38RI | pdb_000038ri

Structure of the DAB1 Complex in State B

PDB DOI: https://doi.org/10.2210/pdb38RI/pdb
EM Map EMD-79080: EMDB EMDataResource

Classification: LYASE
Organism(s): Thermocrinis albus DSM 14484
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2026-09-15 Released: 2026-09-30
Deposition Author(s): Phillips, N.R., Oltrogge, L.M., Remis, J.P., Savage, D.F.
Funding Organization(s): Department of Energy (DOE, United States)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.29 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 38RI

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

Literature

Structural insights into the coupling mechanism of vectorial CO2 uptake by DAB1

Phillips, N.R., Oltrogge, L.M., Remis, J.P., Savage, D.F.

To be published.

Macromolecule Content

Total Structure Weight: 207.35 kDa
Atom Count: 14,196
Modeled Residue Count: 1,678
Deposited Residue Count: 1,804
Unique protein chains: 2

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable inorganic carbon transporter subunit DabA	A	1,031	Thermocrinis albus DSM 14484	Mutation(s): 0 Gene Names: dabA, Thal_0253
UniProt
Find proteins for D3SP01 (Thermocrinis albus (strain DSM 14484 / JCM 11386 / HI 11/12)) Explore D3SP01 Go to UniProtKB: D3SP01
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	D3SP01
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH/Ubiquinone/plastoquinone (Complex I)	B	773	Thermocrinis albus DSM 14484	Mutation(s): 0 Gene Names: Thal_0254
UniProt
Find proteins for D3SP02 (Thermocrinis albus (strain DSM 14484 / JCM 11386 / HI 11/12)) Explore D3SP02 Go to UniProtKB: D3SP02
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	D3SP02
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.29 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	dev-6003
RECONSTRUCTION	cryoSPARC	4.7.0

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-09-30

Deposition Author(s):

Funding Organization	Location	Grant Number
Department of Energy (DOE, United States)	United States	DE-SC0016240 (DFS)

Revision History (Full details and data files)

Version 1.0: 2026-09-30
Type: Initial release