SMTL ID : 9ay1.3 (3 other biounits)

Cryo-EM structure of SINV/EEEV in complex with a potently neutralizing human antibody IgG EEEV-373

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-6-6-24-24-mer

Ligands

18 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.1: 3 residues within 4Å: Chain C: V.34, N.134, R.143 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.2: 3 residues within 4Å: Chain D: N.134, T.136, R.143 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.3: 3 residues within 4Å: Chain E: N.134, W.142, S.144 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.10: 3 residues within 4Å: Chain M: V.34, N.134, R.143 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.11: 3 residues within 4Å: Chain N: N.134, T.136, R.143 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.12: 3 residues within 4Å: Chain O: N.134, W.142, S.144 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.19: 3 residues within 4Å: Chain W: V.34, N.134, R.143 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.20: 3 residues within 4Å: Chain X: N.134, T.136, R.143 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.21: 3 residues within 4Å: Chain Y: N.134, W.142, S.144 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.28: 3 residues within 4Å: Chain 6: V.34, N.134, R.143 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.29: 3 residues within 4Å: Chain 7: N.134, T.136, R.143 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.30: 3 residues within 4Å: Chain 8: N.134, W.142, S.144 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.37: 3 residues within 4Å: Chain g: V.34, N.134, R.143 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.38: 3 residues within 4Å: Chain h: N.134, T.136, R.143 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.39: 3 residues within 4Å: Chain i: N.134, W.142, S.144 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.46: 3 residues within 4Å: Chain q: V.34, N.134, R.143 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.47: 3 residues within 4Å: Chain r: N.134, T.136, R.143 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.48: 3 residues within 4Å: Chain s: N.134, W.142, S.144 No protein-ligand interaction detected (PLIP)

6 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

NAG-NAG.4: 5 residues within 4Å: Chain F: N.134, T.136, S.141, W.142 Ligands: BMA.5 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 5 residues within 4Å: Chain P: N.134, T.136, S.141, W.142 Ligands: BMA.14 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 5 residues within 4Å: Chain Z: N.134, T.136, S.141, W.142 Ligands: BMA.23 No protein-ligand interaction detected (PLIP) NAG-NAG.31: 5 residues within 4Å: Chain 9: N.134, T.136, S.141, W.142 Ligands: BMA.32 No protein-ligand interaction detected (PLIP) NAG-NAG.40: 5 residues within 4Å: Ligands: BMA.41 Chain j: N.134, T.136, S.141, W.142 No protein-ligand interaction detected (PLIP) NAG-NAG.49: 5 residues within 4Å: Ligands: BMA.50 Chain t: N.134, T.136, S.141, W.142 No protein-ligand interaction detected (PLIP)

6 x BMA: beta-D-mannopyranose(Non-functional Binders)

BMA.5: 1 residues within 4Å: Ligands: NAG-NAG.4 No protein-ligand interaction detected (PLIP) BMA.14: 1 residues within 4Å: Ligands: NAG-NAG.13 No protein-ligand interaction detected (PLIP) BMA.23: 1 residues within 4Å: Ligands: NAG-NAG.22 No protein-ligand interaction detected (PLIP) BMA.32: 1 residues within 4Å: Ligands: NAG-NAG.31 No protein-ligand interaction detected (PLIP) BMA.41: 1 residues within 4Å: Ligands: NAG-NAG.40 No protein-ligand interaction detected (PLIP) BMA.50: 1 residues within 4Å: Ligands: NAG-NAG.49 No protein-ligand interaction detected (PLIP)

24 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

NAG.6: 2 residues within 4Å: Chain G: I.281, N.315 Ligand excluded by PLIP NAG.7: 2 residues within 4Å: Chain H: I.281, N.315 Ligand excluded by PLIP NAG.8: 3 residues within 4Å: Chain I: K.276, I.281, N.315 Ligand excluded by PLIP NAG.9: 2 residues within 4Å: Chain J: I.281, N.315 Ligand excluded by PLIP NAG.15: 2 residues within 4Å: Chain Q: I.281, N.315 Ligand excluded by PLIP NAG.16: 2 residues within 4Å: Chain R: I.281, N.315 Ligand excluded by PLIP NAG.17: 3 residues within 4Å: Chain S: K.276, I.281, N.315 Ligand excluded by PLIP NAG.18: 2 residues within 4Å: Chain T: I.281, N.315 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain 0: I.281, N.315 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain 1: I.281, N.315 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain 2: K.276, I.281, N.315 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain 3: I.281, N.315 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain a: I.281, N.315 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain b: I.281, N.315 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain c: K.276, I.281, N.315 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain d: I.281, N.315 Ligand excluded by PLIP NAG.42: 2 residues within 4Å: Chain k: I.281, N.315 Ligand excluded by PLIP NAG.43: 2 residues within 4Å: Chain l: I.281, N.315 Ligand excluded by PLIP NAG.44: 3 residues within 4Å: Chain m: K.276, I.281, N.315 Ligand excluded by PLIP NAG.45: 2 residues within 4Å: Chain n: I.281, N.315 Ligand excluded by PLIP NAG.51: 2 residues within 4Å: Chain u: I.281, N.315 Ligand excluded by PLIP NAG.52: 2 residues within 4Å: Chain v: I.281, N.315 Ligand excluded by PLIP NAG.53: 3 residues within 4Å: Chain w: K.276, I.281, N.315 Ligand excluded by PLIP NAG.54: 2 residues within 4Å: Chain x: I.281, N.315 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bandyopadhyay, A. et al., Cryo-EM structure of SINV/EEEV in complex with a potently neutralizing human antibody IgG EEEV-373. To Be Published

Release Date

2025-06-11

Peptides

IgG EEEV-373 Heavy chain: AKU4eo
IgG EEEV-373 Light chain: BLV5fp
Spike glycoprotein E1: CDEFMNOPWXYZ6789ghijqrst
E2 glycoprotein: GHIJQRST0123abcdklmnuvwx

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
1

K
1

U
1

4
1

e
1

o
1

B
2

L
2

V
2

5
2

f
2

p
2

C
A

D
B

E
C

F
D

M
A

N
B

O
C

P
D

W
A

X
B

Y
C

Z
D

6
A

7
B

8
C

9
D

g
A

h
B

i
C

j
D

q
A

r
B

s
C

t
D

G
a

H
b

I
c

J
d

Q
a

R
b

S
c

T
d

0
a

1
b

2
c

3
d

a
a

b
b

c
c

d
d

k
a

l
b

m
c

n
d

u
a

v
b

w
c

x
d

IgG EEEV-373 Heavy chain

IgG EEEV-373 Light chain

Spike glycoprotein E1

E2 glycoprotein

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