9YIN | pdb_00009yin

Sf11 bacteriophage portal

PDB DOI: https://doi.org/10.2210/pdb9YIN/pdb
EM Map EMD-72999: EMDB EMDataResource

Classification: VIRUS
Organism(s): Shigella phage Sf11 SMD-2017
Expression System: Shigella flexneri Y
Mutation(s): No

Deposited: 2025-10-01 Released: 2025-11-12
Deposition Author(s): Subramanian, S., Parent, K.N.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Science Foundation (NSF, United States)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.40 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 9YIN

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

Literature

Structure of Shigella bacteriophage Sf11

Subramanian, S., Dover, J.A., Parent, K.N.

To be published.

Macromolecule Content

Total Structure Weight: 52.37 kDa
Atom Count: 2,964
Modeled Residue Count: 382
Deposited Residue Count: 470
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sf11 portal	A	470	Shigella phage Sf11 SMD-2017	Mutation(s): 0 Gene Names: Sf11_gp63
UniProt
Find proteins for A0A291AXK9 (Shigella phage Sf11 SMD-2017) Explore A0A291AXK9 Go to UniProtKB: A0A291AXK9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A291AXK9
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.40 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.20.1_4487:
RECONSTRUCTION	cryoSPARC

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2025-11-12

Deposition Author(s):

Subramanian, S.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM116789
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM140803
National Science Foundation (NSF, United States)	United States	1750125

Revision History (Full details and data files)

Version 1.0: 2025-11-12
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.