SMTL ID : 6f2s.1 (1 other biounit)

CryoEM structure of Ageratum Yellow Vein virus (AYVV)

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY 3.30 Å

Oligo State

hetero-9-1-1-mer

Ligands

10 x DC- DA- DA- DC- DC- DA- DC: ssDNA loop(Non-covalent)

DC-DA-DA-DC-DC-DA-DC.1: 9 residues within 4Å: Chain A: D.2, C.11, K.51, S.52, Y.54, F.141, R.186, Y.188, Y.190 Protein-ligand interaction information (PLIP) not available DC-DA-DA-DC-DC-DA-DC.2: 20 residues within 4Å: Chain B: D.2, C.11, V.13, K.51, S.52, Y.54, F.141, R.186, Y.188, Y.190 Chain F: R.80, R.82, T.106, R.112, D.113, Q.116, V.117, L.118, R.119, K.120 Protein-ligand interaction information (PLIP) not available DC-DA-DA-DC-DC-DA-DC.3: 20 residues within 4Å: Chain A: R.47, E.163, N.195 Chain B: R.80, R.82, R.112, D.113, Q.116, V.117, L.118, R.119, K.120 Chain C: D.2, C.11, K.51, S.52, Y.54, F.141, R.186, Y.188 Protein-ligand interaction information (PLIP) not available DC-DA-DA-DC-DC-DA-DC.4: 20 residues within 4Å: Chain C: R.80, R.82, T.106, R.112, D.113, Q.116, V.117, L.118, R.119, K.120 Chain D: D.2, C.11, V.13, K.51, S.52, Y.54, F.141, R.186, Y.188, Y.190 Protein-ligand interaction information (PLIP) not available DC-DA-DA-DC-DC-DA-DC.5: 20 residues within 4Å: Chain D: R.80, R.82, R.112, D.113, Q.116, V.117, L.118, R.119, K.120 Chain E: D.2, C.11, K.51, S.52, Y.54, F.141, R.186, Y.188, Y.190 Chain K: R.47, N.195 Protein-ligand interaction information (PLIP) not available DC-DA-DA-DC-DC-DA-DC.6: 20 residues within 4Å: Chain E: R.80, R.82, R.112, D.113, Q.116, V.117, L.118, R.119, K.120 Chain F: D.2, C.11, V.13, K.51, S.52, Y.54, L.56, F.141, R.186, Y.188, Y.190 Protein-ligand interaction information (PLIP) not available DC-DA-DA-DC-DC-DA-DC.7: 21 residues within 4Å: Chain D: R.47, E.163, N.195 Chain G: D.2, C.11, V.13, K.51, S.52, Y.54, F.141, R.186, Y.188 Chain K: R.80, R.82, R.112, D.113, Q.116, V.117, L.118, R.119, K.120 Protein-ligand interaction information (PLIP) not available DC-DA-DA-DC-DC-DA-DC.8: 19 residues within 4Å: Chain G: R.80, R.82, R.112, D.113, Q.116, V.117, L.118, R.119, K.120 Chain H: D.2, C.11, V.13, K.51, S.52, Y.54, F.141, R.186, Y.188, Y.190 Protein-ligand interaction information (PLIP) not available DC-DA-DA-DC-DC-DA-DC.9: 19 residues within 4Å: Chain H: R.80, R.82, T.106, R.112, D.113, Q.116, V.117, L.118, R.119, K.120 Chain I: C.19, V.21, K.59, S.60, Y.62, F.149, R.194, Y.196, Y.198 Protein-ligand interaction information (PLIP) not available DC-DA-DA-DC-DC-DA-DC.11: 20 residues within 4Å: Chain J: R.103, R.105, T.129, R.135, D.136, Q.139, V.140, L.141, R.142, K.143 Chain K: D.2, C.11, V.13, K.51, S.52, Y.54, F.141, R.186, Y.188, Y.190 Protein-ligand interaction information (PLIP) not available

1 x DC- DA- DA- DC- DC- DA: ssDNA loop associated with subunit H(Non-covalent)

DC-DA-DA-DC-DC-DA.10: 21 residues within 4Å: Chain I: R.88, R.90, T.114, R.120, D.121, Q.124, V.125, L.126, R.127, K.128 Chain J: R.2, D.25, C.34, V.36, K.74, S.75, Y.77, F.164, R.209, Y.211, Y.213 Protein-ligand interaction information (PLIP) not available

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hesketh, E.L. et al., The 3.3 angstrom structure of a plant geminivirus using cryo-EM. Nat Commun (2018)

Release Date

2018-06-27

Peptides

Capsid protein: ABCDEFGHK
coat protein subunit I: I
coat protein subunit H: J

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
F

D
E

E
D

F
C

G
K

H
J

K
G

I
I

J
H

Capsid protein

coat protein subunit I

coat protein subunit H

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