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

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

Find similar proteins by:

(by identity cutoff) | 3D Structure

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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	K8WC63
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

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% Identity50% Identity70% Identity90% Identity95% Identity100% 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 EB [auth f] SDF format, chain GA [auth A] SDF format, chain GB [auth Z] SDF format, chain IA [auth B] 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 YA [auth e] SDF format, chain WA [auth Y] SDF format, chain IB [auth V] SDF format, chain CB [auth U] MOL2 format, chain AB [auth W] 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 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 YA [auth e] MOL2 format, chain WA [auth Y] MOL2 format, chain IB [auth V] MOL2 format, chain CB [auth U] mmCIF format, chain AB [auth W] 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 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 YA [auth e] mmCIF format, chain WA [auth Y] mmCIF format, chain IB [auth V] mmCIF format, chain CB [auth U]	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 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 PA [auth J] SDF format, chain RA [auth I] SDF format, chain TA [auth K] SDF format, chain XA [auth Y] SDF format, chain ZA [auth e] SDF format, chain VA [auth L] SDF format, chain NA [auth D] SDF 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 PA [auth J] MOL2 format, chain RA [auth I] MOL2 format, chain TA [auth K] MOL2 format, chain XA [auth Y] MOL2 format, chain ZA [auth e] MOL2 format, chain VA [auth L] MOL2 format, chain NA [auth D] MOL2 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 PA [auth J] mmCIF format, chain RA [auth I] mmCIF format, chain TA [auth K] mmCIF format, chain XA [auth Y] mmCIF format, chain ZA [auth e] mmCIF format, chain VA [auth L] mmCIF format, chain NA [auth D] mmCIF format, chain BB [auth W]	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]