9MFE | pdb_00009mfe

cryoEM structure of Escherichia phage YDC107 tail core

PDB DOI: https://doi.org/10.2210/pdb9MFE/pdb
EM Map EMD-48226: EMDB EMDataResource

Classification: VIRAL PROTEIN
Organism(s): Escherichia phage YDC107_1
Mutation(s): No

Deposited: 2024-12-09 Released: 2025-01-01
Deposition Author(s): Kopylov, M.
Funding Organization(s): Simons Foundation

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.22 Å
Aggregation State: FILAMENT
Reconstruction Method: HELICAL

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 9MFE

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

Literature

Identification and cryoEM structure determination of Escherichia phage YDC107 tail found in a bacteria-contaminated buffer

Kopylov, M., Jenkins, M.C.

To be published.

Macromolecule Content

Total Structure Weight: 154.2 kDa
Atom Count: 7,110
Modeled Residue Count: 924
Deposited Residue Count: 1,470
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Major tail protein V	A, B, C, D, E A, B, C, D, E, F	245	Escherichia phage YDC107_1	Mutation(s): 0
UniProt
Find proteins for A0ACD6B915 (Escherichia phage YDC107_1) Explore A0ACD6B915 Go to UniProtKB: A0ACD6B915
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0ACD6B915
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.22 Å
Aggregation State: FILAMENT
Reconstruction Method: HELICAL

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21.2_5419

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-01-01

Deposition Author(s):

Funding Organization	Location	Grant Number
Simons Foundation	United States	SF349247

Revision History (Full details and data files)

Version 1.0: 2025-01-01
Type: Initial release

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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.