21FY | pdb_000021fy

The cryo-EM structure of IscS-PptA complex

PDB DOI: https://doi.org/10.2210/pdb21FY/pdb
EM Map EMD-67634: EMDB EMDataResource

Classification: VIRAL PROTEIN
Organism(s): Escherichia coli K-12, Psychrobacter phage vB_PmaS_Y8A
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2025-12-11 Released: 2026-04-15
Deposition Author(s): Wang, Y.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.85 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 21FY

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

Literature

The cryo-EM structure of IscS-PptA complex

Wang, Y.

To be published.

Macromolecule Content

Total Structure Weight: 152 kDa
Atom Count: 9,912
Modeled Residue Count: 1,258
Deposited Residue Count: 1,348
Unique protein chains: 2

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cysteine desulfurase IscS	A, B	404	Escherichia coli K-12	Mutation(s): 0 Gene Names: iscS, nuvC, yfhO, yzzO, b2530, JW2514 EC: 2.8.1.7
UniProt
Find proteins for P0A6B7 (Escherichia coli (strain K12)) Explore P0A6B7 Go to UniProtKB: P0A6B7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0A6B7
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PptA	C, D	270	Psychrobacter phage vB_PmaS_Y8A	Mutation(s): 0
UniProt
Find proteins for A0A5Q2WBY0 (Vibrio phage vB_VhaP_VH-5) Explore A0A5Q2WBY0 Go to UniProtKB: A0A5Q2WBY0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A5Q2WBY0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SF4 (Subject of Investigation/LOI) Query on SF4 Download:Ideal Coordinates CCD File SDF format, chain E [auth C] SDF format, chain F [auth D] MOL2 format, chain E [auth C] MOL2 format, chain F [auth D] mmCIF format, chain E [auth C] mmCIF format, chain F [auth D]	E [auth C], F [auth D]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain E [auth C] Focus chain F [auth D] Interactions & Density Focus chain E [auth C] Focus chain F [auth D]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
LLP Query on LLP	A, B	L-PEPTIDE LINKING	C₁₄ H₂₂ N₃ O₇ P		LYS

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.85 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2026-04-15

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History (Full details and data files)

Version 1.0: 2026-04-15
Type: Initial release

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.