7EAK

Echovirus3 full particle in complex with 5G3 fab

PDB DOI: https://doi.org/10.2210/pdb7EAK/pdb
EM Map EMD-31046: EMDB EMDataResource

Classification: VIRUS
Organism(s): Echovirus E3, Mus musculus
Mutation(s): No

Deposited: 2021-03-07 Released: 2021-07-14
Deposition Author(s): Feng, R.

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.90 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Structural basis for neutralization of an anicteric hepatitis associated echovirus by a potent neutralizing antibody.

Feng, R., Wang, L., Shi, D., Zheng, B., Zhang, L., Hou, H., Xia, D., Cui, L., Wang, X., Xu, S., Wang, K., Zhu, L.

(2021) Cell Discov 7: 35-35

PubMed: 34035235 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/s41421-021-00264-3
Primary Citation of Related Structures:
7EAH, 7EAI, 7EAJ, 7EAK

Organizational Affiliation

CAS Key Laboratory of Infection and Immunity, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.

Macromolecule Content

Total Structure Weight: 121.36 kDa
Atom Count: 8,291
Modelled Residue Count: 1,056
Deposited Residue Count: 1,086
Unique protein chains: 6

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsid protein VP1	A	292	Echovirus E3	Mutation(s): 0
UniProt
Find proteins for A0A060BKX4 (Echovirus E3) Explore A0A060BKX4 Go to UniProtKB: A0A060BKX4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A060BKX4
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsid protein VP2	B	261	Echovirus E3	Mutation(s): 0
UniProt
Find proteins for A0A0K0LDT3 (Echovirus E3) Explore A0A0K0LDT3 Go to UniProtKB: A0A0K0LDT3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0K0LDT3
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsid protein VP3	C	238	Echovirus E3	Mutation(s): 0
UniProt
Find proteins for A0A125RY26 (Echovirus E3) Explore A0A125RY26 Go to UniProtKB: A0A125RY26
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A125RY26
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsid protein VP4	D	68	Echovirus E3	Mutation(s): 0
UniProt
Find proteins for A0A291S400 (Echovirus E3) Explore A0A291S400 Go to UniProtKB: A0A291S400
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A291S400
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
heavy chain of 5G3 fab	E [auth F]	112	Mus musculus	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
light chain of 5G3 fab	F [auth L]	115	Mus musculus	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SPH Query on SPH Download Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A]	G [auth A]	SPHINGOSINE C₁₈ H₃₇ N O₂ WWUZIQQURGPMPG-MSOLQXFVSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
MYR Query on MYR Download Ideal Coordinates CCD File SDF format, chain H [auth D] MOL2 format, chain H [auth D]	H [auth D]	MYRISTIC ACID C₁₄ H₂₈ O₂ TUNFSRHWOTWDNC-UHFFFAOYSA-N		Interactions Focus chain H [auth D] Interactions & Density Focus chain H [auth D]