8QP7

Crystal structure of Hepatitis C Virus E2 glycoprotein epitopeI 411-424 scaffold design 4CIL_04

PDB DOI: https://doi.org/10.2210/pdb8QP7/pdb

Classification: STRUCTURAL PROTEIN
Organism(s): Yersinia enterocolitica
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2023-09-30 Released: 2024-10-09
Deposition Author(s): Nagarathinam, K., Cramer, J.T., Krey, T.
Funding Organization(s): German Research Foundation (DFG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free: 0.262
R-Value Work: 0.214
R-Value Observed: 0.217

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of Hepatitis C Virus E2 glycoprotein epitopeI 411-424 scaffold design 4CIL_04

Nagarathinam, K., Krey, T., Scheck, A., Labuhn, M., Stroeh, L.J., Herold, E., Veselkova, B., Cramer, J.T., Rosset, S., Vollers, S.S., Bankwitz, D., Ballmaier, M., Boening, H., Roth, E., Khera, T., Ahsendorf, H., Tune, S., Dittrich-Breiholz, O., Obleser, J., Nassal, M., Jaeck, H.M., Pietschmann, T., Correia, B.E.

To be published.

Macromolecule Content

Total Structure Weight: 33.07 kDa
Atom Count: 2,211
Modelled Residue Count: 274
Deposited Residue Count: 296
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Yop effector YopM,Internalin B	A	296	Yersinia enterocolitica	Mutation(s): 21 Gene Names: yopM, inlB
UniProt
Find proteins for P0DQD2 (Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e)) Explore P0DQD2 Go to UniProtKB: P0DQD2
Find proteins for P74988 (Yersinia enterocolitica W22703) Explore P74988 Go to UniProtKB: P74988
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Groups	P74988P0DQD2
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free: 0.262
R-Value Work: 0.214
R-Value Observed: 0.217
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.29	α = 90
b = 31.67	β = 94.314
c = 135.75	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Coot	model building
XDS	data reduction
XDS	data scaling
PHENIX	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2024-10-09

Deposition Author(s):

Nagarathinam, K.

Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	KR 2880 / 3-1

Revision History (Full details and data files)

Version 1.0: 2024-10-09
Type: Initial release

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.