7BN1 | pdb_00007bn1

Clathrin heavy chain N-terminal domain complexed with peptide from Protein mu-NS of Reovirus type 1

PDB DOI: https://doi.org/10.2210/pdb7BN1/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Homo sapiens, Mammalian orthoreovirus 1 Lang
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: 1.97 Å
R-Value Free:
0.215 (Depositor), 0.219 (DCC)
R-Value Work:
0.184 (Depositor), 0.191 (DCC)
R-Value Observed:
0.185 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment

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: 84.94 kDa
Atom Count: 6,282
Modeled Residue Count: 738
Deposited Residue Count: 762
Unique protein chains: 2

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Clathrin heavy chain 1	A, B	364	Homo sapiens	Mutation(s): 0 Gene Names: CLTC, CLH17, CLTCL2, KIAA0034
UniProt & NIH Common Fund Data Resources
Find proteins for Q00610 (Homo sapiens) Explore Q00610 Go to UniProtKB: Q00610
PHAROS: Q00610 GTEx: ENSG00000141367
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q00610
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein mu-NS from Reovirus type 1	C [auth E], D [auth F]	17	Mammalian orthoreovirus 1 Lang	Mutation(s): 0
UniProt
Find proteins for Q9PY83 (Reovirus type 1 (strain Lang)) Explore Q9PY83 Go to UniProtKB: Q9PY83
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9PY83
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PG4 (Subject of Investigation/LOI) Query on PG4 Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.97 Å
R-Value Free: 0.215 (Depositor), 0.219 (DCC)
R-Value Work: 0.184 (Depositor), 0.191 (DCC)
R-Value Observed: 0.185 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 137.533	α = 90
b = 128.932	β = 115.5
c = 78.1	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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Ligand Structure Quality Assessment

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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.