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- PDB-9ufe: Cryo-EM structure of the tubular mastigoneme (the central tube) f... -

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Basic information

Entry
Database: PDB / ID: 9ufe
TitleCryo-EM structure of the tubular mastigoneme (the central tube) from golden algae 2.17 angstrom resolution
Components
  • (Tubular mastigoneme ...) x 3
  • OCM3
  • OCM5
  • OCM6
KeywordsCARBOHYDRATE / Cryo-EM / Tubular Mastigoneme / Golden algae / N-Glycans
Function / homology
Function and homology information


: / : / : / EGF-like domain, extracellular / EGF-like domain / Epidermal growth factor-like domain. / EGF-like domain profile. / EGF-like domain signature 1. / EGF-like domain signature 2. / EGF-like domain / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
PHOSPHONATE / Tubular mastigoneme protein / Tubular mastigoneme protein / Tubular mastigoneme protein
Similarity search - Component
Biological speciesOchromonas danica (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.17 Å
AuthorsHuang, J. / Tao, H. / Chen, S. / Cui, Y. / Xu, Y. / Yan, C. / Yan, N.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32330052 China
National Natural Science Foundation of China (NSFC)32341016 China
National Natural Science Foundation of China (NSFC)324B2042 China
CitationJournal: Science / Year: 2026
Title: Structural N- and O-glycans revealed by high-resolution cryo-EM analysis of tubular mastigonemes.
Authors: Junhao Huang / Hui Tao / Sheng Chen / Yahua Cui / Yiran Xu / Chuangye Yan / Nieng Yan /
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 ...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, , 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--Asp (AD) 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.
History
DepositionApr 10, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 29, 2026Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
EA: OCM5
FA: OCM6
DA: Tubular mastigoneme protein
CA: OCM3
AA: Tubular mastigoneme protein
BA: Tubular mastigoneme protein
EB: OCM5
FB: OCM6
DB: Tubular mastigoneme protein
CB: OCM3
AB: Tubular mastigoneme protein
BB: Tubular mastigoneme protein
EC: OCM5
FC: OCM6
DC: Tubular mastigoneme protein
CC: OCM3
AC: Tubular mastigoneme protein
BC: Tubular mastigoneme protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,006,780154
Polymers907,32918
Non-polymers99,451136
Water120,4666687
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 , 3 types, 9 molecules EAEBECFAFBFCCACBCC

#1: Protein OCM5


Mass: 40219.859 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Ochromonas danica (eukaryote)
#2: Protein OCM6


Mass: 78780.789 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Ochromonas danica (eukaryote)
#4: Protein OCM3


Mass: 36806.273 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Ochromonas danica (eukaryote)

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Tubular mastigoneme ... , 3 types, 9 molecules DADBDCAAABACBABBBC

#3: Protein Tubular mastigoneme protein


Mass: 22290.113 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Ochromonas danica (eukaryote) / References: UniProt: C4B7Q8
#5: Protein Tubular mastigoneme protein


Mass: 83365.664 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Ochromonas danica (eukaryote) / References: UniProt: A6P4C0
#6: Protein Tubular mastigoneme protein


Mass: 40980.375 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Ochromonas danica (eukaryote) / References: UniProt: C4B7Q7

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Sugars , 15 types, 57 molecules

#7: Polysaccharide beta-D-xylopyranose-(1-2)-beta-D-xylopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)][2-acetamido-2- ...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-glucopyranose


Type: oligosaccharide / Mass: 2362.116 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DXylpb1-2DXylpb1-6[DManpa1-3][DGlcpNAcb1-4]DManpa1-3[DGlcpNAcb1-2DManpa1-6][DXylpb1-2]DManpa1-6[DManpa1-2][DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/4,14,13/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a212h-1b_1-5]/1-1-2-3-3-3-4-3-3-1-4-4-3-1/a4-b1_b4-c1_c2-d1_c3-e1_c6-f1_f2-g1_f3-h1_f6-m1_h3-i1_h4-j1_h6-k1_k2-l1_m2-n1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(2+1)][a-D-Manp]{}[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(2+1)][b-D-Xylp]{}[(3+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}[(4+1)][b-D-GlcpNAc]{}[(6+1)][b-D-Xylp]{[(2+1)][b-D-Xylp]{}}}[(6+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}}}}}}}LINUCSPDB-CARE
#8: Polysaccharide alpha-D-mannopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-D-mannopyranose-(1- ...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-glucopyranose


Type: oligosaccharide / Mass: 2656.372 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DGlcpNAcb1-4[DManpb1-2DXylpb1-6][DXylpb1-3]DManpa1-3[DManpb1-3DGlcpNAcb1-2[DXylpb1-3]DManpa1-6][DXylpb1-2]DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/4,16,15/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a212h-1b_1-5]/1-1-2-3-3-4-3-4-1-3-4-2-3-1-2-4/a4-b1_b4-c1_c3-d1_c6-e1_e2-f1_e3-g1_e6-m1_g3-h1_g4-i1_g6-k1_i3-j1_k2-l1_m2-n1_m3-p1_n3-o1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(2+1)][b-D-Xylp]{}[(3+1)][a-D-Manp]{[(3+1)][b-D-Xylp]{}[(4+1)][b-D-GlcpNAc]{[(3+1)][a-D-Manp]{}}[(6+1)][b-D-Xylp]{[(2+1)][b-D-Manp]{}}}[(6+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{[(3+1)][b-D-Manp]{}}[(3+1)][b-D-Xylp]{}}}}}}}LINUCSPDB-CARE
#9: Polysaccharide alpha-D-mannopyranose-(1-3)-[beta-D-mannopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...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-glucopyranose


Type: oligosaccharide / Mass: 2686.398 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpb1-4]DGlcpNAcb1-4[DXylpb1-2DXylpb1-6][DGlcpb1-3]DManpa1-3[DGlcpNAcb1-2DManpa1-6][DXylpb1-2]DManpa1-6[DManpa1-2][DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/5,16,15/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a212h-1b_1-5][a2122h-1b_1-5]/1-1-2-3-3-3-4-3-5-1-3-2-4-4-3-1/a4-b1_b4-c1_c2-d1_c3-e1_c6-f1_f2-g1_f3-h1_f6-o1_h3-i1_h4-j1_h6-m1_j3-k1_j4-l1_m2-n1_o2-p1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(2+1)][a-D-Manp]{}[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(2+1)][b-D-Xylp]{}[(3+1)][a-D-Manp]{[(3+1)][b-D-Glcp]{}[(4+1)][b-D-GlcpNAc]{[(3+1)][a-D-Manp]{}[(4+1)][b-D-Manp]{}}[(6+1)][b-D-Xylp]{[(2+1)][b-D-Xylp]{}}}[(6+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}}}}}}}LINUCSPDB-CARE
#10: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D- ...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-glucopyranose


Type: oligosaccharide / Mass: 1559.386 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-2DManpa1-3[DManpa1-2DManpa1-3DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,9,8/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-g1_d2-e1_e2-f1_g3-h1_h2-i1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}}}}}LINUCSPDB-CARE
#11: Polysaccharide beta-D-xylopyranose-(1-2)-beta-D-xylopyranose-(1-6)-[beta-D-xylopyranose-(1-3)][2-acetamido-2-deoxy- ...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-glucopyranose


Type: oligosaccharide / Mass: 2464.205 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DXylpb1-2DXylpb1-6[DXylpb1-3][DGlcpNAcb1-4]DManpa1-3[DGlcpNAcb1-2[DXylpb1-3]DManpa1-6][DXylpb1-2]DManpa1-6[DManpb1-2][DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/4,15,14/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a212h-1b_1-5]/1-1-2-2-3-3-4-3-4-1-4-4-3-1-4/a4-b1_b4-c1_c2-d1_c3-e1_c6-f1_f2-g1_f3-h1_f6-m1_h3-i1_h4-j1_h6-k1_k2-l1_m2-n1_m3-o1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(2+1)][b-D-Manp]{}[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(2+1)][b-D-Xylp]{}[(3+1)][a-D-Manp]{[(3+1)][b-D-Xylp]{}[(4+1)][b-D-GlcpNAc]{}[(6+1)][b-D-Xylp]{[(2+1)][b-D-Xylp]{}}}[(6+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}[(3+1)][b-D-Xylp]{}}}}}}}LINUCSPDB-CARE
#12: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D- ...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-glucopyranose


Type: oligosaccharide / Mass: 1559.386 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-3[DManpa1-2DManpa1-6]DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,9,8/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-e1_e3-f1_e6-h1_f2-g1_h2-i1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}[(6+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}}}}}LINUCSPDB-CARE
#13: Polysaccharide alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-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-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpa1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c6-d1_d3-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#14: Polysaccharide beta-D-xylopyranose-(1-6)-alpha-D-mannopyranose-(1-3)-[alpha-D-xylopyranose-(1-2)][alpha-D- ...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-glucopyranose


Type: oligosaccharide / Mass: 1661.475 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DXylpb1-6DManpa1-3[DXylpa1-2][DManpa1-6]DManpa1-6[DManpb1-2][DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/5,10,9/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a212h-1a_1-5][a212h-1b_1-5]/1-1-2-2-3-3-4-3-5-3/a4-b1_b4-c1_c2-d1_c3-e1_c6-f1_f2-g1_f3-h1_f6-j1_h6-i1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(2+1)][b-D-Manp]{}[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(2+1)][a-D-Xylp]{}[(3+1)][a-D-Manp]{[(6+1)][b-D-Xylp]{}}[(6+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#15: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-xylopyranose


Type: oligosaccharide / Mass: 636.552 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-2DManpa1-3DXylpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,4,3/[a212h-1b_1-5][a1122h-1a_1-5]/1-2-2-2/a3-b1_b2-c1_c2-d1WURCSPDB2Glycan 1.1.0
[][<C5O3>]{[(1+1)][a-D-Manp]{[(2+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#16: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D- ...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-xylopyranose


Type: oligosaccharide / Mass: 1122.975 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-2DManpa1-2DManpa1-2DManpa1-2DManpa1-3DXylpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,7,6/[a212h-1b_1-5][a1122h-1a_1-5]/1-2-2-2-2-2-2/a3-b1_b2-c1_c2-d1_d2-e1_e2-f1_f2-g1WURCSPDB2Glycan 1.1.0
[][<C5O3>]{[(1+1)][a-D-Manp]{[(2+1)][a-D-Manp]{[(2+1)][a-D-Manp]{[(2+1)][a-D-Manp]{[(2+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}}}}}LINUCSPDB-CARE
#17: Polysaccharide
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D- ...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


Type: oligosaccharide / Mass: 1883.668 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-2DManpa1-3[DManpa1-2DManpa1-3[DManpa1-2DManpa1-6]DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,11,10/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-g1_d2-e1_e2-f1_g3-h1_g6-j1_h2-i1_j2-k1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}[(6+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}}}}}LINUCSPDB-CARE
#18: Polysaccharide alpha-D-xylopyranose-(1-2)-beta-D-xylopyranose-(1-6)-[beta-D-glucopyranose-(1-3)][2-acetamido-2- ...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-glucopyranose


Type: oligosaccharide / Mass: 2332.090 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DXylpa1-2DXylpb1-6[DGlcpb1-3][DGlcpNAcb1-4]DManpa1-3[DGlcpNAcb1-2[DXylpb1-3]DManpa1-6][DXylpb1-2]DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/6,14,13/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a212h-1b_1-5][a2122h-1b_1-5][a212h-1a_1-5]/1-1-2-3-3-4-3-5-1-4-6-3-1-4/a4-b1_b4-c1_c3-d1_c6-e1_e2-f1_e3-g1_e6-l1_g3-h1_g4-i1_g6-j1_j2-k1_l2-m1_l3-n1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(2+1)][b-D-Xylp]{}[(3+1)][a-D-Manp]{[(3+1)][b-D-Glcp]{}[(4+1)][b-D-GlcpNAc]{}[(6+1)][b-D-Xylp]{[(2+1)][a-D-Xylp]{}}}[(6+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}[(3+1)][b-D-Xylp]{}}}}}}}LINUCSPDB-CARE
#19: Polysaccharide
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D- ...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


Type: oligosaccharide / Mass: 1721.527 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-3[DManpa1-2DManpa1-6]DManpa1-6[DManpa1-2DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,10,9/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-f1_d2-e1_f3-g1_f6-i1_g2-h1_i2-j1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}[(6+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}}}}}LINUCSPDB-CARE
#20: Polysaccharide alpha-D-xylopyranose-(1-2)-beta-D-xylopyranose-(1-6)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4) ...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-glucopyranose


Type: oligosaccharide / Mass: 2332.090 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DXylpa1-2DXylpb1-6[DGlcpNAcb1-4]DManpa1-3[DGlcpNAcb1-2[DXylpa1-3]DManpa1-6][DXylpb1-2]DManpa1-6[DManpa1-2][DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/5,14,13/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a212h-1b_1-5][a212h-1a_1-5]/1-1-2-3-3-3-4-3-1-4-5-3-1-5/a4-b1_b4-c1_c2-d1_c3-e1_c6-f1_f2-g1_f3-h1_f6-l1_h4-i1_h6-j1_j2-k1_l2-m1_l3-n1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(2+1)][a-D-Manp]{}[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(2+1)][b-D-Xylp]{}[(3+1)][a-D-Manp]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][b-D-Xylp]{[(2+1)][a-D-Xylp]{}}}[(6+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}[(3+1)][a-D-Xylp]{}}}}}}}LINUCSPDB-CARE
#22: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

-
Non-polymers , 4 types, 6766 molecules

#21: Chemical...
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 55 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#23: Chemical...
ChemComp-2PO / PHOSPHONATE


Mass: 79.980 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: HO3P
#24: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#25: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6687 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: tubular mastigoneme / Type: COMPLEX / Entity ID: #1-#6 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Ochromonas danica (eukaryote)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
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: 1200 nm / Nominal defocus min: 600 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

-
Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.17 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 104125 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 16.39 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.005366666
ELECTRON MICROSCOPYf_angle_d0.712690732
ELECTRON MICROSCOPYf_chiral_restr0.047610902
ELECTRON MICROSCOPYf_plane_restr0.005611037
ELECTRON MICROSCOPYf_dihedral_angle_d9.624213119

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