8ZSH | pdb_00008zsh

Cryo-EM Helical Structure of dITP-activated KomBC complex

PDB DOI: https://doi.org/10.2210/pdb8ZSH/pdb
EM Map EMD-60415: 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., Kai, S., Bin, W., Min, L.
Funding Organization(s): Ministry of Education (MoE, Singapore)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.00 Å
Aggregation State: FILAMENT
Reconstruction Method: HELICAL

wwPDB Validation 3D Report Full Report

Validation slider image for 8ZSH

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

Literature

Cryo-EM Helical Structure of dITP-activated KomBC complex

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

To be published.

Macromolecule Content

Total Structure Weight: 833.62 kDa
Atom Count: 58,704
Modeled Residue Count: 7,168
Deposited Residue Count: 7,168
Unique protein chains: 2

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
KomB, HAM-like protein, Non-canonical purine NTP pyrophosphatase	A AA [auth V] B BA [auth X] C A, AA [auth V], B, BA [auth X], C, D, I [auth J], J [auth I], K, L, Q [auth Y], R [auth e], S [auth W], T [auth U], Y [auth f], Z	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
KomC, SIR2 domain protein, NADase	CA [auth h] DA [auth j] E EA [auth l] F CA [auth h], DA [auth j], E, EA [auth l], F, FA [auth n], G, H, M, N, O, P, U [auth g], V [auth i], W [auth k], X [auth m]	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
Y43 (Subject of Investigation/LOI) Query on Y43 Download:Ideal Coordinates CCD File SDF format, chain AB [auth W] SDF format, chain CB [auth U] SDF format, chain EB [auth f] SDF format, chain GA [auth A] SDF format, chain GB [auth Z] SDF format, chain IA [auth B] SDF format, chain IB [auth V] SDF format, chain KA [auth C] SDF format, chain KB [auth X] SDF format, chain MA [auth D] SDF format, chain OA [auth J] SDF format, chain QA [auth I] SDF format, chain SA [auth K] SDF format, chain UA [auth L] SDF format, chain WA [auth Y] SDF format, chain YA [auth e] MOL2 format, chain AB [auth W] MOL2 format, chain CB [auth U] MOL2 format, chain EB [auth f] MOL2 format, chain GA [auth A] MOL2 format, chain GB [auth Z] MOL2 format, chain IA [auth B] MOL2 format, chain IB [auth V] MOL2 format, chain KA [auth C] MOL2 format, chain KB [auth X] MOL2 format, chain MA [auth D] MOL2 format, chain OA [auth J] MOL2 format, chain QA [auth I] MOL2 format, chain SA [auth K] MOL2 format, chain UA [auth L] MOL2 format, chain WA [auth Y] MOL2 format, chain YA [auth e] mmCIF format, chain AB [auth W] mmCIF format, chain CB [auth U] mmCIF format, chain EB [auth f] mmCIF format, chain GA [auth A] mmCIF format, chain GB [auth Z] mmCIF format, chain IA [auth B] mmCIF format, chain IB [auth V] mmCIF format, chain KA [auth C] mmCIF format, chain KB [auth X] mmCIF format, chain MA [auth D] mmCIF format, chain OA [auth J] mmCIF format, chain QA [auth I] mmCIF format, chain SA [auth K] mmCIF format, chain UA [auth L] mmCIF format, chain WA [auth Y] mmCIF format, chain YA [auth e]	AB [auth W] CB [auth U] EB [auth f] GA [auth A] GB [auth Z] AB [auth W], CB [auth U], EB [auth f], GA [auth A], GB [auth Z], IA [auth B], IB [auth V], KA [auth C], KB [auth X], MA [auth D], OA [auth J], QA [auth I], SA [auth K], UA [auth L], WA [auth Y], YA [auth e]	2'-deoxyinosine 5'-triphosphate C₁₀ H₁₅ N₄ O₁₃ P₃ UFJPAQSLHAGEBL-RRKCRQDMSA-N		Interactions Focus chain AB [auth W] Focus chain CB [auth U] Focus chain EB [auth f] Focus chain GA [auth A] Focus chain GB [auth Z] Focus chain IA [auth B] Focus chain IB [auth V] Focus chain KA [auth C] Focus chain KB [auth X] Focus chain MA [auth D] Focus chain OA [auth J] Focus chain QA [auth I] Focus chain SA [auth K] Focus chain UA [auth L] Focus chain WA [auth Y] Focus chain YA [auth e] Interactions & Density Focus chain AB [auth W] Focus chain CB [auth U] Focus chain EB [auth f] Focus chain GA [auth A] Focus chain GB [auth Z] Focus chain IA [auth B] Focus chain IB [auth V] Focus chain KA [auth C] Focus chain KB [auth X] Focus chain MA [auth D] Focus chain OA [auth J] Focus chain QA [auth I] Focus chain SA [auth K] Focus chain UA [auth L] Focus chain WA [auth Y] Focus chain YA [auth e]
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain BB [auth W] SDF format, chain DB [auth U] SDF format, chain FB [auth f] SDF format, chain HA [auth A] SDF format, chain HB [auth Z] SDF format, chain JA [auth B] SDF format, chain JB [auth V] SDF format, chain LA [auth C] SDF format, chain LB [auth X] SDF format, chain NA [auth D] SDF format, chain PA [auth J] SDF format, chain RA [auth I] SDF format, chain TA [auth K] SDF format, chain VA [auth L] SDF format, chain XA [auth Y] SDF format, chain ZA [auth e] MOL2 format, chain BB [auth W] MOL2 format, chain DB [auth U] MOL2 format, chain FB [auth f] MOL2 format, chain HA [auth A] MOL2 format, chain HB [auth Z] MOL2 format, chain JA [auth B] MOL2 format, chain JB [auth V] MOL2 format, chain LA [auth C] MOL2 format, chain LB [auth X] MOL2 format, chain NA [auth D] MOL2 format, chain PA [auth J] MOL2 format, chain RA [auth I] MOL2 format, chain TA [auth K] MOL2 format, chain VA [auth L] MOL2 format, chain XA [auth Y] MOL2 format, chain ZA [auth e] mmCIF format, chain BB [auth W] mmCIF format, chain DB [auth U] mmCIF format, chain FB [auth f] mmCIF format, chain HA [auth A] mmCIF format, chain HB [auth Z] mmCIF format, chain JA [auth B] mmCIF format, chain JB [auth V] mmCIF format, chain LA [auth C] mmCIF format, chain LB [auth X] mmCIF format, chain NA [auth D] mmCIF format, chain PA [auth J] mmCIF format, chain RA [auth I] mmCIF format, chain TA [auth K] mmCIF format, chain VA [auth L] mmCIF format, chain XA [auth Y] mmCIF format, chain ZA [auth e]	BB [auth W] DB [auth U] FB [auth f] HA [auth A] HB [auth Z] BB [auth W], DB [auth U], FB [auth f], HA [auth A], HB [auth Z], JA [auth B], JB [auth V], LA [auth C], LB [auth X], NA [auth D], PA [auth J], RA [auth I], TA [auth K], VA [auth L], XA [auth Y], ZA [auth e]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain BB [auth W] Focus chain DB [auth U] Focus chain FB [auth f] Focus chain HA [auth A] Focus chain HB [auth Z] Focus chain JA [auth B] Focus chain JB [auth V] Focus chain LA [auth C] Focus chain LB [auth X] Focus chain NA [auth D] Focus chain PA [auth J] Focus chain RA [auth I] Focus chain TA [auth K] Focus chain VA [auth L] Focus chain XA [auth Y] Focus chain ZA [auth e] Interactions & Density Focus chain BB [auth W] Focus chain DB [auth U] Focus chain FB [auth f] Focus chain HA [auth A] Focus chain HB [auth Z] Focus chain JA [auth B] Focus chain JB [auth V] Focus chain LA [auth C] Focus chain LB [auth X] Focus chain NA [auth D] Focus chain PA [auth J] Focus chain RA [auth I] Focus chain TA [auth K] Focus chain VA [auth L] Focus chain XA [auth Y] Focus chain ZA [auth e]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.00 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.