6JJD | pdb_00006jjd

Cryo-EM structure of giant freshwater prawn Macrobrachium rosenbergii nodavirus (MrNV) full VLP

PDB DOI: https://doi.org/10.2210/pdb6JJD/pdb
EM Map EMD-9707: EMDB EMDataResource

Classification: VIRUS LIKE PARTICLE
Organism(s): Macrobrachium rosenbergii nodavirus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2019-02-25 Released: 2019-05-01
Deposition Author(s): Chang, W.H., Wang, C.H., Lin, H.H., Lin, S.Y., Chong, S.C., Wu, Y.Y.
Funding Organization(s): Ministry of Science and Technology (Taiwan), Academia Sinica (Taiwan)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.21 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 6JJD

This is version 1.1 of the entry. See complete history.

Literature

Cryo-EM structure of giant freshwater prawn Macrobrachium rosenbergii nodavirus (MrNV) full VLP

Chang, W.H., Wang, C.H., Lin, H.H., Lin, S.Y., Chong, S.C., Wu, Y.Y.

To be published.

Macromolecule Content

Total Structure Weight: 124.72 kDa
Atom Count: 4,753
Modeled Residue Count: 602
Deposited Residue Count: 1,113
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsid protein	A, B, C	371	Macrobrachium rosenbergii nodavirus	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain I [auth B] SDF format, chain H [auth B] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain J [auth B] MOL2 format, chain I [auth B] MOL2 format, chain H [auth B] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain J [auth B] mmCIF format, chain I [auth B] mmCIF format, chain H [auth B] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A] E [auth A] F [auth A] G [auth A] H [auth B] D [auth A], E [auth A], F [auth A], G [auth A], H [auth B], I [auth B], J [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.21 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	2.0
MODEL REFINEMENT	PHENIX	3374

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2019-05-01

Deposition Author(s):

Funding Organization	Location	Grant Number
Ministry of Science and Technology (Taiwan)	Taiwan	MOST 103-2321-B-001-048
Ministry of Science and Technology (Taiwan)	Taiwan	MOST 104-2321-B-001-019
Ministry of Science and Technology (Taiwan)	Taiwan	MOST 105-2321-B-001-009
Ministry of Science and Technology (Taiwan)	Taiwan	MOST 106-0210-01-15-02
Ministry of Science and Technology (Taiwan)	Taiwan	MOST 106-0210-01-15-04
Ministry of Science and Technology (Taiwan)	Taiwan	MOST 107-0210-01-19-01
Ministry of Science and Technology (Taiwan)	Taiwan	MOST 107-0210-01-19-02
Academia Sinica (Taiwan)	Taiwan	AS-103-TP-B12

Revision History (Full details and data files)

Version 1.0: 2019-05-01
Type: Initial release
Version 1.1: 2024-03-27
Changes: Data collection, Database references, Derived calculations

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.