7BN2 | pdb_00007bn2

Clathrin heavy chain N-terminal domain bound to Non structured protein 3 from Eastern Equine Encephalitis Virus

PDB DOI: https://doi.org/10.2210/pdb7BN2/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Homo sapiens, Eastern equine encephalitis virus
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:
0.219 (Depositor), 0.224 (DCC)
R-Value Work:
0.181 (Depositor), 0.188 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7BN2

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: 85.13 kDa
Atom Count: 6,323
Modeled Residue Count: 737
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 [auth AAA], B [auth BBB]	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
Non structured protein 3 from Eastern Equine Encephalitis Virus	C [auth CCC], D [auth DDD]	17	Eastern equine encephalitis virus	Mutation(s): 0

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 E [auth AAA] MOL2 format, chain E [auth AAA] mmCIF format, chain E [auth AAA]	E [auth AAA]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth AAA] Interactions & Density Focus chain E [auth AAA]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain F [auth BBB] MOL2 format, chain F [auth BBB] mmCIF format, chain F [auth BBB]	F [auth BBB]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain F [auth BBB] Interactions & Density Focus chain F [auth BBB]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.97 Å
R-Value Free: 0.219 (Depositor), 0.224 (DCC)
R-Value Work: 0.181 (Depositor), 0.188 (DCC)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 136.9	α = 90
b = 129.119	β = 115.294
c = 77.881	γ = 90

Software Package:

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

Structure Validation

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View more in-depth experimental data

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, Derived calculations
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.