9LSJ

Cryo-EM structure of the G15C-R66C and T83C-T83C diabody complex (CitS-diabody #7-TLR3)

PDB DOI: https://doi.org/10.2210/pdb9LSJ/pdb
EM Map EMD-63357: EMDB EMDataResource

Classification: STRUCTURAL PROTEIN/IMMUNE SYSTEM
Organism(s): Klebsiella pneumoniae, Homo sapiens, synthetic construct
Expression System: Escherichia coli, Trichoplusia ni
Mutation(s): No

Deposited: 2025-02-04 Released: 2025-03-12
Deposition Author(s): Kim, S., Kim, J.W., Park, J.G., Lee, S.S., Choi, S.H., Lee, J.-O., Jin, M.S.
Funding Organization(s): Samsung Science and Technology Foundation, National Research Foundation (NRF, Korea)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.10 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

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

Literature

Disulfide-stabilized diabodies enable near-atomic cryo-EM imaging of small proteins: A case study of the bacterial Na+/citrate symporter CitS

Kim, S., Kim, J.W., Park, J.G., Lee, S.S., Choi, S.H., Lee, J.-O., Jin, M.S.

To be published.

Macromolecule Content

Total Structure Weight: 257.89 kDa
Atom Count: 15,438
Modelled Residue Count: 1,989
Deposited Residue Count: 2,318
Unique protein chains: 4

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Citrate/sodium symporter	A, B	446	Klebsiella pneumoniae	Mutation(s): 0 Gene Names: citS
UniProt
Find proteins for P31602 (Klebsiella pneumoniae) Explore P31602 Go to UniProtKB: P31602
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P31602
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Toll-like receptor 3	C	904	Homo sapiens	Mutation(s): 0 Gene Names: TLR3
UniProt & NIH Common Fund Data Resources
Find proteins for O15455 (Homo sapiens) Explore O15455 Go to UniProtKB: O15455
PHAROS: O15455 GTEx: ENSG00000164342
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O15455
Glycosylation
Glycosylation Sites: 8	Glycosylation Focus chain C	Go to GlyGen: O15455-1
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Diabody (CitS VH-TLR3 VL)	D	256	synthetic construct	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Diabody (TLR3 VH-CitS VL)	E	266	synthetic construct	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	F [auth H], G [auth F], I	2		N-Glycosylation	Interactions Focus chain F [auth H] Focus chain G [auth F] Focus chain I Interactions & Density Focus chain F [auth H] Focus chain G [auth F] Focus chain I

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	H [auth G]	3		N-Glycosylation	Interactions Focus chain H [auth G] Interactions & Density Focus chain H [auth G]

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PLM Query on PLM Download Ideal Coordinates CCD File SDF format, chain K [auth A] MOL2 format, chain K [auth A] mmCIF format, chain K [auth A]	K [auth A]	PALMITIC ACID C₁₆ H₃₂ O₂ IPCSVZSSVZVIGE-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Interactions & Density Focus chain K [auth A]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain L [auth C] SDF format, chain M [auth C] SDF format, chain N [auth C] SDF format, chain O [auth C] MOL2 format, chain L [auth C] MOL2 format, chain M [auth C] MOL2 format, chain N [auth C] MOL2 format, chain O [auth C] mmCIF format, chain L [auth C] mmCIF format, chain M [auth C] mmCIF format, chain N [auth C] mmCIF format, chain O [auth C]	L [auth C], M [auth C], N [auth C], O [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain L [auth C] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth C] Interactions & Density Focus chain L [auth C] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth C]
CIT (Subject of Investigation/LOI) Query on CIT Download Ideal Coordinates CCD File SDF format, chain J [auth A] MOL2 format, chain J [auth A] mmCIF format, chain J [auth A]	J [auth A]	CITRIC ACID C₆ H₈ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Interactions & Density Focus chain J [auth A]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.10 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.18.2_3874

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-03-12

Deposition Author(s):

Funding Organization	Location	Grant Number
Samsung Science and Technology Foundation	Korea, Republic Of	SSTF-BA1702-14
National Research Foundation (NRF, Korea)	Korea, Republic Of	RS-2024-00344154
National Research Foundation (NRF, Korea)	Korea, Republic Of	RS-2024-00440614