7BN3 | pdb_00007bn3

Crystal structure of C-terminal domain of PABPC1 in complex with Nucleoprotein from Human Coronavirus 229E

PDB DOI: https://doi.org/10.2210/pdb7BN3/pdb

Classification: TRANSCRIPTION
Organism(s): Homo sapiens, Human coronavirus 229E
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2021-01-21 Released: 2022-03-02
Deposition Author(s): Badgujar, D.C., Dobritzsch, D.
Funding Organization(s): The Swedish Foundation for Strategic Research, Swedish Research Council

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.93 Å
R-Value Free:
0.228 (Depositor), 0.236 (DCC)
R-Value Work:
0.193 (Depositor), 0.203 (DCC)
R-Value Observed:
0.195 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7BN3

This is version 1.2 of the entry. See complete history.

Literature

Large-scale phage-based screening reveals extensive pan-viral mimicry of host short linear motifs

Mihalic, F., Simonetti, L., Giudice, G., Sander, M.R., Lindqvist, R., Peters, M.B.A., Benz, C., Kassa, E., Badgujar, D., Inturi, R., Ali, M., Krystkowiak, I., Sayadi, A., Andersson, E., Aronsson, H., Soderberg, O., Dobritzsch, D., Petsalaki, E., Overby, A.K., Jemth, P., Davey, N.E., Ivarsson, Y.

(2023) Nat Commun 14

DOI: https://doi.org/10.1038/s41467-023-38015-5

Macromolecule Content

Total Structure Weight: 35.08 kDa
Atom Count: 2,253
Modeled Residue Count: 286
Deposited Residue Count: 327
Unique protein chains: 2

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isoform 2 of Polyadenylate-binding protein 1	A, B, C	92	Homo sapiens	Mutation(s): 0 Gene Names: PABPC1, PAB1, PABP1, PABPC2
UniProt & NIH Common Fund Data Resources
Find proteins for P11940 (Homo sapiens) Explore P11940 Go to UniProtKB: P11940
PHAROS: P11940 GTEx: ENSG00000070756
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P11940
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleoprotein from Human Coronavirus 229E	D [auth F], E [auth D], F [auth E]	17	Human coronavirus 229E	Mutation(s): 0
UniProt
Find proteins for P15130 (Human coronavirus 229E) Explore P15130 Go to UniProtKB: P15130
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P15130
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain I [auth C] SDF format, chain H [auth B] SDF format, chain G [auth B] MOL2 format, chain I [auth C] MOL2 format, chain H [auth B] MOL2 format, chain G [auth B] mmCIF format, chain I [auth C] mmCIF format, chain H [auth B] mmCIF format, chain G [auth B]	G [auth B], H [auth B], I [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth C] Interactions & Density Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth C]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain J [auth E] MOL2 format, chain J [auth E] mmCIF format, chain J [auth E]	J [auth E]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain J [auth E] Interactions & Density Focus chain J [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.93 Å
R-Value Free: 0.228 (Depositor), 0.236 (DCC)
R-Value Work: 0.193 (Depositor), 0.203 (DCC)
R-Value Observed: 0.195 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.509	α = 90
b = 150.065	β = 90
c = 65.502	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2022-03-02

Deposition Author(s):

Funding Organization	Location	Grant Number
The Swedish Foundation for Strategic Research	Sweden	SB16-0039
Swedish Research Council	Sweden	2016-04965
Swedish Research Council	Sweden	2016-04134

Revision History (Full details and data files)

Version 1.0: 2022-03-02
Type: Initial release
Version 1.1: 2023-05-10
Changes: Database references
Version 1.2: 2024-02-07
Changes: Data collection, Refinement description

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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.