9X1E | pdb_00009x1e

Cryo-EM structure of the dITP-bound intermediate form of the KomBC filament

PDB DOI: https://doi.org/10.2210/pdb9X1E/pdb
EM Map EMD-66459: EMDB EMDataResource

Classification: ANTIVIRAL PROTEIN
Organism(s): Escherichia coli
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2025-10-01 Released: 2026-10-28
Deposition Author(s): Li, X., Liu, M., Jiang, W.X., Xing, Q., Ma, L.X., Huang, F.T.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.20 Å
Aggregation State: FILAMENT
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 9X1E

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

Literature

Cryo-EM structure of the dITP-bound intermediate form of the KomBC filament

Li, X., Liu, M., Jiang, W.X., Xing, Q., Ma, L.X., Huang, F.T.

To be published.

Macromolecule Content

Total Structure Weight: 1,497.99 kDa
Atom Count: 103,012
Modeled Residue Count: 12,600
Deposited Residue Count: 12,908
Unique protein chains: 2

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
KomB	A [auth AA] CA [auth FG] CB [auth CA] D [auth CG] DA [auth FH] A [auth AA], CA [auth FG], CB [auth CA], D [auth CG], DA [auth FH], DB [auth CB], E [auth CH], GA, H [auth DA], HA [auth GB], I [auth DB], L [auth DG], LA [auth GG], M [auth DH], MA [auth GH], P [auth EA], Q [auth EB], QA [auth AG], RA [auth AH], T [auth AB], U [auth EG], UA [auth BA], V [auth EH], VA [auth BB], Y [auth FA], YA [auth BG], Z [auth FB], ZA [auth BH]	197	Escherichia coli	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
KomC	AA [auth FC] AB [auth BI] B [auth CC] BA [auth FD] BB [auth BJ] AA [auth FC], AB [auth BI], B [auth CC], BA [auth FD], BB [auth BJ], C [auth CD], EA [auth FI], F [auth CI], FA [auth FJ], G [auth CJ], IA [auth GC], J [auth DC], JA [auth GD], K [auth DD], KA [auth AC], N [auth DI], NA [auth GI], O [auth DJ], OA [auth GJ], PA [auth AD], R [auth EC], S [auth ED], SA [auth AI], TA [auth AJ], W [auth EI], WA [auth BC], X [auth EJ], XA [auth BD]	264	Escherichia coli	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 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 AC [auth BA] SDF format, chain BC [auth BB] SDF format, chain CC [auth BG] SDF format, chain DC [auth BH] SDF format, chain EB [auth AA] SDF format, chain EC [auth CA] SDF format, chain FB [auth CG] SDF format, chain FC [auth CB] SDF format, chain GB [auth CH] SDF format, chain HB [auth DA] SDF format, chain IB [auth DB] SDF format, chain JB [auth DG] SDF format, chain KB [auth DH] SDF format, chain LB [auth EA] SDF format, chain MB [auth EB] SDF format, chain NB [auth AB] SDF format, chain OB [auth EG] SDF format, chain PB [auth EH] SDF format, chain SB [auth FG] SDF format, chain TB [auth FH] SDF format, chain UB [auth GA] SDF format, chain VB [auth GB] SDF format, chain WB [auth GG] SDF format, chain ZB [auth AH] SDF format, chain YB [auth AG] SDF format, chain XB [auth GH] SDF format, chain RB [auth FB] SDF format, chain QB [auth FA] MOL2 format, chain AC [auth BA] MOL2 format, chain BC [auth BB] MOL2 format, chain CC [auth BG] MOL2 format, chain DC [auth BH] MOL2 format, chain EB [auth AA] MOL2 format, chain EC [auth CA] MOL2 format, chain FB [auth CG] MOL2 format, chain FC [auth CB] MOL2 format, chain GB [auth CH] MOL2 format, chain HB [auth DA] MOL2 format, chain IB [auth DB] MOL2 format, chain JB [auth DG] MOL2 format, chain KB [auth DH] MOL2 format, chain LB [auth EA] MOL2 format, chain MB [auth EB] MOL2 format, chain NB [auth AB] MOL2 format, chain OB [auth EG] MOL2 format, chain PB [auth EH] MOL2 format, chain SB [auth FG] MOL2 format, chain TB [auth FH] MOL2 format, chain UB [auth GA] MOL2 format, chain VB [auth GB] MOL2 format, chain WB [auth GG] MOL2 format, chain ZB [auth AH] MOL2 format, chain YB [auth AG] MOL2 format, chain XB [auth GH] MOL2 format, chain RB [auth FB] MOL2 format, chain QB [auth FA] mmCIF format, chain AC [auth BA] mmCIF format, chain BC [auth BB] mmCIF format, chain CC [auth BG] mmCIF format, chain DC [auth BH] mmCIF format, chain EB [auth AA] mmCIF format, chain EC [auth CA] mmCIF format, chain FB [auth CG] mmCIF format, chain FC [auth CB] mmCIF format, chain GB [auth CH] mmCIF format, chain HB [auth DA] mmCIF format, chain IB [auth DB] mmCIF format, chain JB [auth DG] mmCIF format, chain KB [auth DH] mmCIF format, chain LB [auth EA] mmCIF format, chain MB [auth EB] mmCIF format, chain NB [auth AB] mmCIF format, chain OB [auth EG] mmCIF format, chain PB [auth EH] mmCIF format, chain SB [auth FG] mmCIF format, chain TB [auth FH] mmCIF format, chain UB [auth GA] mmCIF format, chain VB [auth GB] mmCIF format, chain WB [auth GG] mmCIF format, chain ZB [auth AH] mmCIF format, chain YB [auth AG] mmCIF format, chain XB [auth GH] mmCIF format, chain RB [auth FB] mmCIF format, chain QB [auth FA]	AC [auth BA] BC [auth BB] CC [auth BG] DC [auth BH] EB [auth AA] AC [auth BA], BC [auth BB], CC [auth BG], DC [auth BH], EB [auth AA], EC [auth CA], FB [auth CG], FC [auth CB], GB [auth CH], HB [auth DA], IB [auth DB], JB [auth DG], KB [auth DH], LB [auth EA], MB [auth EB], NB [auth AB], OB [auth EG], PB [auth EH], QB [auth FA], RB [auth FB], SB [auth FG], TB [auth FH], UB [auth GA], VB [auth GB], WB [auth GG], XB [auth GH], YB [auth AG], ZB [auth AH]	2'-deoxyinosine 5'-triphosphate C₁₀ H₁₅ N₄ O₁₃ P₃ UFJPAQSLHAGEBL-RRKCRQDMSA-N		Interactions Focus chain AC [auth BA] Focus chain BC [auth BB] Focus chain CC [auth BG] Focus chain DC [auth BH] Focus chain EB [auth AA] Focus chain EC [auth CA] Focus chain FB [auth CG] Focus chain FC [auth CB] Focus chain GB [auth CH] Focus chain HB [auth DA] Focus chain IB [auth DB] Focus chain JB [auth DG] Focus chain KB [auth DH] Focus chain LB [auth EA] Focus chain MB [auth EB] Focus chain NB [auth AB] Focus chain OB [auth EG] Focus chain PB [auth EH] Focus chain QB [auth FA] Focus chain RB [auth FB] Focus chain SB [auth FG] Focus chain TB [auth FH] Focus chain UB [auth GA] Focus chain VB [auth GB] Focus chain WB [auth GG] Focus chain XB [auth GH] Focus chain YB [auth AG] Focus chain ZB [auth AH] Interactions & Density Focus chain AC [auth BA] Focus chain BC [auth BB] Focus chain CC [auth BG] Focus chain DC [auth BH] Focus chain EB [auth AA] Focus chain EC [auth CA] Focus chain FB [auth CG] Focus chain FC [auth CB] Focus chain GB [auth CH] Focus chain HB [auth DA] Focus chain IB [auth DB] Focus chain JB [auth DG] Focus chain KB [auth DH] Focus chain LB [auth EA] Focus chain MB [auth EB] Focus chain NB [auth AB] Focus chain OB [auth EG] Focus chain PB [auth EH] Focus chain QB [auth FA] Focus chain RB [auth FB] Focus chain SB [auth FG] Focus chain TB [auth FH] Focus chain UB [auth GA] Focus chain VB [auth GB] Focus chain WB [auth GG] Focus chain XB [auth GH] Focus chain YB [auth AG] Focus chain ZB [auth AH]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.20 Å
Aggregation State: FILAMENT
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	cryoSPARC

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2026-10-28

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32371277

Revision History (Full details and data files)

Version 1.0: 2026-10-28
Type: Initial release