9WXP | pdb_00009wxp

cryo-EM structure of a mammalian collagen fibril


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: SINGLE PARTICLE 

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This is version 1.1 of the entry. See complete history

Literature

The molecular architecture of mammalian vitreous body collagen fibrils.

Lou, X.Cong, Y.Xu, Y.Liu, Y.Li, Y.Yan, C.

(2026) Science 393: 509-513

  • DOI: https://doi.org/10.1126/science.aec2906
  • Primary Citation Related Structures: 
    9WXP

  • PubMed Abstract: 

    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.


  • Organizational Affiliation
    • State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structures, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China.

Macromolecule Content 

  • Total Structure Weight: 4,134.99 kDa 
  • Atom Count: 279,032 
  • Modeled Residue Count: 42,376 
  • Deposited Residue Count: 43,552 
  • Unique protein chains: 30

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Collagen alpha-1(V) chainA [auth AA],
DB [auth FA],
GD [auth KA],
JF [auth PA]
246Sus scrofaMutation(s): 0 
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Fibrillar collagen NC1 domain-containing proteinB [auth BA],
EB [auth GA],
HD [auth LA],
KF [auth QA]
233Sus scrofaMutation(s): 0 
UniProt
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Fibrillar collagen NC1 domain-containing proteinC [auth CA],
FB [auth HA],
ID [auth MA],
LF [auth RA]
234Sus scrofaMutation(s): 0 
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Fibrillar collagen NC1 domain-containing proteinD [auth DA],
GB [auth IA],
JD [auth NA],
MF [auth SA]
237Sus scrofaMutation(s): 0 
UniProt
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Fibrillar collagen NC1 domain-containing proteinE [auth EA],
HB [auth JA],
KD [auth OA],
NF [auth TA]
77Sus scrofaMutation(s): 0 
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Collagen type XI alpha 1 chainF [auth AC],
IB [auth FC],
LD [auth KC],
OF [auth PC]
246Sus scrofaMutation(s): 0 
UniProt
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Reference Sequence
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
Collagen type XI alpha 1 chainG [auth BC],
JB [auth GC],
MD [auth LC],
PF [auth QC]
233Sus scrofaMutation(s): 0 
UniProt
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Reference Sequence
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
Collagen type XI alpha 1 chainH [auth CC],
KB [auth HC],
ND [auth MC],
QF [auth RC]
235Sus scrofaMutation(s): 0 
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Reference Sequence
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
Fibrillar collagen NC1 domain-containing proteinI [auth DC],
LB [auth IC],
OD [auth NC],
RF [auth SC]
236Sus scrofaMutation(s): 0 
UniProt
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Reference Sequence
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
Fibrillar collagen NC1 domain-containing proteinJ [auth EC],
MB [auth JC],
PD [auth OC],
SF [auth TC]
76Sus scrofaMutation(s): 0 
UniProt
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Reference Sequence
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
Chromaffin granule amine transporter isoform X1K [auth AB],
NB [auth FB],
QD [auth KB],
TF [auth PB]
231Sus scrofaMutation(s): 0 
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Reference Sequence
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Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
Collagen type V alpha 2 chainL [auth BB],
OB [auth GB],
RD [auth LB],
UF [auth QB]
233Sus scrofaMutation(s): 0 
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Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
Collagen type V alpha 2 chainM [auth CB],
PB [auth HB],
SD [auth MB],
VF [auth RB]
234Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 14
MoleculeChains  Sequence LengthOrganismDetailsImage
Collagen alpha-2(V) chain preproproteinN [auth DB],
QB [auth IB],
TD [auth NB],
WF [auth SB]
237Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 15
MoleculeChains  Sequence LengthOrganismDetailsImage
Collagen alpha-2(V) chain preproproteinO [auth EB],
RB [auth JB],
UD [auth OB],
XF [auth TB]
76Sus scrofaMutation(s): 0 
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Entity ID: 16
MoleculeChains  Sequence LengthOrganismDetailsImage
Collagen type II alpha 1 chain169Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 17
MoleculeChains  Sequence LengthOrganismDetailsImage
Collagen type II alpha 1 chain248Sus scrofaMutation(s): 0 
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Entity ID: 18
MoleculeChains  Sequence LengthOrganismDetailsImage
Collagen type II alpha 1 chain223Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 19
MoleculeChains  Sequence LengthOrganismDetailsImage
Collagen type II alpha 1 chain237Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 20
MoleculeChains  Sequence LengthOrganismDetailsImage
Collagen type II alpha 1 chain162Sus scrofaMutation(s): 0 
UniProt
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Reference Sequence
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Entity ID: 21
MoleculeChains  Sequence LengthOrganismDetailsImage
Collagen type IX alpha 1 chainCH [auth JJ],
TA [auth AJ],
WC [auth DJ],
ZE [auth GJ]
58Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 22
MoleculeChains  Sequence LengthOrganismDetailsImage
Collagen alpha-1(IX) chainAF [auth HJ],
DH [auth KJ],
UA [auth BJ],
XC [auth EJ]
231Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 23
MoleculeChains  Sequence LengthOrganismDetailsImage
Collagen alpha-1(IX) chainBF [auth IJ],
EH [auth LJ],
VA [auth CJ],
YC [auth FJ]
171Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 24
MoleculeChains  Sequence LengthOrganismDetailsImage
Collagen type IX alpha 2 chainCF [auth GK],
FH [auth JK],
WA [auth AK],
ZC [auth DK]
58Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 25
MoleculeChains  Sequence LengthOrganismDetailsImage
Collagen type IX alpha 2 chainAD [auth EK],
DF [auth HK],
GH [auth KK],
XA [auth BK]
232Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 26
MoleculeChains  Sequence LengthOrganismDetailsImage
Collagen type IX alpha 2 chainBD [auth FK],
EF [auth IK],
HH [auth LK],
YA [auth CK]
170Sus scrofaMutation(s): 0 
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Entity ID: 27
MoleculeChains  Sequence LengthOrganismDetailsImage
Collagen alpha-3(IX) chainCD [auth DL],
FF [auth GL],
IH [auth JL],
ZA [auth AL]
58Sus scrofaMutation(s): 0 
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Entity ID: 28
MoleculeChains  Sequence LengthOrganismDetailsImage
Collagen alpha-3(IX) chainAB [auth BL],
DD [auth EL],
GF [auth HL],
JH [auth KL]
232Sus scrofaMutation(s): 0 
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Entity ID: 29
MoleculeChains  Sequence LengthOrganismDetailsImage
Collagen alpha-3(IX) chainBB [auth CL],
ED [auth FL],
HF [auth IL],
KH [auth LL]
170Sus scrofaMutation(s): 0 
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Entity ID: 30
MoleculeChains  Sequence LengthOrganismDetailsImage
OpticinCB [auth AM],
FD [auth BM],
IF [auth CM],
LH [auth DM]
210Sus scrofaMutation(s): 0 
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Reference Sequence

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Entity ID: 31
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-glucopyranose-(1-2)-beta-D-galactopyranose
AI [auth Qa],
AJ [auth De],
AK [auth Li],
AL [auth ri],
AM [auth fb],
AI [auth Qa],
AJ [auth De],
AK [auth Li],
AL [auth ri],
AM [auth fb],
AN [auth Pf],
AO [auth Zj],
AP [auth Mc],
AQ [auth sc],
AR [auth Hk],
AS [auth nk],
AT [auth ad],
AU [auth Lh],
AV [auth Tl],
BI [auth Ra],
BJ [auth Ee],
BK [auth Mi],
BL [auth Ab],
BM [auth hb],
BN [auth Rf],
BO [auth bj],
BP [auth Nc],
BQ [auth Ag],
BR [auth Ik],
BS [auth ok],
BT [auth cd],
BU [auth Mh],
BV [auth Ul],
CI [auth Ta],
CJ [auth Ge],
CK [auth Ni],
CL [auth Bb],
CM [auth jb],
CN [auth Sf],
CO [auth cj],
CP [auth Oc],
CQ [auth Bg],
CR [auth Jk],
CS [auth pk],
CT [auth dd],
CU [auth Nh],
CV [auth Xl],
DI [auth Ua],
DJ [auth He],
DK [auth Oi],
DL [auth Cb],
DM [auth kb],
DN [auth Vf],
DO [auth dj],
DP [auth Pc],
DQ [auth Cg],
DR [auth Kk],
DS [auth qk],
DT [auth ed],
DU [auth Oh],
DV [auth Yl],
EI [auth Va],
EJ [auth Ie],
EK [auth Pi],
EL [auth Eb],
EM [auth lb],
EN [auth Wf],
EO [auth ej],
EP [auth Qc],
EQ [auth Dg],
ER [auth Lk],
ES [auth rk],
ET [auth fd],
EU [auth Ph],
EV [auth Zl],
FI [auth Ya],
FJ [auth Je],
FK [auth Qi],
FL [auth Gb],
FM [auth mb],
FN [auth Aj],
FO [auth gj],
FP [auth Rc],
FQ [auth Eg],
FR [auth Mk],
FS [auth Ad],
FT [auth hd],
FU [auth Rh],
FV [auth bl],
GI [auth Za],
GJ [auth Ke],
GK [auth Si],
GL [auth Hb],
GM [auth nb],
GN [auth Bj],
GO [auth ij],
GP [auth Tc],
GQ [auth Gg],
GR [auth Nk],
GS [auth Bd],
GT [auth jd],
GU [auth Sh],
GV [auth cl],
HI [auth aa],
HJ [auth Le],
HK [auth Ti],
HL [auth Ib],
HM [auth ob],
HN [auth Cj],
HO [auth jj],
HP [auth Uc],
HQ [auth Hg],
HR [auth Ok],
HS [auth Cd],
HT [auth kd],
HU [auth Vh],
HV [auth dl],
II [auth ca],
IJ [auth Me],
IK [auth Ui],
IL [auth Jb],
IM [auth pb],
IN [auth Dj],
IO [auth kj],
IP [auth Vc],
IQ [auth Ig],
IR [auth Pk],
IS [auth Ed],
IT [auth ld],
IU [auth Wh],
IV [auth el],
JI [auth da],
JJ [auth Ne],
JK [auth Xi],
JL [auth Kb],
JM [auth qb],
JN [auth Fj],
JO [auth lj],
JP [auth Yc],
JQ [auth Jg],
JR [auth Qk],
JS [auth Gd],
JT [auth md],
JU [auth Al],
JV [auth gl],
KI [auth ea],
KJ [auth Oe],
KK [auth Yi],
KL [auth Lb],
KM [auth rb],
KN [auth Gj],
KO [auth mj],
KP [auth Zc],
KQ [auth Kg],
KR [auth Sk],
KS [auth Hd],
KT [auth nd],
KU [auth Bl],
KV [auth il],
LI [auth fa],
LJ [auth Pe],
LK [auth Zi],
LL [auth Mb],
LM [auth sb],
LN [auth Hj],
LO [auth nj],
LP [auth ac],
LQ [auth Lg],
LR [auth Tk],
LS [auth Id],
LT [auth od],
LU [auth Cl],
LV [auth jl],
MH [auth Aa],
MI [auth ha],
MJ [auth Re],
MK [auth bi],
ML [auth Nb],
MM [auth Af],
MN [auth Ij],
MO [auth oj],
MP [auth cc],
MQ [auth Mg],
MR [auth Uk],
MS [auth Jd],
MT [auth pd],
MU [auth Dl],
MV [auth kl],
NH [auth Ba],
NI [auth ja],
NJ [auth Se],
NK [auth ci],
NL [auth Ob],
NM [auth Bf],
NN [auth Jj],
NO [auth pj],
NP [auth dc],
NQ [auth Ng],
NR [auth Xk],
NS [auth Kd],
NT [auth qd],
NU [auth Fl],
NV [auth ll],
OH [auth Ca],
OI [auth ka],
OJ [auth Ve],
OK [auth di],
OL [auth Pb],
OM [auth Cf],
ON [auth Kj],
OO [auth qj],
OP [auth ec],
OQ [auth Og],
OR [auth Yk],
OS [auth Ld],
OT [auth rd],
OU [auth Gl],
OV [auth ml],
PH [auth Ea],
PI [auth la],
PJ [auth We],
PK [auth ei],
PL [auth Qb],
PM [auth Df],
PN [auth Lj],
PO [auth rj],
PP [auth fc],
PQ [auth Pg],
PR [auth Zk],
PS [auth Md],
PT [auth sd],
PU [auth Hl],
PV [auth nl],
QH [auth Ga],
QI [auth ma],
QJ [auth Ai],
QK [auth gi],
QL [auth Rb],
QM [auth Ef],
QN [auth Mj],
QO [auth Ac],
QP [auth hc],
QQ [auth Rg],
QR [auth bk],
QS [auth Nd],
QT [auth Ah],
QU [auth Il],
QV [auth ol],
RH [auth Ha],
RI [auth na],
RJ [auth Bi],
RK [auth ii],
RL [auth Tb],
RM [auth Gf],
RN [auth Nj],
RO [auth Bc],
RP [auth jc],
RQ [auth Sg],
RR [auth ck],
RS [auth Od],
RT [auth Bh],
RU [auth Jl],
RV [auth pl],
SH [auth Ia],
SI [auth oa],
SJ [auth Ci],
SK [auth ji],
SL [auth Ub],
SM [auth Hf],
SN [auth Oj],
SO [auth Cc],
SP [auth kc],
SQ [auth Vg],
SR [auth dk],
SS [auth Pd],
ST [auth Ch],
SU [auth Kl],
SV [auth ql],
TH [auth Ja],
TI [auth pa],
TJ [auth Di],
TK [auth ki],
TL [auth Vb],
TM [auth If],
TN [auth Pj],
TO [auth Ec],
TP [auth lc],
TQ [auth Wg],
TR [auth ek],
TS [auth Qd],
TT [auth Dh],
TU [auth Ll],
TV [auth rl],
UH [auth Ka],
UI [auth qa],
UJ [auth Fi],
UK [auth li],
UL [auth Yb],
UM [auth Jf],
UN [auth Qj],
UO [auth Gc],
UP [auth mc],
UQ [auth Ak],
UR [auth gk],
US [auth Rd],
UT [auth Eh],
UU [auth Ml],
VH [auth La],
VI [auth ra],
VJ [auth Gi],
VK [auth mi],
VL [auth Zb],
VM [auth Kf],
VN [auth Sj],
VO [auth Hc],
VP [auth nc],
VQ [auth Bk],
VR [auth ik],
VS [auth Td],
VT [auth Gh],
VU [auth Nl],
WH [auth Ma],
WI [auth sa],
WJ [auth Hi],
WK [auth ni],
WL [auth ab],
WM [auth Lf],
WN [auth Tj],
WO [auth Ic],
WP [auth oc],
WQ [auth Ck],
WR [auth jk],
WS [auth Ud],
WT [auth Hh],
WU [auth Ol],
XH [auth Na],
XI [auth Ae],
XJ [auth Ii],
XK [auth oi],
XL [auth cb],
XM [auth Mf],
XN [auth Uj],
XO [auth Jc],
XP [auth pc],
XQ [auth Dk],
XR [auth kk],
XS [auth Vd],
XT [auth Ih],
XU [auth Pl],
YH [auth Oa],
YI [auth Be],
YJ [auth Ji],
YK [auth pi],
YL [auth db],
YM [auth Nf],
YN [auth Xj],
YO [auth Kc],
YP [auth qc],
YQ [auth Fk],
YR [auth lk],
YS [auth Yd],
YT [auth Jh],
YU [auth Ql],
ZH [auth Pa],
ZI [auth Ce],
ZJ [auth Ki],
ZK [auth qi],
ZL [auth eb],
ZM [auth Of],
ZN [auth Yj],
ZO [auth Lc],
ZP [auth rc],
ZQ [auth Gk],
ZR [auth mk],
ZS [auth Zd],
ZT [auth Kh],
ZU [auth Sl]
2N/A
Glycosylation Resources
GlyTouCan: G50348ER
GlyCosmos: G50348ER
GlyGen: G50348ER

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GLC

Query on GLC



Download:Ideal Coordinates CCD File
AW [auth RC],
UV [auth CC],
WV [auth HC],
YV [auth MC]
alpha-D-glucopyranose
C6 H12 O6
WQZGKKKJIJFFOK-DVKNGEFBSA-N
GAL

Query on GAL



Download:Ideal Coordinates CCD File
BW [auth PB],
VV [auth AB],
XV [auth FB],
ZV [auth KB]
beta-D-galactopyranose
C6 H12 O6
WQZGKKKJIJFFOK-FPRJBGLDSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
LYZ
Query on LYZ
A [auth AA],
DB [auth FA],
GD [auth KA],
JF [auth PA]
L-PEPTIDE LINKINGC6 H14 N2 O3LYS

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21.1_5286
RECONSTRUCTIONcryoSPARC

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China32341016

Revision History  (Full details and data files)

  • Version 1.0: 2026-08-05
    Type: Initial release
  • Version 1.1: 2026-08-12
    Changes: Data collection, Database references