9UFE | pdb_00009ufe

Cryo-EM structure of the tubular mastigoneme (the central tube) from golden algae 2.17 angstrom resolution

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.17 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 9UFE

This is version 1.1 of the entry. See complete history. 

Literature

Structural N- and O-glycans revealed by high-resolution cryo-EM analysis of tubular mastigonemes.

Huang, J., Tao, H., Chen, S., Cui, Y., Xu, Y., Yan, C., Yan, N.

(2026) Science : eaef4958-eaef4958

  • DOI: https://doi.org/10.1126/science.aef4958
  • Primary Citation Related Structures: 
    9UFE

  • PubMed Abstract: 

    The chemical complexity and non-templated biosynthesis of glycans have posed significant challenges for establishing sequence-structure relationships. Here we report cryo-EM structures of tubular mastigonemes from a golden alga species, Ochromonas danica , in which a large number of N- and O-glycans are resolved at 1.8-2.2 Å resolution. Beyond high-mannose and complex N-glycans, we identify a non-canonical N-glycan on the Ala- Asn -Asp (A N D) motif. The surface spikes comprise dense O-glycans coating PSXX tetrapeptide repeats, with two glycans linked on trihydroxylated proline and one on serine per repeat. In addition to various types of sugars and their covalent modifiers, water molecules (>10% of resolved volume) and cations are clearly resolved and mediate the structural assembly. Our study establishes a framework for investigating glycan folding in high-order biological assemblies.

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

Macromolecule Content 

  • Total Structure Weight: 1,006.78 kDa 
  • Atom Count: 71,986 
  • Modeled Residue Count: 7,632 
  • Deposited Residue Count: 8,289 
  • Unique protein chains: 6

Macromolecules

Find similar proteins by:
|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
OCM5A [auth EA],
G [auth EB],
M [auth EC]		368Ochromonas danicaMutation(s): 0 
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|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
OCM6B [auth FA],
H [auth FB],
N [auth FC]		723Ochromonas danicaMutation(s): 0 
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|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Tubular mastigoneme proteinC [auth DA],
I [auth DB],
O [auth DC]		209Ochromonas danicaMutation(s): 0 
UniProt
Find proteins for C4B7Q8 (Ochromonas danica)
Explore C4B7Q8 
Go to UniProtKB:  C4B7Q8
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC4B7Q8
Sequence Annotations
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Reference Sequence
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|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
OCM3D [auth CA],
J [auth CB],
P [auth CC]		349Ochromonas danicaMutation(s): 0 
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|  3D Structure
Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Tubular mastigoneme proteinE [auth AA],
K [auth AB],
Q [auth AC]		748Ochromonas danicaMutation(s): 0 
UniProt
Find proteins for A6P4C0 (Ochromonas danica)
Explore A6P4C0 
Go to UniProtKB:  A6P4C0
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA6P4C0
Glycosylation
Glycosylation Sites: 5
Sequence Annotations
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Reference Sequence
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|  3D Structure
Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Tubular mastigoneme proteinF [auth BA],
L [auth BB],
R [auth BC]		366Ochromonas danicaMutation(s): 0 
UniProt
Find proteins for C4B7Q7 (Ochromonas danica)
Explore C4B7Q7 
Go to UniProtKB:  C4B7Q7
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC4B7Q7
Glycosylation
Glycosylation Sites: 3
Sequence Annotations
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Reference Sequence

Oligosaccharides

Help  
Entity ID: 7
MoleculeChains Length2D Diagram GlycosylationD Interactions
beta-D-xylopyranose-(1-2)-beta-D-xylopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)][2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)][beta-D-xylopyranose-(1-2)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-2)][alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseAB [auth aK],
JA [auth aF],
S [auth aA]		14N-Glycosylation
Entity ID: 8
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-mannopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-D-mannopyranose-(1-2)-beta-D-xylopyranose-(1-6)][beta-D-xylopyranose-(1-3)]alpha-D-mannopyranose-(1-3)-[beta-D-mannopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-[beta-D-xylopyranose-(1-3)]alpha-D-mannopyranose-(1-6)][beta-D-xylopyranose-(1-2)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseBB [auth aL],
KA [auth aG],
T [auth aB]		16N-Glycosylation
Entity ID: 9
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-mannopyranose-(1-3)-[beta-D-mannopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-D-xylopyranose-(1-2)-beta-D-xylopyranose-(1-6)][beta-D-glucopyranose-(1-3)]alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)][beta-D-xylopyranose-(1-2)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-2)][alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseCB [auth aM],
LA [auth aH],
U [auth aC]		16N-Glycosylation
Entity ID: 10
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseDB [auth aN],
MA [auth aI],
V [auth aD]		9N-Glycosylation
Glycosylation Resources
GlyTouCan: G04216GB
GlyCosmos: G04216GB
GlyGen: G04216GB
Entity ID: 11
MoleculeChains Length2D Diagram GlycosylationD Interactions
beta-D-xylopyranose-(1-2)-beta-D-xylopyranose-(1-6)-[beta-D-xylopyranose-(1-3)][2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-[beta-D-xylopyranose-(1-3)]alpha-D-mannopyranose-(1-6)][beta-D-xylopyranose-(1-2)]alpha-D-mannopyranose-(1-6)-[beta-D-mannopyranose-(1-2)][alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseEB [auth aO],
NA [auth aJ],
W [auth aE]		15N-Glycosylation
Entity ID: 12
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseFB [auth bG],
OA [auth bD],
X [auth bA]		9N-Glycosylation
Glycosylation Resources
GlyTouCan: G37135JQ
GlyCosmos: G37135JQ
GlyGen: G37135JQ
Entity ID: 13
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseGB [auth bH],
PA [auth bE],
Y [auth bB]		5N-Glycosylation
Glycosylation Resources
GlyTouCan: G10756ZZ
GlyCosmos: G10756ZZ
GlyGen: G10756ZZ
Entity ID: 14
MoleculeChains Length2D Diagram GlycosylationD Interactions
beta-D-xylopyranose-(1-6)-alpha-D-mannopyranose-(1-3)-[alpha-D-xylopyranose-(1-2)][alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[beta-D-mannopyranose-(1-2)][alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseHB [auth bI],
QA [auth bF],
Z [auth bC]		10N-Glycosylation
Entity ID: 15
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-xylopyranoseAA [auth cA],
IB [auth cC],
RA [auth cB]		4N/A
Entity ID: 16
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-xylopyranoseBA [auth dA],
JB [auth dC],
SA [auth dB]		7N/A
Entity ID: 17
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
CA [auth eA],
FA [auth fC],
GA [auth fD],
KB [auth eE],
NB [auth fM],
CA [auth eA],
FA [auth fC],
GA [auth fD],
KB [auth eE],
NB [auth fM],
OB [auth fN],
TA [auth eC],
WA [auth fH],
XA [auth fI]
11N-Glycosylation
Glycosylation Resources
GlyTouCan: G60230HH
GlyCosmos: G60230HH
GlyGen: G60230HH
Entity ID: 18
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-xylopyranose-(1-2)-beta-D-xylopyranose-(1-6)-[beta-D-glucopyranose-(1-3)][2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-[beta-D-xylopyranose-(1-3)]alpha-D-mannopyranose-(1-6)][beta-D-xylopyranose-(1-2)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseDA [auth eB],
LB [auth eF],
UA [auth eD]		14N-Glycosylation
Entity ID: 19
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
EA [auth fB],
HA [auth fE],
MB [auth fL],
PB [auth fO],
VA [auth fG],
EA [auth fB],
HA [auth fE],
MB [auth fL],
PB [auth fO],
VA [auth fG],
YA [auth fJ]
10N-Glycosylation
Glycosylation Resources
GlyTouCan: G89864BN
GlyCosmos: G89864BN
GlyGen: G89864BN
Entity ID: 20
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-xylopyranose-(1-2)-beta-D-xylopyranose-(1-6)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-[alpha-D-xylopyranose-(1-3)]alpha-D-mannopyranose-(1-6)][beta-D-xylopyranose-(1-2)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-2)][alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseIA [auth fF],
QB [auth fP],
ZA [auth fK]		14N-Glycosylation

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
(Subject of Investigation/LOI)

Query on NAG


Download:Ideal Coordinates CCD File
SB [auth EA]
UC [auth EB]
VB [auth FA]
WD [auth EC]
XC [auth FB]
SB [auth EA],
UC [auth EB],
VB [auth FA],
WD [auth EC],
XC [auth FB],
ZD [auth FC]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
2PO

Query on 2PO


Download:Ideal Coordinates CCD File
AE [auth FC]
FC [auth AA]
GC [auth AA]
HC [auth AA]
HD [auth AB]
AE [auth FC],
FC [auth AA],
GC [auth AA],
HC [auth AA],
HD [auth AB],
ID [auth AB],
JD [auth AB],
JE [auth AC],
KE [auth AC],
LE [auth AC],
PC [auth BA],
QC [auth BA],
RD [auth BB],
SD [auth BB],
TB [auth EA],
TE [auth BC],
UE [auth BC],
VC [auth EB],
WB [auth FA],
XD [auth EC],
YC [auth FB]
PHOSPHONATE
H O3 P
ABLZXFCXXLZCGV-UHFFFAOYSA-L
CA
(Subject of Investigation/LOI)

Query on CA


Download:Ideal Coordinates CCD File
AC [auth FA]
AD [auth FB]
BC [auth FA]
BD [auth FB]
BE [auth FC]
AC [auth FA],
AD [auth FB],
BC [auth FA],
BD [auth FB],
BE [auth FC],
CC [auth FA],
CD [auth FB],
CE [auth FC],
DD [auth FB],
DE [auth FC],
EC [auth CA],
ED [auth FB],
EE [auth FC],
FE [auth FC],
GD [auth CB],
GE [auth FC],
IC [auth AA],
IE [auth CC],
JC [auth AA],
KC [auth AA],
KD [auth AB],
LC [auth AA],
LD [auth AB],
MC [auth AA],
MD [auth AB],
ME [auth AC],
NC [auth AA],
ND [auth AB],
NE [auth AC],
OC [auth AA],
OD [auth AB],
OE [auth AC],
PD [auth AB],
PE [auth AC],
QD [auth AB],
QE [auth AC],
RB [auth EA],
RC [auth BA],
RE [auth AC],
SC [auth BA],
SE [auth AC],
TC [auth BA],
TD [auth BB],
UB [auth EA],
UD [auth BB],
VD [auth BB],
VE [auth BC],
WC [auth EB],
WE [auth BC],
XB [auth FA],
XE [auth BC],
YB [auth FA],
YD [auth EC],
ZB [auth FA],
ZC [auth FB]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL
(Subject of Investigation/LOI)

Query on CL


Download:Ideal Coordinates CCD File
DC [auth DA],
FD [auth DB],
HE [auth DC]		CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.17 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC

Structure Validation

View Full Validation Report



View more in-depth experimental data

Entry History 

& Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China32330052
National Natural Science Foundation of China (NSFC)China32341016
National Natural Science Foundation of China (NSFC)China324B2042

Revision History  (Full details and data files)

  • Version 1.0: 2026-04-29
    Type: Initial release
  • Version 1.1: 2026-05-06
    Changes: Data collection, Database references