9WXP image
Deposition Date 2025-09-25
Release Date 2026-08-05
Last Version Date 2026-08-12
Entry Detail
PDB ID:
9WXP
Keywords:
PROTEIN FIBRIL
Title:
cryo-EM structure of a mammalian collagen fibril
Biological Source:
Source Organism(s):
Sus scrofa (Taxon ID: 9823)
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
3.20 Å
Aggregation State:
FILAMENT
Reconstruction Method:
SINGLE PARTICLE
9WXP validation report missing
Macromolecular Entities
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Collagen alpha-1(V) chain
Chain IDs:A (auth: AA), DB (auth: FA), GD (auth: KA), JF (auth: PA)
Chain Length:0
Number of Molecules:4
Biological Source:Sus scrofa
UniProt ID:A0A480MJQ8
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Chromaffin granule amine tran
Chain IDs:K (auth: AB), NB (auth: FB), QD (auth: KB), TF (auth: PB)
Chain Length:0
Number of Molecules:4
Biological Source:Sus scrofa
UniProt ID:A0A480YT77
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Collagen type XI alpha 1 chai
Gene (Uniprot):COL11A1
Chain IDs:F (auth: AC), IB (auth: FC), LD (auth: KC), OF (auth: PC)
Chain Length:0
Number of Molecules:4
Biological Source:Sus scrofa
UniProt ID:A0A4X1TLK6
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Collagen type II alpha 1 chai
Gene (Uniprot):COL2A1
Chain IDs:P (auth: AD), Q (auth: AE), R (auth: AF), EA (auth: AG), FA (auth: AH), GA (auth: AI), SB (auth: FD), TB (auth: FE), UB (auth: FF), HC (auth: FG), IC (auth: FH), JC (auth: FI), VD (auth: KD), WD (auth: KE), XD (auth: KF), KE (auth: KG), LE (auth: KH), ME (auth: KI), YF (auth: PD), ZF (auth: PE), AG (auth: PF), NG (auth: PG), OG (auth: PH), PG (auth: PI)
Chain Length:0
Number of Molecules:24
Biological Source:Sus scrofa
UniProt ID:A0A8D1U0L9
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Collagen type IX alpha 1 chai
Gene (Uniprot):COL9A1
Chain IDs:TA (auth: AJ), WC (auth: DJ), ZE (auth: GJ), CH (auth: JJ)
Chain Length:0
Number of Molecules:4
Biological Source:Sus scrofa
UniProt ID:A0A8X9AEQ8 Pfam ID:PF01391
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Collagen type IX alpha 2 chai
Gene (Uniprot):COL9A2
Chain IDs:WA (auth: AK), ZC (auth: DK), CF (auth: GK), FH (auth: JK)
Chain Length:0
Number of Molecules:4
Biological Source:Sus scrofa
UniProt ID:A0A8D0V1I3
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Collagen alpha-3(IX) chain
Gene (Uniprot):COL9A3
Chain IDs:ZA (auth: AL), CD (auth: DL), FF (auth: GL), IH (auth: JL)
Chain Length:0
Number of Molecules:4
Biological Source:Sus scrofa
UniProt ID:A0A8D1N974
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Opticin
Gene (Uniprot):OPTC
Chain IDs:CB (auth: AM), FD (auth: BM), IF (auth: CM), LH (auth: DM)
Chain Length:0
Number of Molecules:4
Biological Source:Sus scrofa
UniProt ID:A0A8D0IR51
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Fibrillar collagen NC1 domain
Chain IDs:B (auth: BA), EB (auth: GA), HD (auth: LA), KF (auth: QA)
Chain Length:0
Number of Molecules:4
Biological Source:Sus scrofa
UniProt ID:A0A8D1DM46
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Collagen type V alpha 2 chain
Gene (Uniprot):COL5A2
Chain IDs:L (auth: BB), OB (auth: GB), RD (auth: LB), UF (auth: QB)
Chain Length:0
Number of Molecules:4
Biological Source:Sus scrofa
UniProt ID:A0A8D0XPB4
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Collagen type XI alpha 1 chai
Gene (Uniprot):COL11A1
Chain IDs:G (auth: BC), JB (auth: GC), MD (auth: LC), PF (auth: QC)
Chain Length:0
Number of Molecules:4
Biological Source:Sus scrofa
UniProt ID:A0A5G2RGP6
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Collagen type II alpha 1 chai
Gene (Uniprot):COL2A1
Chain IDs:S (auth: BD), T (auth: BE), U (auth: BF), HA (auth: BG), IA (auth: BH), JA (auth: BI), VB (auth: GD), WB (auth: GE), XB (auth: GF), KC (auth: GG), LC (auth: GH), MC (auth: GI), YD (auth: LD), ZD (auth: LE), AE (auth: LF), NE (auth: LG), OE (auth: LH), PE (auth: LI), BG (auth: QD), CG (auth: QE), DG (auth: QF), QG, RG (auth: QH), SG (auth: QI)
Chain Length:0
Number of Molecules:24
Biological Source:Sus scrofa
UniProt ID:A0A8D1U0L9
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Collagen alpha-1(IX) chain
Gene (Uniprot):COL9A1
Chain IDs:UA (auth: BJ), XC (auth: EJ), AF (auth: HJ), DH (auth: KJ)
Chain Length:0
Number of Molecules:4
Biological Source:Sus scrofa
UniProt ID:A0A8D0XSJ2
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Collagen type IX alpha 2 chai
Gene (Uniprot):COL9A2
Chain IDs:XA (auth: BK), AD (auth: EK), DF (auth: HK), GH (auth: KK)
Chain Length:0
Number of Molecules:4
Biological Source:Sus scrofa
UniProt ID:A0A4X1VU67
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Collagen alpha-3(IX) chain
Chain IDs:AB (auth: BL), DD (auth: EL), GF (auth: HL), JH (auth: KL)
Chain Length:0
Number of Molecules:4
Biological Source:Sus scrofa
UniProt ID:A0A4X1SJL5
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Fibrillar collagen NC1 domain
Chain IDs:C (auth: CA), FB (auth: HA), ID (auth: MA), LF (auth: RA)
Chain Length:0
Number of Molecules:4
Biological Source:Sus scrofa
UniProt ID:A0A8D1DM46
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Collagen type V alpha 2 chain
Chain IDs:M (auth: CB), PB (auth: HB), SD (auth: MB), VF (auth: RB)
Chain Length:0
Number of Molecules:4
Biological Source:Sus scrofa
UniProt ID:A0A4X1TRM1
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Collagen type XI alpha 1 chai
Gene (Uniprot):COL11A1
Chain IDs:H (auth: CC), KB (auth: HC), ND (auth: MC), QF (auth: RC)
Chain Length:0
Number of Molecules:4
Biological Source:Sus scrofa
UniProt ID:A0A4X1TLK6
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Collagen type II alpha 1 chai
Gene (Uniprot):COL2A1
Chain IDs:V (auth: CD), W (auth: CE), X (auth: CF), KA (auth: CG), LA (auth: CH), MA (auth: CI), YB (auth: HD), ZB (auth: HE), AC (auth: HF), NC (auth: HG), OC (auth: HH), PC (auth: HI), BE (auth: MD), CE (auth: ME), DE (auth: MF), QE (auth: MG), RE (auth: MH), SE (auth: MI), EG (auth: RD), FG (auth: RE), GG (auth: RF), TG (auth: RG), UG (auth: RH), VG (auth: RI)
Chain Length:0
Number of Molecules:24
Biological Source:Sus scrofa
UniProt ID:A0A8D1VPS8
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Collagen alpha-1(IX) chain
Gene (Uniprot):COL9A1
Chain IDs:VA (auth: CJ), YC (auth: FJ), BF (auth: IJ), EH (auth: LJ)
Chain Length:0
Number of Molecules:4
Biological Source:Sus scrofa
UniProt ID:A0A8D1PQ72
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Collagen type IX alpha 2 chai
Gene (Uniprot):COL9A2
Chain IDs:YA (auth: CK), BD (auth: FK), EF (auth: IK), HH (auth: LK)
Chain Length:0
Number of Molecules:4
Biological Source:Sus scrofa
UniProt ID:A0A4X1VU67
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Collagen alpha-3(IX) chain
Gene (Uniprot):COL9A3
Chain IDs:BB (auth: CL), ED (auth: FL), HF (auth: IL), KH (auth: LL)
Chain Length:0
Number of Molecules:4
Biological Source:Sus scrofa
UniProt ID:A0A8D1N974
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Fibrillar collagen NC1 domain
Chain IDs:D (auth: DA), GB (auth: IA), JD (auth: NA), MF (auth: SA)
Chain Length:0
Number of Molecules:4
Biological Source:Sus scrofa
UniProt ID:A0A8D1DM80
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Collagen alpha-2(V) chain pre
Gene (Uniprot):COL5A2
Chain IDs:N (auth: DB), QB (auth: IB), TD (auth: NB), WF (auth: SB)
Chain Length:0
Number of Molecules:4
Biological Source:Sus scrofa
UniProt ID:F1RXW0 Pfam ID:PF01391
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Fibrillar collagen NC1 domain
Chain IDs:I (auth: DC), LB (auth: IC), OD (auth: NC), RF (auth: SC)
Chain Length:0
Number of Molecules:4
Biological Source:Sus scrofa
UniProt ID:A0A8D1N6J3
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Collagen type II alpha 1 chai
Gene (Uniprot):COL2A1
Chain IDs:Y (auth: DD), Z (auth: DE), AA (auth: DF), NA (auth: DG), OA (auth: DH), PA (auth: DI), BC (auth: ID), CC (auth: IE), DC (auth: IF), QC (auth: IG), RC (auth: IH), SC (auth: II), EE (auth: ND), FE (auth: NE), GE (auth: NF), TE (auth: NG), UE (auth: NH), VE (auth: NI), HG (auth: SD), IG (auth: SE), JG (auth: SF), WG (auth: SG), XG (auth: SH), YG (auth: SI)
Chain Length:0
Number of Molecules:24
Biological Source:Sus scrofa
UniProt ID:A0A8D1U0L9
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Fibrillar collagen NC1 domain
Chain IDs:E (auth: EA), HB (auth: JA), KD (auth: OA), NF (auth: TA)
Chain Length:0
Number of Molecules:4
Biological Source:Sus scrofa
UniProt ID:A0A8D1DM46
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Collagen alpha-2(V) chain pre
Gene (Uniprot):COL5A2
Chain IDs:O (auth: EB), RB (auth: JB), UD (auth: OB), XF (auth: TB)
Chain Length:0
Number of Molecules:4
Biological Source:Sus scrofa
UniProt ID:F1RXW0 Pfam ID:PF01391
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Fibrillar collagen NC1 domain
Chain IDs:J (auth: EC), MB (auth: JC), PD (auth: OC), SF (auth: TC)
Chain Length:0
Number of Molecules:4
Biological Source:Sus scrofa
UniProt ID:A0A8D1N6J3
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Collagen type II alpha 1 chai
Gene (Uniprot):COL2A1
Chain IDs:BA (auth: ED), CA (auth: EE), DA (auth: EF), QA (auth: EG), RA (auth: EH), SA (auth: EI), EC (auth: JD), FC (auth: JE), GC (auth: JF), TC (auth: JG), UC (auth: JH), VC (auth: JI), HE (auth: OD), IE (auth: OE), JE (auth: OF), WE (auth: OG), XE (auth: OH), YE (auth: OI), KG (auth: TD), LG (auth: TE), MG (auth: TF), ZG (auth: TG), AH (auth: TH), BH (auth: TI)
Chain Length:0
Number of Molecules:24
Biological Source:Sus scrofa
UniProt ID:A0A8D1U0L9
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
LYZ A LYS modified residue
Ligand Molecules
GAL
GLC
Primary Citation
The molecular architecture of mammalian vitreous body collagen fibrils.
Science 393 509 513 (2026)
PMID: 42531406 DOI: 10.1126/science.aec2906

Abstact

Collagen, a fundamental constituent of the extracellular matrix, has long remained elusive to high-resolution structural characterization. Using a tailored system and optimized cryo-electron microscopy processing for long-period filaments, we determined the structure of native collagen fibrils from the porcine vitreous body, with local resolutions extending from 2.6 to 7 angstroms. Each 67-nanometer periodic unit contains type II, V/XI, and IX collagen triple helices together with opticin, at a stoichiometry of 8:4:4:4, which reveals their detailed higher-order molecular packing. Abundant galactose-glucose disaccharides modify hydroxylysine residues in conserved -glycine-X-hydroxylysine- motifs, mediating fibril packing and structural stability. Our structure uncovers the glycan-mediated assembly principle of collagen fibrils and clarifies the structure-function basis of collagens in the vitreous body.

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Protein

Chemical

Disease

Primary Citation of related structures
9WXP
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