGEKGPQGKP GLAGLPGADG PPGHPG KEG QSGE(LYZ)GSLGP PGPQGPIGY

UniProtKB: Collagen type XI alpha 1 chain

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Macromolecule #7: Collagen type XI alpha 1 chain

MacromoleculeName: Collagen type XI alpha 1 chain / type: protein_or_peptide / ID: 7 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 22.244246 KDa
SequenceString: PGPRGV(LYZ)GAD GVRGL(LYZ)GS(LYZ)G E(LYZ)GEDGFPGF (LYZ)GDMGL(LYZ)GDR GEVGQVGPRG EDGPEG P(LYZ)G RAGPTGDPGP SGQAGE(LYZ)GKL GVPGLPGYPG RQGP(LYZ)GSTGF PGFPGANGE(LYZ) GARGVAGKPG P RGQRGPTG ...String:
PGPRGV(LYZ)GAD GVRGL(LYZ)GS(LYZ)G E(LYZ)GEDGFPGF (LYZ)GDMGL(LYZ)GDR GEVGQVGPRG EDGPEG P(LYZ)G RAGPTGDPGP SGQAGE(LYZ)GKL GVPGLPGYPG RQGP(LYZ)GSTGF PGFPGANGE(LYZ) GARGVAGKPG P RGQRGPTG PRGSRGARGP TGKPGP(LYZ)GTS GGDGPPGPPG ERGPQGPQGP VGFPGPKGPP GPPGKDGLPG HPGQRGET G FQGKTGPPGP GGVVGPQGPT GETGPIGERG HPGPPG

UniProtKB: Collagen type XI alpha 1 chain

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Macromolecule #8: Collagen type XI alpha 1 chain

MacromoleculeName: Collagen type XI alpha 1 chain / type: protein_or_peptide / ID: 8 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 21.615338 KDa
SequenceString: PPGEQGLPGA AGKEGA(LYZ)GDP GPQGVSGKDG PAGLRGFPGE RGLPGAQGAP GL(LYZ)GGEGPQG PPGPVGSPGE RG SAGTAGP IGLPGRPGPQ GPPGPAGE(LYZ)G APGEKGPQGP AGRDGVQGPV GLPGPAGPAG SPGEDGDKGE IGEPGQ (LYZ)GS (LYZ) ...String:
PPGEQGLPGA AGKEGA(LYZ)GDP GPQGVSGKDG PAGLRGFPGE RGLPGAQGAP GL(LYZ)GGEGPQG PPGPVGSPGE RG SAGTAGP IGLPGRPGPQ GPPGPAGE(LYZ)G APGEKGPQGP AGRDGVQGPV GLPGPAGPAG SPGEDGDKGE IGEPGQ (LYZ)GS (LYZ)GD(LYZ)GENGPP GPPGLQGPVG APGIAGGDGE PGPRGQQGMF GQ(LYZ)GDEGARG FPGPPGPIGL Q GLPGPPGE (LYZ)GENGDVGPM GPPGPPGP

UniProtKB: Collagen type XI alpha 1 chain

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Macromolecule #9: Fibrillar collagen NC1 domain-containing protein

MacromoleculeName: Fibrillar collagen NC1 domain-containing protein / type: protein_or_peptide / ID: 9 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 21.355842 KDa
SequenceString: RGPQGPNGAD GPQGPPGSIG SVGGVGE(LYZ)GE PGEAGNPGPP GEAGTGGP(LYZ)G ERGE(LYZ)GEAGP PGAAGPPG A KGPPGDDGP(LYZ) GNPGPVGFPG DPGPPGEPGP AGQDGVGGDK GEDGDPGQPG PPGPSGEAGP PGPPGKRGPP GAAGA EGRQ GE(LYZ) ...String:
RGPQGPNGAD GPQGPPGSIG SVGGVGE(LYZ)GE PGEAGNPGPP GEAGTGGP(LYZ)G ERGE(LYZ)GEAGP PGAAGPPG A KGPPGDDGP(LYZ) GNPGPVGFPG DPGPPGEPGP AGQDGVGGDK GEDGDPGQPG PPGPSGEAGP PGPPGKRGPP GAAGA EGRQ GE(LYZ)GA(LYZ)GEAG AEGPPGKTGP VGPQGPAGKP GPEGLRGIPG PVGEQGLPGA AGQDGPPGPM GPPGLPGL (LYZ) GDPGS(LYZ)GE(LYZ)G HPGLIGLIG

UniProtKB: Collagen type XI alpha 1 chain

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Macromolecule #10: Fibrillar collagen NC1 domain-containing protein

MacromoleculeName: Fibrillar collagen NC1 domain-containing protein / type: protein_or_peptide / ID: 10 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 6.852358 KDa
SequenceString:
PPGEQGE(LYZ)GD RGLPGAQGST GA(LYZ)GDGGIPG PAGPIGPPGP PGLPGPQGP(LYZ) GT(LYZ)GSTGPAG Q (LYZ)GDSGLPG PPGPPGP

UniProtKB: Collagen type XI alpha 1 chain

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Macromolecule #11: Chromaffin granule amine transporter isoform X1

MacromoleculeName: Chromaffin granule amine transporter isoform X1 / type: protein_or_peptide / ID: 11 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 21.432652 KDa
SequenceString: PVGPRGPQGL QGQQGGAGPM GPPGEPGEPG PMGPIGARGP EGPPGKPGED GEPGRNGNPG EVGFAGSPGA RGFPGAPGLP GL(LYZ)GHRGH(LYZ) GLEGP(LYZ)GEVG ATGS(LYZ)GEAGP TGPMGAMGPM GPRGMPGERG RLGPQGAPGQ RGAHG MPGK PGPMGPLGIP ...String:
PVGPRGPQGL QGQQGGAGPM GPPGEPGEPG PMGPIGARGP EGPPGKPGED GEPGRNGNPG EVGFAGSPGA RGFPGAPGLP GL(LYZ)GHRGH(LYZ) GLEGP(LYZ)GEVG ATGS(LYZ)GEAGP TGPMGAMGPM GPRGMPGERG RLGPQGAPGQ RGAHG MPGK PGPMGPLGIP GSPGFPGNPG M(LYZ)GEAGPTGA RGPEGPQGQR GETGPPGPVG SQGLPGAVGT DGTPGAKGPT GS PGTSGPP GLAG

UniProtKB: Chromaffin granule amine transporter isoform X1

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Macromolecule #12: Collagen type V alpha 2 chain

MacromoleculeName: Collagen type V alpha 2 chain / type: protein_or_peptide / ID: 12 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 21.671557 KDa
SequenceString: PPGSPGPQGS TGPPGIRGQP GDPGVPGF(LYZ)G EAGP(LYZ)GEPGP HGIQGPIGPP GEEGKRGPRG DPGTVGPPGP MG ERGAPGN RGFPGSDGLP GP(LYZ)GAQGERG PVGSSGP(LYZ)GG QGDPGRPGEP GLPGARGLTG NPGVQGPEGK LGPLG APGE DGRPGPPGSI ...String:
PPGSPGPQGS TGPPGIRGQP GDPGVPGF(LYZ)G EAGP(LYZ)GEPGP HGIQGPIGPP GEEGKRGPRG DPGTVGPPGP MG ERGAPGN RGFPGSDGLP GP(LYZ)GAQGERG PVGSSGP(LYZ)GG QGDPGRPGEP GLPGARGLTG NPGVQGPEGK LGPLG APGE DGRPGPPGSI GIRGQPGSMG LPGP(LYZ)GSSGD PGKPGEAGNA GVPGQRGAPG KDGEVGPSGP VGPPGLAGER GE QGPPGPT GFQGLP

UniProtKB: Collagen type V alpha 2 chain

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Macromolecule #13: Collagen type V alpha 2 chain

MacromoleculeName: Collagen type V alpha 2 chain / type: protein_or_peptide / ID: 13 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 21.379926 KDa
SequenceString: GPPGPPGEGG KPGDQGVPGD PGAVGPLGPR GERGNPGERG EPGITGLPGE (LYZ)GMAGGHGPD GP(LYZ)GSPGPSG TP GDTGPPG LQGMPGERGI AGTPGP(LYZ)GDR GGIGE(LYZ)GAEG TAGNDGARGL PGPLGPPGPA GPTGE(LYZ)GEPG P RGLVGPPG ...String:
GPPGPPGEGG KPGDQGVPGD PGAVGPLGPR GERGNPGERG EPGITGLPGE (LYZ)GMAGGHGPD GP(LYZ)GSPGPSG TP GDTGPPG LQGMPGERGI AGTPGP(LYZ)GDR GGIGE(LYZ)GAEG TAGNDGARGL PGPLGPPGPA GPTGE(LYZ)GEPG P RGLVGPPG SRGNPGSRGE NGPTGAVGFA GPQGPDGQPG VKGEPGEPGQ (LYZ)GDAGSPGPQ GLAGSPGPHG PNGVPGL (LYZ)G GRGTQGPPGA TGFPGSA

UniProtKB: Collagen type V alpha 2 chain

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Macromolecule #14: Collagen alpha-2(V) chain preproprotein

MacromoleculeName: Collagen alpha-2(V) chain preproprotein / type: protein_or_peptide / ID: 14 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 22.060861 KDa
SequenceString: GRVGPPGPTG APGPAGPLGE PGKEGPPGLR GDPGSHGRVG DRGPAGPPGG PGDKGDPGED GQPGPDGPPG PAGTTGQRGI VGMPGQRGE RGMPGLPGPA GTPGKVGPTG APGDKGPPGP VGPPGSNGPV GEPGPEGPAG NDGTPGRDGA VGERGDRGDP G PAGLPGSR ...String:
GRVGPPGPTG APGPAGPLGE PGKEGPPGLR GDPGSHGRVG DRGPAGPPGG PGDKGDPGED GQPGPDGPPG PAGTTGQRGI VGMPGQRGE RGMPGLPGPA GTPGKVGPTG APGDKGPPGP VGPPGSNGPV GEPGPEGPAG NDGTPGRDGA VGERGDRGDP G PAGLPGSR GAPGTPGPVG APGDAGQRGD PGSRGPIGPP GRAGKRGLLG PQGPRGD(LYZ)GD HGDRGDRGQ(LYZ) GHRG FTGLQ

UniProtKB: Collagen type V alpha 2 chain

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Macromolecule #15: Collagen alpha-2(V) chain preproprotein

MacromoleculeName: Collagen alpha-2(V) chain preproprotein / type: protein_or_peptide / ID: 15 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 6.758372 KDa
SequenceString:
GLPGPPGPNG EQGSAGIPGP FGPRGPPGPV GPSGKEGNPG PLGPVGPPGV RGSVGEAGPE GPPGEPGPPG PPGPPG

UniProtKB: Collagen type V alpha 2 chain

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Macromolecule #16: Collagen type II alpha 1 chain

MacromoleculeName: Collagen type II alpha 1 chain / type: protein_or_peptide / ID: 16 / Number of copies: 24 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 15.503065 KDa
SequenceString:
MGVMQGPMGP MGPRGPPGPA GAPGPQGFQG NPGEPGEPGV SGPMGPRGPP GPPGKPGDDG EAGKPGKSGE RGPPGPQGAR GFPGTPGLP GVKGHRGYPG LDGAKGEAGA PGVKGESGSP GENGSPGPMG PRGLPGERGR TGPAGAAGAR GNDGQPGPAG P PGPVGPAG G

UniProtKB: Collagen type II alpha 1 chain

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Macromolecule #17: Collagen type II alpha 1 chain

MacromoleculeName: Collagen type II alpha 1 chain / type: protein_or_peptide / ID: 17 / Number of copies: 24 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 22.314205 KDa
SequenceString: PGFPGAPGAK GEAGPTGARG PEGAQGPRGE PGNPGSPGPA GASGNPGTDG IPGAKGSAGA PGIAGAPGFP GPRGPPGPQG ATGPLGPKG QTGEPGIAGF KGEQGPKGEP GPAGPQGAPG PAGEEGKRGA RGEPGGAGPA GPPGERGAPG NRGFPGQDGL A GPKGAPGE ...String:
PGFPGAPGAK GEAGPTGARG PEGAQGPRGE PGNPGSPGPA GASGNPGTDG IPGAKGSAGA PGIAGAPGFP GPRGPPGPQG ATGPLGPKG QTGEPGIAGF KGEQGPKGEP GPAGPQGAPG PAGEEGKRGA RGEPGGAGPA GPPGERGAPG NRGFPGQDGL A GPKGAPGE RGPSGLAGPK GANGDPGRPG EPGLPGARGL TGRPGDAGPQ GKVGPSGAPG EDGRPGPPGP QGARGQPGVM GF PGPKGAN G

UniProtKB: Collagen type II alpha 1 chain

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Macromolecule #18: Collagen type II alpha 1 chain

MacromoleculeName: Collagen type II alpha 1 chain / type: protein_or_peptide / ID: 18 / Number of copies: 24 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 20.160889 KDa
SequenceString: EPGKAGEKGL PGAPGLRGLP GKDGETGAAG PPGPAGPAGE RGEQGAPGPS GFQGLPGPPG APGEGGKPGD QGVPGEAGAP GLVGPRGER GFPGERGSPG SQGLQGPRGL PGTPGTDGPK GASGPAGPPG AQGPPGLQGM PGERGAAGIA GPKGDRGDVG E KGPEGAPG ...String:
EPGKAGEKGL PGAPGLRGLP GKDGETGAAG PPGPAGPAGE RGEQGAPGPS GFQGLPGPPG APGEGGKPGD QGVPGEAGAP GLVGPRGER GFPGERGSPG SQGLQGPRGL PGTPGTDGPK GASGPAGPPG AQGPPGLQGM PGERGAAGIA GPKGDRGDVG E KGPEGAPG KDGGRGLTGP IGPPGPAGAN GEKGEVGPPG PAGTAGARGA PGERGETGPP GPAGF

UniProtKB: Collagen type II alpha 1 chain

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Macromolecule #19: Collagen type II alpha 1 chain

MacromoleculeName: Collagen type II alpha 1 chain / type: protein_or_peptide / ID: 19 / Number of copies: 24 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 21.32877 KDa
SequenceString: GETGPPGPAG FAGPPGADGQ PGAKGEQGEA GQKGDAGAPG PQGPSGAPGP QGPTGVTGPK GARGAQGPPG ATGFPGAAGR VGPPGSNGN PGPPGPPGPS GKDGPKGARG DSGPPGRAGD PGLQGPAGPP GEKGEPGEDG PSGPDGPPGP QGLAGQRGIV G LPGQRGER ...String:
GETGPPGPAG FAGPPGADGQ PGAKGEQGEA GQKGDAGAPG PQGPSGAPGP QGPTGVTGPK GARGAQGPPG ATGFPGAAGR VGPPGSNGN PGPPGPPGPS GKDGPKGARG DSGPPGRAGD PGLQGPAGPP GEKGEPGEDG PSGPDGPPGP QGLAGQRGIV G LPGQRGER GFPGLPGPSG EPGKQGAPGA SGDRGPPGPV GPPGLTGPSG EPGREGSPGA DGPPGRDGAA GVKGDRGET

UniProtKB: Collagen type II alpha 1 chain

+
Macromolecule #20: Collagen type II alpha 1 chain

MacromoleculeName: Collagen type II alpha 1 chain / type: protein_or_peptide / ID: 20 / Number of copies: 24 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 14.454652 KDa
SequenceString:
GDRGETGAAG APGAPGPPGS PGPAGPTGKQ GDRGEAGAQG PMGPAGPAGA RGMPGPQGPR GDKGEAGEAG ERGLKGHRGF TGLQGLPGP PGPSGDQGAS GPAGPSGPRG PPGPVGPSGK DGANGIPGPI GPPGPRGRSG ETGPAGPPGT PGPPGPPGPP G PG

UniProtKB: Collagen type II alpha 1 chain

+
Macromolecule #21: Collagen type IX alpha 1 chain

MacromoleculeName: Collagen type IX alpha 1 chain / type: protein_or_peptide / ID: 21 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 5.459867 KDa
SequenceString:
QGHKGEEGDQ GEPGEVGAQG PPGAQGLRGI TGIAGAKGEK GARGLDGEPG PQGLPGAP

UniProtKB: Collagen type IX alpha 1 chain

+
Macromolecule #22: Collagen alpha-1(IX) chain

MacromoleculeName: Collagen alpha-1(IX) chain / type: protein_or_peptide / ID: 22 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 21.57192 KDa
SequenceString: GAPGDQGQRG PPGEIGPKGD RGAQGSRGIP GLPGPKGDTG LPGVDGREGI PGMPGTKGEP GKPGPPGEAG LQGLPGIGIP GAKGVAGEK GNTGAPGKPG QLGNSGKPGQ QGPPGEVGPR GPRGLPGSRG EIGPVGPPGP PGKLGSLGSP GLPGLPGPPG L PGMKGDRG ...String:
GAPGDQGQRG PPGEIGPKGD RGAQGSRGIP GLPGPKGDTG LPGVDGREGI PGMPGTKGEP GKPGPPGEAG LQGLPGIGIP GAKGVAGEK GNTGAPGKPG QLGNSGKPGQ QGPPGEVGPR GPRGLPGSRG EIGPVGPPGP PGKLGSLGSP GLPGLPGPPG L PGMKGDRG VVGEPGPKGE QGVSGEEGEA GERGELGDIG LPGPKGSVGN PGEPGLRGPE GSRGLPGVEG PRG

UniProtKB: Collagen alpha-1(IX) chain

+
Macromolecule #23: Collagen alpha-1(IX) chain

MacromoleculeName: Collagen alpha-1(IX) chain / type: protein_or_peptide / ID: 23 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 16.613785 KDa
SequenceString:
GPPGPRGVQG EQGATGLPGI EGPPGRAPTD QHIKQVCMRV MQEHFAAMAA SLKRPESGAS GLPGRPGPPG PPGPPGENGF PGQMGLRGL PGMKGPPGAL GLRGPKGDMG ERGDRGPPGR GPKGLPGATG LPGDPGPASY GRNGRDGERG PPGVAGIPGV P GPPGPPGP PGF

UniProtKB: Collagen alpha-1(IX) chain

+
Macromolecule #24: Collagen type IX alpha 2 chain

MacromoleculeName: Collagen type IX alpha 2 chain / type: protein_or_peptide / ID: 24 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 5.336972 KDa
SequenceString:
GKPGPKGDVG ASGEQGIPGP PGPQGVRGYP GMAGPKGEMG PQGYKGMVGS VGAAGSPG

UniProtKB: Collagen type IX alpha 2 chain

+
Macromolecule #25: Collagen type IX alpha 2 chain

MacromoleculeName: Collagen type IX alpha 2 chain / type: protein_or_peptide / ID: 25 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 21.813746 KDa
SequenceString: SPGEEGPRGP PGRAGEKGDV GSQGVRGPQG ITGPKGATGP PGIDGKDGTP GTPGMKGSAG QAGRPGNPGH QGLAGMPGQP GTKGGPGDK GEPGQRGFPG VSGPPGKEGE PGPQGEIGPQ GIMGQKGDHG ERGPVGQPGP QGRQGPKGEQ GPPGIPGPQG L PGIKGDKG ...String:
SPGEEGPRGP PGRAGEKGDV GSQGVRGPQG ITGPKGATGP PGIDGKDGTP GTPGMKGSAG QAGRPGNPGH QGLAGMPGQP GTKGGPGDK GEPGQRGFPG VSGPPGKEGE PGPQGEIGPQ GIMGQKGDHG ERGPVGQPGP QGRQGPKGEQ GPPGIPGPQG L PGIKGDKG SPGKTGPRGG VGDPGVAGLP GEKGEKGESG EPGPKGQQGV RGEPGYPGPS GDAGAPGVQG YPGP

UniProtKB: Collagen type IX alpha 2 chain

+
Macromolecule #26: Collagen type IX alpha 2 chain

MacromoleculeName: Collagen type IX alpha 2 chain / type: protein_or_peptide / ID: 26 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 16.681969 KDa
SequenceString:
PPGPRGLVGD RGLPGLPGRQ GVAGRDASDQ HIEDVMLKMM QEQLAEMAVS AKREALGATG MVGPPGPPGP PGYPGKQGPH GHPGPRGIP GIVGAVGQIG NTGPKGKRGE KGDRGEVGRG HPGMPGPPGI PGLPGRPGQA INGKDGDRGA PGAPGEAGRP G LPGPMGLP GF

UniProtKB: Collagen type IX alpha 2 chain

+
Macromolecule #27: Collagen alpha-3(IX) chain

MacromoleculeName: Collagen alpha-3(IX) chain / type: protein_or_peptide / ID: 27 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 5.475208 KDa
SequenceString:
KDGEKGDPGP PGPPGIPGTV GLQGPRGLRG LPGPLGPSGD RGPIGFRGPP GIPGAPGK

UniProtKB: Collagen type IX alpha 3 chain

+
Macromolecule #28: Collagen alpha-3(IX) chain

MacromoleculeName: Collagen alpha-3(IX) chain / type: protein_or_peptide / ID: 28 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 21.48548 KDa
SequenceString: PGKVGDRGER GPEGVRGPKG DLGRPGPKGV PGMAGPGGEP GMPGKDGRDG VPGLDGEKGE AGRSGAPGEK GPDGLPGLPG RAGSKGEKG ELGRAGELGE AGPSGEPGVP GDVGAPGERG EAGHRGSAGA LGPQGPPGAP GVRGFQGQKG SAGAPGLPGP Q GLRGGMGD ...String:
PGKVGDRGER GPEGVRGPKG DLGRPGPKGV PGMAGPGGEP GMPGKDGRDG VPGLDGEKGE AGRSGAPGEK GPDGLPGLPG RAGSKGEKG ELGRAGELGE AGPSGEPGVP GDVGAPGERG EAGHRGSAGA LGPQGPPGAP GVRGFQGQKG SAGAPGLPGP Q GLRGGMGD RGPGGATGPK GDQGIAGSDG LPGDKGELGP SGPVGPKGEA GSRGELGPKG IQGPNGTSGV DGLP

UniProtKB: Collagen alpha-3(IX) chain

+
Macromolecule #29: Collagen alpha-3(IX) chain

MacromoleculeName: Collagen alpha-3(IX) chain / type: protein_or_peptide / ID: 29 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 16.272949 KDa
SequenceString:
PGPPGPPGLQ GVRGMPGITG KPGVPGKEAS EQHIRELCGG VISEQIAQLA AHLRKPLAPG SIGRPGPAGP PGPPGPPGSM GHPGARGPP GYRGPTGELG DPGPRGSQGD RGDKGSAGEG LDGPDGDQGL QGPQGVPGVS KDGRDGAHGE PGFPGDPGRP G AVGAQGPP GI

UniProtKB: Collagen type IX alpha 3 chain

+
Macromolecule #30: Opticin

MacromoleculeName: Opticin / type: protein_or_peptide / ID: 30 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 23.67427 KDa
SequenceString: PGLPTCLVCV CLGSSVYCDD TDLENIPPLP QTTTYLYARF NRINHIRAGD FKGLTKLKRI DLSSNFISSI DDDALLLLPD LQDLILIEN QLAALPTLPT AIEVLDVRLN RLRSSGIQPG AFRALEKLQF LYLADNLLDS IPGPLPLSLR SLHLQNNMIE T LQRDTFCD ...String:
PGLPTCLVCV CLGSSVYCDD TDLENIPPLP QTTTYLYARF NRINHIRAGD FKGLTKLKRI DLSSNFISSI DDDALLLLPD LQDLILIEN QLAALPTLPT AIEVLDVRLN RLRSSGIQPG AFRALEKLQF LYLADNLLDS IPGPLPLSLR SLHLQNNMIE T LQRDTFCD PEEHKHTRRQ LEDIRLDGNP INLSLFPSAY FCLPRLPIGR FT

UniProtKB: Opticin

+
Macromolecule #32: alpha-D-glucopyranose

MacromoleculeName: alpha-D-glucopyranose / type: ligand / ID: 32 / Number of copies: 4 / Formula: GLC
Molecular weightTheoretical: 180.156 Da
Chemical component information

ChemComp-GLC:
alpha-D-glucopyranose

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Macromolecule #33: beta-D-galactopyranose

MacromoleculeName: beta-D-galactopyranose / type: ligand / ID: 33 / Number of copies: 4 / Formula: GAL
Molecular weightTheoretical: 180.156 Da
Chemical component information

ChemComp-GAL:
beta-D-galactopyranose

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Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statefilament

-
Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 600039
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD

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