4ADJ

Crystal structure of the Rubella virus glycoprotein E1 in its post-fusion form crystallized in presence of 1mM of calcium acetate

PDB DOI: https://doi.org/10.2210/pdb4ADJ/pdb

Classification: VIRAL PROTEIN
Organism(s): Rubella virus
Expression System: Drosophila melanogaster
Mutation(s): No

Deposited: 2011-12-26 Released: 2013-01-09
Deposition Author(s): DuBois, R.M., Vaney, M.C., Tortorici, M.A., Al Kurdi, R., Barba-Spaeth, G., Rey, F.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.94 Å
R-Value Free: 0.194
R-Value Work: 0.182
R-Value Observed: 0.182

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 153.38 kDa
Atom Count: 11,033
Modelled Residue Count: 1,294
Deposited Residue Count: 1,419
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E1 ENVELOPE GLYCOPROTEIN	A, B, C	473	Rubella virus	Mutation(s): 0
UniProt
Find proteins for P08563 (Rubella virus (strain M33)) Explore P08563 Go to UniProtKB: P08563
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P08563
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain T [auth C] SDF format, chain D [auth A] SDF format, chain J [auth B] SDF format, chain O [auth C] MOL2 format, chain T [auth C] MOL2 format, chain D [auth A] MOL2 format, chain J [auth B] MOL2 format, chain O [auth C]	D [auth A], J [auth B], O [auth C], T [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain D [auth A] Focus chain J [auth B] Focus chain O [auth C] Focus chain T [auth C] Interactions & Density Focus chain D [auth A] Focus chain J [auth B] Focus chain O [auth C] Focus chain T [auth C]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain P [auth C] SDF format, chain K [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain P [auth C] MOL2 format, chain K [auth B]	E [auth A], F [auth A], K [auth B], P [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain K [auth B] Focus chain P [auth C] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain K [auth B] Focus chain P [auth C]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain M [auth B] SDF format, chain Q [auth C] SDF format, chain I [auth A] SDF format, chain N [auth B] MOL2 format, chain M [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain I [auth A] MOL2 format, chain N [auth B]	I [auth A], M [auth B], N [auth B], Q [auth C]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain I [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain Q [auth C] Interactions & Density Focus chain I [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain Q [auth C]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain S [auth C] SDF format, chain L [auth B] MOL2 format, chain H [auth A] MOL2 format, chain S [auth C] MOL2 format, chain L [auth B]	H [auth A], L [auth B], S [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain L [auth B] Focus chain S [auth C] Interactions & Density Focus chain H [auth A] Focus chain L [auth B] Focus chain S [auth C]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain R [auth C] MOL2 format, chain G [auth A] MOL2 format, chain R [auth C]	G [auth A], R [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain R [auth C] Interactions & Density Focus chain G [auth A] Focus chain R [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.94 Å
R-Value Free: 0.194
R-Value Work: 0.182
R-Value Observed: 0.182
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 121.875	α = 90
b = 126.899	β = 90
c = 130.946	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2013-01-09

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-01-09
Type: Initial release
Version 1.1: 2013-01-23
Changes: Database references
Version 1.2: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Other, Structure summary
Version 1.3: 2023-12-20
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary