25IP | pdb_000025ip

Mtb galactan transporter Rv3781/3783, translocating intermediate state

PDB DOI: https://doi.org/10.2210/pdb25IP/pdb
EM Map EMD-80145: EMDB EMDataResource

Classification: TRANSPORT PROTEIN
Organism(s): Mycobacterium tuberculosis H37Rv
Expression System: Mycolicibacterium smegmatis MC2 155
Mutation(s): Yes

Deposited: 2026-04-06 Released: 2026-10-07
Deposition Author(s): Wei, C., Zhang, L.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.61 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 25IP

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

Literature

Rv3781/3783 complex, DDM_bound

Wei, C., Zhang, L.

To be published.

Macromolecule Content

Total Structure Weight: 128.32 kDa
Atom Count: 8,564
Modeled Residue Count: 1,044
Deposited Residue Count: 1,106
Unique protein chains: 2

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable O-antigen/lipopolysaccharide transport integral membrane protein ABC transporter RfbD	A, D [auth B]	280	Mycobacterium tuberculosis H37Rv	Mutation(s): 0 Gene Names: rfbD, Rv3783
UniProt
Find proteins for P72049 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P72049 Go to UniProtKB: P72049
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P72049
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable O-antigen/lipopolysaccharide transport ATP-binding protein ABC transporter RfbE	B [auth C], C [auth D]	273	Mycobacterium tuberculosis H37Rv	Mutation(s): 1 Gene Names: rfbE, Rv3781
UniProt
Find proteins for P72047 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P72047 Go to UniProtKB: P72047
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P72047
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-L-rhamnopyranose-(1-3)-2-acetamido-2-deoxy-1-O-phosphono-alpha-D-glucopyranose	E [auth F], F [auth G]	2		N/A	Interactions Focus chain E [auth F] Focus chain F [auth G] Interactions & Density Focus chain E [auth F] Focus chain F [auth G]

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
LMT (Subject of Investigation/LOI) Query on LMT Download:Ideal Coordinates CCD File SDF format, chain M [auth B] SDF format, chain N [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B]	M [auth B], N [auth B]	DODECYL-BETA-D-MALTOSIDE C₂₄ H₄₆ O₁₁ NLEBIOOXCVAHBD-QKMCSOCLSA-N		Interactions Focus chain M [auth B] Focus chain N [auth B] Interactions & Density Focus chain M [auth B] Focus chain N [auth B]
ATP (Subject of Investigation/LOI) Query on ATP Download:Ideal Coordinates CCD File SDF format, chain H [auth C] SDF format, chain J [auth D] MOL2 format, chain H [auth C] MOL2 format, chain J [auth D] mmCIF format, chain H [auth C] mmCIF format, chain J [auth D]	H [auth C], J [auth D]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain H [auth C] Focus chain J [auth D] Interactions & Density Focus chain H [auth C] Focus chain J [auth D]
A1E8P( Subject of Investigation/LOI) Query on A1E8P Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain L [auth B] MOL2 format, chain G [auth A] MOL2 format, chain L [auth B] mmCIF format, chain G [auth A] mmCIF format, chain L [auth B]	G [auth A], L [auth B]	[(2~{Z},6~{E})-3,7,11-trimethyldodeca-2,6,10-trienyl] dihydrogen phosphate C₁₅ H₂₇ O₄ P ALEWCKXBHSDCCT-PVMFERMNSA-N		Interactions Focus chain G [auth A] Focus chain L [auth B] Interactions & Density Focus chain G [auth A] Focus chain L [auth B]
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain I [auth C] SDF format, chain K [auth D] MOL2 format, chain I [auth C] MOL2 format, chain K [auth D] mmCIF format, chain I [auth C] mmCIF format, chain K [auth D]	I [auth C], K [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain I [auth C] Focus chain K [auth D] Interactions & Density Focus chain I [auth C] Focus chain K [auth D]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.61 Å
Aggregation State: PARTICLE
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: 2026-10-07

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32394011

Revision History (Full details and data files)

Version 1.0: 2026-10-07
Type: Initial release