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- PDB-9wxp: cryo-EM structure of a mammalian collagen fibril -

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Basic information

Entry
Database: PDB / ID: 9wxp
Titlecryo-EM structure of a mammalian collagen fibril
Components
  • (Collagen alpha-1(IX) ...) x 2
  • (Collagen alpha-2(V) chain ...) x 2
  • (Collagen alpha-3(IX) ...) x 3
  • (Collagen type II alpha 1 ...) x 5
  • (Collagen type IX alpha 2 ...) x 3
  • (Collagen type V alpha 2 ...) x 2
  • (Collagen type XI alpha 1 ...) x 3
  • (Fibrillar collagen NC1 domain-containing ...) x 6
  • Chromaffin granule amine transporter isoform X1
  • Collagen alpha-1(V) chain
  • Collagen type IX alpha 1 chain
  • Opticin
KeywordsPROTEIN FIBRIL / collagen / glycan
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
beta-D-galactopyranose / alpha-D-glucopyranose / 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 ...beta-D-galactopyranose / alpha-D-glucopyranose / 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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsLou, X. / Cong, Y. / Xu, Y. / Yan, C.
Funding support China, 1items
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, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Aug 5, 2026Provider: repository / Type: Initial release
Revision 1.0Aug 5, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Aug 5, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Aug 5, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AA: Collagen alpha-1(V) chain
BA: Fibrillar collagen NC1 domain-containing protein
CA: Fibrillar collagen NC1 domain-containing protein
DA: Fibrillar collagen NC1 domain-containing protein
EA: Fibrillar collagen NC1 domain-containing protein
AC: Collagen type XI alpha 1 chain
BC: Collagen type XI alpha 1 chain
CC: Collagen type XI alpha 1 chain
DC: Fibrillar collagen NC1 domain-containing protein
EC: Fibrillar collagen NC1 domain-containing protein
AB: Chromaffin granule amine transporter isoform X1
BB: Collagen type V alpha 2 chain
CB: Collagen type V alpha 2 chain
DB: Collagen alpha-2(V) chain preproprotein
EB: Collagen alpha-2(V) chain preproprotein
AD: Collagen type II alpha 1 chain
AE: Collagen type II alpha 1 chain
AF: Collagen type II alpha 1 chain
BD: Collagen type II alpha 1 chain
BE: Collagen type II alpha 1 chain
BF: Collagen type II alpha 1 chain
CD: Collagen type II alpha 1 chain
CE: Collagen type II alpha 1 chain
CF: Collagen type II alpha 1 chain
DD: Collagen type II alpha 1 chain
DE: Collagen type II alpha 1 chain
DF: Collagen type II alpha 1 chain
ED: Collagen type II alpha 1 chain
EE: Collagen type II alpha 1 chain
EF: Collagen type II alpha 1 chain
AG: Collagen type II alpha 1 chain
AH: Collagen type II alpha 1 chain
AI: Collagen type II alpha 1 chain
BG: Collagen type II alpha 1 chain
BH: Collagen type II alpha 1 chain
BI: Collagen type II alpha 1 chain
CG: Collagen type II alpha 1 chain
CH: Collagen type II alpha 1 chain
CI: Collagen type II alpha 1 chain
DG: Collagen type II alpha 1 chain
DH: Collagen type II alpha 1 chain
DI: Collagen type II alpha 1 chain
EG: Collagen type II alpha 1 chain
EH: Collagen type II alpha 1 chain
EI: Collagen type II alpha 1 chain
AJ: Collagen type IX alpha 1 chain
BJ: Collagen alpha-1(IX) chain
CJ: Collagen alpha-1(IX) chain
AK: Collagen type IX alpha 2 chain
BK: Collagen type IX alpha 2 chain
CK: Collagen type IX alpha 2 chain
AL: Collagen alpha-3(IX) chain
BL: Collagen alpha-3(IX) chain
CL: Collagen alpha-3(IX) chain
AM: Opticin
FA: Collagen alpha-1(V) chain
GA: Fibrillar collagen NC1 domain-containing protein
HA: Fibrillar collagen NC1 domain-containing protein
IA: Fibrillar collagen NC1 domain-containing protein
JA: Fibrillar collagen NC1 domain-containing protein
FC: Collagen type XI alpha 1 chain
GC: Collagen type XI alpha 1 chain
HC: Collagen type XI alpha 1 chain
IC: Fibrillar collagen NC1 domain-containing protein
JC: Fibrillar collagen NC1 domain-containing protein
FB: Chromaffin granule amine transporter isoform X1
GB: Collagen type V alpha 2 chain
HB: Collagen type V alpha 2 chain
IB: Collagen alpha-2(V) chain preproprotein
JB: Collagen alpha-2(V) chain preproprotein
FD: Collagen type II alpha 1 chain
FE: Collagen type II alpha 1 chain
FF: Collagen type II alpha 1 chain
GD: Collagen type II alpha 1 chain
GE: Collagen type II alpha 1 chain
GF: Collagen type II alpha 1 chain
HD: Collagen type II alpha 1 chain
HE: Collagen type II alpha 1 chain
HF: Collagen type II alpha 1 chain
ID: Collagen type II alpha 1 chain
IE: Collagen type II alpha 1 chain
IF: Collagen type II alpha 1 chain
JD: Collagen type II alpha 1 chain
JE: Collagen type II alpha 1 chain
JF: Collagen type II alpha 1 chain
FG: Collagen type II alpha 1 chain
FH: Collagen type II alpha 1 chain
FI: Collagen type II alpha 1 chain
GG: Collagen type II alpha 1 chain
GH: Collagen type II alpha 1 chain
GI: Collagen type II alpha 1 chain
HG: Collagen type II alpha 1 chain
HH: Collagen type II alpha 1 chain
HI: Collagen type II alpha 1 chain
IG: Collagen type II alpha 1 chain
IH: Collagen type II alpha 1 chain
II: Collagen type II alpha 1 chain
JG: Collagen type II alpha 1 chain
JH: Collagen type II alpha 1 chain
JI: Collagen type II alpha 1 chain
DJ: Collagen type IX alpha 1 chain
EJ: Collagen alpha-1(IX) chain
FJ: Collagen alpha-1(IX) chain
DK: Collagen type IX alpha 2 chain
EK: Collagen type IX alpha 2 chain
FK: Collagen type IX alpha 2 chain
DL: Collagen alpha-3(IX) chain
EL: Collagen alpha-3(IX) chain
FL: Collagen alpha-3(IX) chain
BM: Opticin
KA: Collagen alpha-1(V) chain
LA: Fibrillar collagen NC1 domain-containing protein
MA: Fibrillar collagen NC1 domain-containing protein
NA: Fibrillar collagen NC1 domain-containing protein
OA: Fibrillar collagen NC1 domain-containing protein
KC: Collagen type XI alpha 1 chain
LC: Collagen type XI alpha 1 chain
MC: Collagen type XI alpha 1 chain
NC: Fibrillar collagen NC1 domain-containing protein
OC: Fibrillar collagen NC1 domain-containing protein
KB: Chromaffin granule amine transporter isoform X1
LB: Collagen type V alpha 2 chain
MB: Collagen type V alpha 2 chain
NB: Collagen alpha-2(V) chain preproprotein
OB: Collagen alpha-2(V) chain preproprotein
KD: Collagen type II alpha 1 chain
KE: Collagen type II alpha 1 chain
KF: Collagen type II alpha 1 chain
LD: Collagen type II alpha 1 chain
LE: Collagen type II alpha 1 chain
LF: Collagen type II alpha 1 chain
MD: Collagen type II alpha 1 chain
ME: Collagen type II alpha 1 chain
MF: Collagen type II alpha 1 chain
ND: Collagen type II alpha 1 chain
NE: Collagen type II alpha 1 chain
NF: Collagen type II alpha 1 chain
OD: Collagen type II alpha 1 chain
OE: Collagen type II alpha 1 chain
OF: Collagen type II alpha 1 chain
KG: Collagen type II alpha 1 chain
KH: Collagen type II alpha 1 chain
KI: Collagen type II alpha 1 chain
LG: Collagen type II alpha 1 chain
LH: Collagen type II alpha 1 chain
LI: Collagen type II alpha 1 chain
MG: Collagen type II alpha 1 chain
MH: Collagen type II alpha 1 chain
MI: Collagen type II alpha 1 chain
NG: Collagen type II alpha 1 chain
NH: Collagen type II alpha 1 chain
NI: Collagen type II alpha 1 chain
OG: Collagen type II alpha 1 chain
OH: Collagen type II alpha 1 chain
OI: Collagen type II alpha 1 chain
GJ: Collagen type IX alpha 1 chain
HJ: Collagen alpha-1(IX) chain
IJ: Collagen alpha-1(IX) chain
GK: Collagen type IX alpha 2 chain
HK: Collagen type IX alpha 2 chain
IK: Collagen type IX alpha 2 chain
GL: Collagen alpha-3(IX) chain
HL: Collagen alpha-3(IX) chain
IL: Collagen alpha-3(IX) chain
CM: Opticin
PA: Collagen alpha-1(V) chain
QA: Fibrillar collagen NC1 domain-containing protein
RA: Fibrillar collagen NC1 domain-containing protein
SA: Fibrillar collagen NC1 domain-containing protein
TA: Fibrillar collagen NC1 domain-containing protein
PC: Collagen type XI alpha 1 chain
QC: Collagen type XI alpha 1 chain
RC: Collagen type XI alpha 1 chain
SC: Fibrillar collagen NC1 domain-containing protein
TC: Fibrillar collagen NC1 domain-containing protein
PB: Chromaffin granule amine transporter isoform X1
QB: Collagen type V alpha 2 chain
RB: Collagen type V alpha 2 chain
SB: Collagen alpha-2(V) chain preproprotein
TB: Collagen alpha-2(V) chain preproprotein
PD: Collagen type II alpha 1 chain
PE: Collagen type II alpha 1 chain
PF: Collagen type II alpha 1 chain
QD: Collagen type II alpha 1 chain
QE: Collagen type II alpha 1 chain
QF: Collagen type II alpha 1 chain
RD: Collagen type II alpha 1 chain
RE: Collagen type II alpha 1 chain
RF: Collagen type II alpha 1 chain
SD: Collagen type II alpha 1 chain
SE: Collagen type II alpha 1 chain
SF: Collagen type II alpha 1 chain
TD: Collagen type II alpha 1 chain
TE: Collagen type II alpha 1 chain
TF: Collagen type II alpha 1 chain
PG: Collagen type II alpha 1 chain
PH: Collagen type II alpha 1 chain
PI: Collagen type II alpha 1 chain
QG: Collagen type II alpha 1 chain
QH: Collagen type II alpha 1 chain
QI: Collagen type II alpha 1 chain
RG: Collagen type II alpha 1 chain
RH: Collagen type II alpha 1 chain
RI: Collagen type II alpha 1 chain
SG: Collagen type II alpha 1 chain
SH: Collagen type II alpha 1 chain
SI: Collagen type II alpha 1 chain
TG: Collagen type II alpha 1 chain
TH: Collagen type II alpha 1 chain
TI: Collagen type II alpha 1 chain
JJ: Collagen type IX alpha 1 chain
KJ: Collagen alpha-1(IX) chain
LJ: Collagen alpha-1(IX) chain
JK: Collagen type IX alpha 2 chain
KK: Collagen type IX alpha 2 chain
LK: Collagen type IX alpha 2 chain
JL: Collagen alpha-3(IX) chain
KL: Collagen alpha-3(IX) chain
LL: Collagen alpha-3(IX) chain
DM: Opticin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,134,991600
Polymers4,006,215220
Non-polymers128,776380
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 4 types, 16 molecules AAFAKAPAABFBKBPBAJDJGJJJAMBMCMDM

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


Mass: 23201.516 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A480MJQ8
#11: Protein
Chromaffin granule amine transporter isoform X1 / Collagen alpha-2(V) chain preproprotein


Mass: 21432.652 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A480YT77
#21: Protein
Collagen type IX alpha 1 chain


Mass: 5459.867 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A8X9AEQ8
#30: Protein
Opticin


Mass: 23674.270 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A8D0IR51

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Fibrillar collagen NC1 domain-containing ... , 6 types, 24 molecules BAGALAQACAHAMARADAIANASAEAJAOATADCICNCSCECJCOCTC

#2: Protein
Fibrillar collagen NC1 domain-containing protein


Mass: 22416.535 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A8D1DM46
#3: Protein
Fibrillar collagen NC1 domain-containing protein


Mass: 21669.555 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A8D1DM46
#4: Protein
Fibrillar collagen NC1 domain-containing protein


Mass: 21587.170 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A8D1DM80
#5: Protein
Fibrillar collagen NC1 domain-containing protein


Mass: 6999.511 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A8D1DM46
#9: Protein
Fibrillar collagen NC1 domain-containing protein


Mass: 21355.842 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A8D1N6J3
#10: Protein
Fibrillar collagen NC1 domain-containing protein


Mass: 6852.358 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A8D1N6J3

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Collagen type XI alpha 1 ... , 3 types, 12 molecules ACFCKCPCBCGCLCQCCCHCMCRC

#6: Protein
Collagen type XI alpha 1 chain


Mass: 23352.639 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1TLK6
#7: Protein
Collagen type XI alpha 1 chain


Mass: 22244.246 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A5G2RGP6
#8: Protein
Collagen type XI alpha 1 chain


Mass: 21615.338 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1TLK6

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Collagen type V alpha 2 ... , 2 types, 8 molecules BBGBLBQBCBHBMBRB

#12: Protein
Collagen type V alpha 2 chain


Mass: 21671.557 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A8D0XPB4
#13: Protein
Collagen type V alpha 2 chain


Mass: 21379.926 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1TRM1

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Collagen alpha-2(V) chain ... , 2 types, 8 molecules DBIBNBSBEBJBOBTB

#14: Protein
Collagen alpha-2(V) chain preproprotein / Collagen type V alpha 2 chain


Mass: 22060.861 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1RXW0
#15: Protein
Collagen alpha-2(V) chain preproprotein / Collagen type V alpha 2 chain


Mass: 6758.372 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1RXW0

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Collagen type II alpha 1 ... , 5 types, 120 molecules ADAEAFAGAHAIFDFEFFFGFHFIKDKEKFKGKHKIPDPEPFPGPHPIBDBEBFBGBHBI...

#16: Protein ...
Collagen type II alpha 1 chain


Mass: 15503.065 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A8D1U0L9
#17: Protein ...
Collagen type II alpha 1 chain


Mass: 22314.205 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A8D1U0L9
#18: Protein ...
Collagen type II alpha 1 chain


Mass: 20160.889 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A8D1VPS8
#19: Protein ...
Collagen type II alpha 1 chain


Mass: 21328.770 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A8D1U0L9
#20: Protein ...
Collagen type II alpha 1 chain


Mass: 14454.652 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A8D1U0L9

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Collagen alpha-1(IX) ... , 2 types, 8 molecules BJEJHJKJCJFJIJLJ

#22: Protein
Collagen alpha-1(IX) chain


Mass: 21571.920 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A8D0XSJ2
#23: Protein
Collagen alpha-1(IX) chain


Mass: 16613.785 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A8D1PQ72

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Collagen type IX alpha 2 ... , 3 types, 12 molecules AKDKGKJKBKEKHKKKCKFKIKLK

#24: Protein
Collagen type IX alpha 2 chain


Mass: 5336.972 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A8D0V1I3
#25: Protein
Collagen type IX alpha 2 chain


Mass: 21813.746 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1VU67
#26: Protein
Collagen type IX alpha 2 chain


Mass: 16681.969 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1VU67

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Collagen alpha-3(IX) ... , 3 types, 12 molecules ALDLGLJLBLELHLKLCLFLILLL

#27: Protein
Collagen alpha-3(IX) chain


Mass: 5475.208 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A8D1N974
#28: Protein
Collagen alpha-3(IX) chain


Mass: 21485.480 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1SJL5
#29: Protein
Collagen alpha-3(IX) chain


Mass: 16272.949 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A8D1N974

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Sugars , 3 types, 380 molecules

#31: Polysaccharide...
alpha-D-glucopyranose-(1-2)-beta-D-galactopyranose


Type: oligosaccharide / Mass: 342.297 Da / Num. of mol.: 372
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpa1-2DGalpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2112h-1b_1-5][a2122h-1a_1-5]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-Galp]{[(2+1)][b-D-Glcp]{}}LINUCSPDB-CARE
#32: Sugar
ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H12O6
IdentifierTypeProgram
DGlcpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#33: Sugar
ChemComp-GAL / beta-D-galactopyranose / beta-D-galactose / D-galactose / galactose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H12O6
IdentifierTypeProgram
DGalpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-galactopyranoseCOMMON NAMEGMML 1.0
b-D-GalpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: collagen / Type: COMPLEX / Entity ID: #1-#30 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Sus scrofa (pig)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.21.1_5286model refinement
10cryoSPARCinitial Euler assignment
13cryoSPARC3D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 600039 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 110.85 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0029289008
ELECTRON MICROSCOPYf_angle_d0.7018394328
ELECTRON MICROSCOPYf_chiral_restr0.035736040
ELECTRON MICROSCOPYf_plane_restr0.006759216
ELECTRON MICROSCOPYf_dihedral_angle_d4.54252317

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  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
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External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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