[English] 日本語
Yorodumi
- PDB-8wa2: cryo-EM structure of native mastigonemes isolated from Chlamydomo... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8wa2
Titlecryo-EM structure of native mastigonemes isolated from Chlamydomonas reinhardtii at 3.0 angstrom resolution
Components
  • Mst1
  • Mstax
KeywordsMEMBRANE PROTEIN / Cilia / arabinoglycan / PKD2 / PPII helix / mechanosensation.
Function / homologyTyrosine-protein kinase ephrin type A/B receptor-like / Tyrosine-protein kinase ephrin type A/B receptor-like / Putative ephrin-receptor like / Growth factor receptor cysteine-rich domain superfamily / alpha-L-arabinofuranose / alpha-D-galactopyranose / Tyrosine-protein kinase ephrin type A/B receptor-like domain-containing protein
Function and homology information
Biological speciesChlamydomonas reinhardtii (plant)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å
AuthorsHuang, J. / Tao, H. / Chen, J. / Pan, J. / Yan, C. / Yan, N.
Funding support China, 1items
OrganizationGrant numberCountry
National Basic Research Program of China (973 Program)2020YFA0509301 China
CitationJournal: Cell / Year: 2024
Title: Structure-guided discovery of protein and glycan components in native mastigonemes.
Authors: Junhao Huang / Hui Tao / Jikun Chen / Yang Shen / Jianlin Lei / Junmin Pan / Chuangye Yan / Nieng Yan /
Abstract: Mastigonemes, the hair-like lateral appendages lining cilia or flagella, participate in mechanosensation and cellular motion, but their constituents and structure have remained unclear. Here, we ...Mastigonemes, the hair-like lateral appendages lining cilia or flagella, participate in mechanosensation and cellular motion, but their constituents and structure have remained unclear. Here, we report the cryo-EM structure of native mastigonemes isolated from Chlamydomonas at 3.0 Å resolution. The long stem assembles as a super spiral, with each helical turn comprising four pairs of anti-parallel mastigoneme-like protein 1 (Mst1). A large array of arabinoglycans, which represents a common class of glycosylation in plants and algae, is resolved surrounding the type II poly-hydroxyproline (Hyp) helix in Mst1. The EM map unveils a mastigoneme axial protein (Mstax) that is rich in heavily glycosylated Hyp and contains a PKD2-like transmembrane domain (TMD). Mstax, with nearly 8,000 residues spanning from the intracellular region to the distal end of the mastigoneme, provides the framework for Mst1 assembly. Our study provides insights into the complexity of protein and glycan interactions in native bio-architectures.
History
DepositionSep 6, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 10, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Mst1
B: Mst1
C: Mst1
D: Mst1
E: Mst1
F: Mst1
G: Mstax
H: Mstax
I: Mstax
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,463,403459
Polymers1,256,6169
Non-polymers206,787450
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

-
Components

-
Protein , 2 types, 9 molecules ABCDEFGHI

#1: Protein
Mst1 /


Mass: 206316.203 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8J9H7
#2: Protein Mstax


Mass: 6239.464 Da / Num. of mol.: 3 / Source method: obtained synthetically
Details: Our Mstax sequence in the structure (chain G, H and I) represents the average sequence resulting from the statistical analysis of a segment of 34 repeated sequences in Mstax.
Source: (synth.) synthetic construct (others)

+
Sugars , 25 types, 444 molecules

#3: Polysaccharide...
beta-L-arabinofuranose-(1-2)-beta-L-arabinofuranose-(1-2)-beta-L-arabinofuranose


Type: oligosaccharide / Mass: 414.360 Da / Num. of mol.: 95 / Source method: obtained synthetically
DescriptorTypeProgram
LArafb1-2LArafb1-2LArafb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a211h-1b_1-4]/1-1-1/a2-b1_b2-c1WURCSPDB2Glycan 1.1.0
[][L-1-deoxy-Araf]{[(2+1)][b-L-Araf]{[(2+1)][b-L-Araf]{}}}LINUCSPDB-CARE
#4: Polysaccharide...
alpha-L-arabinofuranose-(1-3)-beta-L-arabinofuranose-(1-2)-beta-L-arabinofuranose-(1-2)-beta-L-arabinofuranose


Type: oligosaccharide / Mass: 546.474 Da / Num. of mol.: 43 / Source method: obtained synthetically
DescriptorTypeProgram
LArafa1-3LArafb1-2LArafb1-2LArafb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,4,3/[a211h-1b_1-4][a211h-1a_1-4]/1-1-1-2/a2-b1_b2-c1_c3-d1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-Xylf]{[(2+1)][b-L-Araf]{[(2+1)][b-L-Araf]{[(3+1)][a-L-Araf]{}}}}LINUCSPDB-CARE
#5: Polysaccharide
alpha-L-arabinofuranose-(1-3)-beta-L-arabinofuranose-(1-2)-beta-L-arabinofuranose-(1-2)-[alpha-L- ...alpha-L-arabinofuranose-(1-3)-beta-L-arabinofuranose-(1-2)-beta-L-arabinofuranose-(1-2)-[alpha-L-arabinofuranose-(1-5)]beta-L-arabinofuranose


Type: oligosaccharide / Mass: 678.589 Da / Num. of mol.: 4 / Source method: obtained synthetically
DescriptorTypeProgram
LArafa1-3LArafb1-2LArafb1-2[LArafa1-5]LArafb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,5,4/[a211h-1b_1-4][a211h-1a_1-4]/1-1-1-2-2/a2-b1_a5-e1_b2-c1_c3-d1WURCSPDB2Glycan 1.1.0
[][L-1-deoxy-Araf]{[(2+1)][b-L-Araf]{[(2+1)][b-L-Araf]{[(3+1)][a-L-Araf]{}}}[(5+1)][a-L-Araf]{}}LINUCSPDB-CARE
#6: Polysaccharide...
beta-D-galactofuranose-(1-2)-beta-L-arabinofuranose-(1-2)-beta-L-arabinofuranose


Type: oligosaccharide / Mass: 444.386 Da / Num. of mol.: 48 / Source method: obtained synthetically
DescriptorTypeProgram
DGalfb1-2LArafb1-2LArafb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a211h-1b_1-4][a2112h-1b_1-4]/1-1-2/a2-b1_b2-c1WURCSPDB2Glycan 1.1.0
[][L-1-deoxy-Araf]{[(2+1)][b-L-Araf]{[(2+1)][b-L-Altf]{}}}LINUCSPDB-CARE
#7: Polysaccharide
beta-L-arabinofuranose-(1-2)-beta-L-arabinofuranose-(1-2)-[alpha-L-arabinofuranose-(1-3)]beta-L- ...beta-L-arabinofuranose-(1-2)-beta-L-arabinofuranose-(1-2)-[alpha-L-arabinofuranose-(1-3)]beta-L-arabinofuranose


Type: oligosaccharide / Mass: 546.474 Da / Num. of mol.: 12 / Source method: obtained synthetically
DescriptorTypeProgram
LArafb1-2LArafb1-2[LArafa1-3]LArafb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,4,3/[a211h-1b_1-4][a211h-1a_1-4]/1-1-1-2/a2-b1_a3-d1_b2-c1WURCSPDB2Glycan 1.1.0
[][L-1-deoxy-Araf]{[(2+1)][b-L-Araf]{[(2+1)][b-L-Araf]{}}[(3+1)][a-L-Araf]{}}LINUCSPDB-CARE
#8: Polysaccharide
alpha-L-arabinofuranose-(1-2)-alpha-L-arabinofuranose-(1-3)-beta-L-arabinofuranose-(1-2)-beta-L- ...alpha-L-arabinofuranose-(1-2)-alpha-L-arabinofuranose-(1-3)-beta-L-arabinofuranose-(1-2)-beta-L-arabinofuranose-(1-2)-beta-L-arabinofuranose


Type: oligosaccharide / Mass: 678.589 Da / Num. of mol.: 4 / Source method: obtained synthetically
DescriptorTypeProgram
LArafa1-2LArafa1-3LArafb1-2LArafb1-2LArafb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,5,4/[a211h-1b_1-4][a211h-1a_1-4]/1-1-1-2-2/a2-b1_b2-c1_c3-d1_d2-e1WURCSPDB2Glycan 1.1.0
[][L-1-deoxy-Araf]{[(2+1)][b-L-Araf]{[(2+1)][b-L-Araf]{[(3+1)][a-L-Araf]{[(2+1)][a-L-Araf]{}}}}}LINUCSPDB-CARE
#9: Polysaccharide
beta-L-arabinofuranose-(1-2)-beta-L-arabinofuranose


Type: oligosaccharide / Mass: 282.245 Da / Num. of mol.: 8 / Source method: obtained synthetically
DescriptorTypeProgram
LArafb1-2LArafb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a211h-1b_1-4]/1-1/a2-b1WURCSPDB2Glycan 1.1.0
[][L-1-deoxy-Araf]{[(2+1)][b-L-Araf]{}}LINUCSPDB-CARE
#10: Polysaccharide
alpha-L-arabinofuranose-(1-3)-beta-L-arabinofuranose-(1-2)-beta-L-arabinofuranose-(1-2)-[alpha-L- ...alpha-L-arabinofuranose-(1-3)-beta-L-arabinofuranose-(1-2)-beta-L-arabinofuranose-(1-2)-[alpha-L-arabinofuranose-(1-3)]beta-L-arabinofuranose


Type: oligosaccharide / Mass: 678.589 Da / Num. of mol.: 16 / Source method: obtained synthetically
DescriptorTypeProgram
LArafa1-3LArafb1-2LArafb1-2[LArafa1-3]LArafb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,5,4/[a211h-1b_1-4][a211h-1a_1-4]/1-1-1-2-2/a2-b1_a3-e1_b2-c1_c3-d1WURCSPDB2Glycan 1.1.0
[][L-1-deoxy-Araf]{[(2+1)][b-L-Araf]{[(2+1)][b-L-Araf]{[(3+1)][a-L-Araf]{}}}[(3+1)][a-L-Araf]{}}LINUCSPDB-CARE
#11: Polysaccharide
alpha-L-arabinofuranose-(1-3)-[alpha-L-arabinofuranose-(1-5)]beta-L-arabinofuranose


Type: oligosaccharide / Mass: 414.360 Da / Num. of mol.: 4 / Source method: obtained synthetically
DescriptorTypeProgram
LArafa1-3[LArafa1-5]LArafb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a211h-1b_1-4][a211h-1a_1-4]/1-2-2/a3-b1_a5-c1WURCSPDB2Glycan 1.1.0
[][L-1-deoxy-Araf]{[(3+1)][a-L-Araf]{}[(5+1)][a-L-Araf]{}}LINUCSPDB-CARE
#12: Polysaccharide
alpha-L-arabinofuranose-(1-3)-beta-D-galactofuranose-(1-2)-beta-L-arabinofuranose-(1-2)-[alpha-L- ...alpha-L-arabinofuranose-(1-3)-beta-D-galactofuranose-(1-2)-beta-L-arabinofuranose-(1-2)-[alpha-L-arabinofuranose-(1-3)]beta-L-arabinofuranose


Type: oligosaccharide / Mass: 708.615 Da / Num. of mol.: 12 / Source method: obtained synthetically
DescriptorTypeProgram
LArafa1-3DGalfb1-2LArafb1-2[LArafa1-3]LArafb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a211h-1b_1-4][a2112h-1b_1-4][a211h-1a_1-4]/1-1-2-3-3/a2-b1_a3-e1_b2-c1_c3-d1WURCSPDB2Glycan 1.1.0
[][L-1-deoxy-Araf]{[(2+1)][b-L-Araf]{[(2+1)][b-L-Altf]{[(3+1)][a-L-Araf]{}}}[(3+1)][a-L-Araf]{}}LINUCSPDB-CARE
#13: Polysaccharide...
alpha-L-arabinofuranose-(1-3)-beta-D-galactofuranose-(1-2)-beta-L-arabinofuranose-(1-2)-beta-L-arabinofuranose


Type: oligosaccharide / Mass: 576.500 Da / Num. of mol.: 30 / Source method: obtained synthetically
DescriptorTypeProgram
LArafa1-3DGalfb1-2LArafb1-2LArafb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a211h-1b_1-4][a2112h-1b_1-4][a211h-1a_1-4]/1-1-2-3/a2-b1_b2-c1_c3-d1WURCSPDB2Glycan 1.1.0
[][L-1-deoxy-Araf]{[(2+1)][b-L-Araf]{[(2+1)][b-L-Altf]{[(3+1)][a-L-Araf]{}}}}LINUCSPDB-CARE
#14: Polysaccharide
beta-L-arabinofuranose-(1-5)-beta-D-galactofuranose-(1-2)-beta-L-arabinofuranose-(1-2)-beta-L-arabinofuranose


Type: oligosaccharide / Mass: 576.500 Da / Num. of mol.: 12 / Source method: obtained synthetically
DescriptorTypeProgram
LArafb1-5DGalfb1-2LArafb1-2LArafb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,4,3/[a211h-1b_1-4][a2112h-1b_1-4]/1-1-2-1/a2-b1_b2-c1_c5-d1WURCSPDB2Glycan 1.1.0
[][L-1-deoxy-Araf]{[(2+1)][b-L-Araf]{[(2+1)][b-L-Altf]{[(5+1)][b-L-Araf]{}}}}LINUCSPDB-CARE
#15: Polysaccharide
alpha-L-arabinofuranose-(1-2)-alpha-L-arabinofuranose-(1-3)-beta-D-galactofuranose-(1-2)-beta-L- ...alpha-L-arabinofuranose-(1-2)-alpha-L-arabinofuranose-(1-3)-beta-D-galactofuranose-(1-2)-beta-L-arabinofuranose-(1-2)-beta-L-arabinofuranose


Type: oligosaccharide / Mass: 708.615 Da / Num. of mol.: 12 / Source method: obtained synthetically
DescriptorTypeProgram
LArafa1-2LArafa1-3DGalfb1-2LArafb1-2LArafb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a211h-1b_1-4][a2112h-1b_1-4][a211h-1a_1-4]/1-1-2-3-3/a2-b1_b2-c1_c3-d1_d2-e1WURCSPDB2Glycan 1.1.0
[][L-1-deoxy-Araf]{[(2+1)][b-L-Araf]{[(2+1)][a-D-Galf]{[(3+1)][a-L-Araf]{[(2+1)][b-L-Araf]{}}}}}LINUCSPDB-CARE
#16: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 3 / Source method: obtained synthetically
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#17: Polysaccharide
alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D- ...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: 1072.964 Da / Num. of mol.: 4 / Source method: obtained synthetically
DescriptorTypeProgram
DManpa1-6DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3/a4-b1_b4-c1_c3-d1_c6-e1_e6-f1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][b-D-Manp]{}[(6+1)][b-D-Manp]{[(6+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#18: Polysaccharide
beta-D-galactofuranose-(1-2)-[alpha-L-arabinofuranose-(1-5)]beta-L-arabinofuranose-(1-2)-[alpha-L- ...beta-D-galactofuranose-(1-2)-[alpha-L-arabinofuranose-(1-5)]beta-L-arabinofuranose-(1-2)-[alpha-L-arabinofuranose-(1-3)]beta-L-arabinofuranose


Type: oligosaccharide / Mass: 708.615 Da / Num. of mol.: 16 / Source method: obtained synthetically
DescriptorTypeProgram
DGalfb1-2[LArafa1-5]LArafb1-2[LArafa1-3]LArafb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a211h-1b_1-4][a2112h-1b_1-4][a211h-1a_1-4]/1-1-2-3-3/a2-b1_a3-e1_b2-c1_b5-d1WURCSPDB2Glycan 1.1.0
[][L-1-deoxy-Araf]{[(2+1)][b-L-Araf]{[(2+1)][a-D-Galf]{}[(5+1)][b-L-Araf]{}}[(3+1)][a-L-Araf]{}}LINUCSPDB-CARE
#19: Polysaccharide
beta-D-galactofuranose-(1-2)-beta-L-arabinofuranose-(1-2)-[alpha-L-arabinofuranose-(1-3)]beta-L- ...beta-D-galactofuranose-(1-2)-beta-L-arabinofuranose-(1-2)-[alpha-L-arabinofuranose-(1-3)]beta-L-arabinofuranose


Type: oligosaccharide / Mass: 576.500 Da / Num. of mol.: 6 / Source method: obtained synthetically
DescriptorTypeProgram
DGalfb1-2LArafb1-2[LArafa1-3]LArafb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a211h-1b_1-4][a2112h-1b_1-4][a211h-1a_1-4]/1-1-2-3/a2-b1_a3-d1_b2-c1WURCSPDB2Glycan 1.1.0
[][L-1-deoxy-Araf]{[(2+1)][b-L-Araf]{[(2+1)][a-D-Galf]{}}[(3+1)][a-L-Araf]{}}LINUCSPDB-CARE
#20: Polysaccharide
beta-D-galactofuranose-(1-2)-[alpha-L-arabinofuranose-(1-5)]beta-L-arabinofuranose-(1-2)-beta-L- ...beta-D-galactofuranose-(1-2)-[alpha-L-arabinofuranose-(1-5)]beta-L-arabinofuranose-(1-2)-beta-L-arabinofuranose


Type: oligosaccharide / Mass: 576.500 Da / Num. of mol.: 12 / Source method: obtained synthetically
DescriptorTypeProgram
DGalfb1-2[LArafa1-5]LArafb1-2LArafb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a211h-1b_1-4][a2112h-1b_1-4][a211h-1a_1-4]/1-1-2-3/a2-b1_b2-c1_b5-d1WURCSPDB2Glycan 1.1.0
[][L-1-deoxy-Araf]{[(2+1)][b-L-Araf]{[(2+1)][a-D-Galf]{}[(5+1)][a-L-Araf]{}}}LINUCSPDB-CARE
#21: Polysaccharide beta-D-galactofuranose-(1-2)-beta-L-arabinofuranose-(1-2)-[alpha-L-arabinofuranose-(1-3)][alpha-L- ...beta-D-galactofuranose-(1-2)-beta-L-arabinofuranose-(1-2)-[alpha-L-arabinofuranose-(1-3)][alpha-L-arabinofuranose-(1-5)]beta-L-arabinofuranose


Type: oligosaccharide / Mass: 708.615 Da / Num. of mol.: 3 / Source method: obtained synthetically
DescriptorTypeProgram
DGalfb1-2LArafb1-2[LArafa1-3][LArafa1-5]LArafb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a211h-1b_1-4][a2112h-1b_1-4][a211h-1a_1-4]/1-1-2-3-3/a2-b1_a3-d1_a5-e1_b2-c1WURCSPDB2Glycan 1.1.0
[][L-1-deoxy-Araf]{[(2+1)][b-L-Araf]{[(2+1)][a-D-Galf]{}}[(3+1)][b-L-Araf]{}[(5+1)][a-L-Lyxf]{}}LINUCSPDB-CARE
#22: Polysaccharide
beta-D-galactofuranose-(1-2)-[alpha-L-arabinofuranose-(1-5)]beta-L-arabinofuranose-(1-2)-[alpha-L- ...beta-D-galactofuranose-(1-2)-[alpha-L-arabinofuranose-(1-5)]beta-L-arabinofuranose-(1-2)-[alpha-L-arabinofuranose-(1-2)-alpha-L-arabinofuranose-(1-3)]beta-L-arabinofuranose


Type: oligosaccharide / Mass: 840.730 Da / Num. of mol.: 8 / Source method: obtained synthetically
DescriptorTypeProgram
DGalfb1-2[LArafa1-5]LArafb1-2[LArafa1-2LArafa1-3]LArafb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a211h-1b_1-4][a2112h-1b_1-4][a211h-1a_1-4]/1-1-2-3-3-3/a2-b1_a3-e1_b2-c1_b5-d1_e2-f1WURCSPDB2Glycan 1.1.0
[][L-1-deoxy-Araf]{[(2+1)][b-L-Araf]{[(2+1)][a-D-Galf]{}[(5+1)][a-L-Araf]{}}[(3+1)][a-L-Araf]{[(2+1)][a-L-Araf]{}}}LINUCSPDB-CARE
#23: Polysaccharide beta-D-galactofuranose-(1-2)-[alpha-L-arabinofuranose-(1-5)]beta-L-arabinofuranose-(1-2)-[alpha-L- ...beta-D-galactofuranose-(1-2)-[alpha-L-arabinofuranose-(1-5)]beta-L-arabinofuranose-(1-2)-[alpha-L-arabinofuranose-(1-3)][alpha-L-arabinofuranose-(1-5)]beta-L-arabinofuranose


Type: oligosaccharide / Mass: 840.730 Da / Num. of mol.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
DGalfb1-2[LArafa1-5]LArafb1-2[LArafa1-3][LArafa1-5]LArafb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a211h-1b_1-4][a2112h-1b_1-4][a211h-1a_1-4]/1-1-2-3-3-3/a2-b1_a3-e1_a5-f1_b2-c1_b5-d1WURCSPDB2Glycan 1.1.0
[][L-1-deoxy-Araf]{[(2+1)][b-L-Araf]{[(2+1)][a-D-Galf]{}[(5+1)][b-L-Araf]{}}[(3+1)][b-L-Araf]{}[(5+1)][a-L-Araf]{}}LINUCSPDB-CARE
#24: Polysaccharide beta-D-galactofuranose-(1-2)-beta-L-arabinofuranose-(1-2)-[alpha-L-arabinofuranose-(1-2)-alpha-L- ...beta-D-galactofuranose-(1-2)-beta-L-arabinofuranose-(1-2)-[alpha-L-arabinofuranose-(1-2)-alpha-L-arabinofuranose-(1-3)][alpha-L-arabinofuranose-(1-5)]beta-L-arabinofuranose


Type: oligosaccharide / Mass: 840.730 Da / Num. of mol.: 2 / Source method: obtained synthetically
DescriptorTypeProgram
DGalfb1-2LArafb1-2[LArafa1-2LArafa1-3][LArafa1-5]LArafb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a211h-1b_1-4][a2112h-1b_1-4][a211h-1a_1-4]/1-1-2-3-3-3/a2-b1_a3-d1_a5-f1_b2-c1_d2-e1WURCSPDB2Glycan 1.1.0
[][L-1-deoxy-Araf]{[(2+1)][b-L-Araf]{[(2+1)][a-D-Galf]{}}[(3+1)][b-L-Araf]{[(2+1)][a-L-Araf]{}}[(5+1)][a-L-Araf]{}}LINUCSPDB-CARE
#26: Sugar
ChemComp-AHR / alpha-L-arabinofuranose / alpha-L-arabinose / L-arabinose / arabinose / Arabinose


Type: L-saccharide, alpha linking / Mass: 150.130 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C5H10O5 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
LArafaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-L-arabinofuranoseCOMMON NAMEGMML 1.0
a-L-ArafIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
AraSNFG CARBOHYDRATE SYMBOLGMML 1.0
#27: Sugar...
ChemComp-GLA / alpha-D-galactopyranose / alpha-D-galactose / D-galactose / galactose / ALPHA D-GALACTOSE / Galactose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 62 / Source method: obtained synthetically / Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGalpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-galactopyranoseCOMMON NAMEGMML 1.0
a-D-GalpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalSNFG CARBOHYDRATE SYMBOLGMML 1.0
#28: 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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 7 / 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 , 1 types, 6 molecules

#25: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: mastigoneme / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1 / Source: NATURAL
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Buffer solutionpH: 8
SpecimenConc.: 5 mg/ml / Embedding 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: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / 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)

-
Processing

CTF correctionType: NONE
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 69065 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.004102182
ELECTRON MICROSCOPYf_angle_d0.955140250
ELECTRON MICROSCOPYf_dihedral_angle_d14.73120699
ELECTRON MICROSCOPYf_chiral_restr0.06219813
ELECTRON MICROSCOPYf_plane_restr0.00615184

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
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

Read more