8ZSI | pdb_00008zsi

CryoEM Helical Structure of HAM-SIR2 with dITP and NAD fragment

PDB DOI: https://doi.org/10.2210/pdb8ZSI/pdb
EM Map EMD-60416: EMDB EMDataResource

Classification: IMMUNE SYSTEM
Organism(s): Escherichia coli
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-06-05 Released: 2025-12-10
Deposition Author(s): Hao, F., Eddie, T., Bin, W., Min, L.
Funding Organization(s): Ministry of Education (MoE, Singapore)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.10 Å
Aggregation State: FILAMENT
Reconstruction Method: HELICAL

wwPDB Validation 3D Report Full Report

Validation slider image for 8ZSI

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

Literature

CryoEM Helical Structure of HAM-SIR2 with dITP and NAD fragment

Hao, F., Eddie, T., Bin, W., Min, L.

To be published.

Macromolecule Content

Total Structure Weight: 209.37 kDa
Atom Count: 14,740
Modeled Residue Count: 1,792
Deposited Residue Count: 1,792
Unique protein chains: 2

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Non-canonical purine NTP pyrophosphatase	A, B, C, D	184	Escherichia coli	Mutation(s): 0 Gene Names: GRW56_02065, GRW57_01900
UniProt
Find proteins for K8WC63 (Providencia sneebia DSM 19967) Explore K8WC63 Go to UniProtKB: K8WC63
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	K8WC63
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Sir2 family NAD-dependent protein deacetylase	E, F, G, H	264	Escherichia coli	Mutation(s): 0 Gene Names: GRW56_02060, GRW57_01895
UniProt
Find proteins for K8WJ15 (Providencia sneebia DSM 19967) Explore K8WJ15 Go to UniProtKB: K8WJ15
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	K8WJ15
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD (Subject of Investigation/LOI) Query on NAD Download:Ideal Coordinates CCD File SDF format, chain N [auth H] SDF format, chain M [auth E] MOL2 format, chain N [auth H] MOL2 format, chain M [auth E] mmCIF format, chain N [auth H] mmCIF format, chain M [auth E]	M [auth E], N [auth H]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain M [auth E] Focus chain N [auth H] Interactions & Density Focus chain M [auth E] Focus chain N [auth H]
Y43 (Subject of Investigation/LOI) Query on Y43 Download:Ideal Coordinates CCD File SDF format, chain L [auth D] SDF format, chain K [auth C] SDF format, chain J [auth B] SDF format, chain I [auth A] MOL2 format, chain L [auth D] MOL2 format, chain K [auth C] MOL2 format, chain J [auth B] MOL2 format, chain I [auth A] mmCIF format, chain L [auth D] mmCIF format, chain K [auth C] mmCIF format, chain J [auth B] mmCIF format, chain I [auth A]	I [auth A], J [auth B], K [auth C], L [auth D]	2'-deoxyinosine 5'-triphosphate C₁₀ H₁₅ N₄ O₁₃ P₃ UFJPAQSLHAGEBL-RRKCRQDMSA-N		Interactions Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth C] Focus chain L [auth D] Interactions & Density Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth C] Focus chain L [auth D]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.10 Å
Aggregation State: FILAMENT
Reconstruction Method: HELICAL

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-12-10

Deposition Author(s):

Funding Organization	Location	Grant Number
Ministry of Education (MoE, Singapore)	Singapore	--

Revision History (Full details and data files)

Version 1.0: 2025-12-10
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.