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- PDB-25ip: Mtb galactan transporter Rv3781/3783, translocating intermediate state -

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Basic information

Entry
Database: PDB / ID: 25ip
TitleMtb galactan transporter Rv3781/3783, translocating intermediate state
Components(Probable O-antigen/lipopolysaccharide transport ...) x 2
KeywordsTRANSPORT PROTEIN
Function / homology
Function and homology information


lipopolysaccharide transport / ABC-type transporter activity / ATP hydrolysis activity / ATP binding / plasma membrane
Similarity search - Function
ABC transporter, teichoic acids export TagH-like / : / ABC-2 type transporter / ABC-2 type transporter / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
: / ADENOSINE-5'-TRIPHOSPHATE / Probable O-antigen/lipopolysaccharide transport ATP-binding protein ABC transporter RfbE / Probable O-antigen/lipopolysaccharide transport integral membrane protein ABC transporter RfbD
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.61 Å
AuthorsWei, C. / Zhang, L.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32394011 China
CitationJournal: To Be Published
Title: Rv3781/3783 complex, DDM_bound
Authors: Wei, C. / Zhang, L.
History
DepositionApr 6, 2026Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Oct 7, 2026Provider: repository / Type: Initial release
Revision 1.0Oct 7, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable O-antigen/lipopolysaccharide transport integral membrane protein ABC transporter RfbD
C: Probable O-antigen/lipopolysaccharide transport ATP-binding protein ABC transporter RfbE
D: Probable O-antigen/lipopolysaccharide transport ATP-binding protein ABC transporter RfbE
B: Probable O-antigen/lipopolysaccharide transport integral membrane protein ABC transporter RfbD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,31914
Polymers124,7354
Non-polymers3,58410
Water724
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Probable O-antigen/lipopolysaccharide transport ... , 2 types, 4 molecules ABCD

#1: Protein Probable O-antigen/lipopolysaccharide transport integral membrane protein ABC transporter RfbD


Mass: 32369.197 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Gene: rfbD, Rv3783
Production host: Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: P72049
#2: Protein Probable O-antigen/lipopolysaccharide transport ATP-binding protein ABC transporter RfbE


Mass: 29998.326 Da / Num. of mol.: 2 / Mutation: E183Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Gene: rfbE, Rv3781
Production host: Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: P72047

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Sugars , 2 types, 4 molecules

#3: Polysaccharide alpha-L-rhamnopyranose-(1-3)-2-acetamido-2-deoxy-1-O-phosphono-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 447.329 Da / Num. of mol.: 2 / Source method: obtained synthetically
DescriptorTypeProgram
WURCS=2.0/2,2,1/[a2122h-1a_1-5_1*OPO/3O/3=O_2*NCC/3=O][a2211m-1a_1-5]/1-2/a3-b1WURCSPDB2Glycan 1.1.0
[][<O2P1>]{[(1+1)][a-D-GlcpNAc]{[(3+1)][a-L-Rhap]{}}}LINUCSPDB-CARE
#7: Sugar ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H46O11 / Feature type: SUBJECT OF INVESTIGATION / Comment: detergent*YM

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Non-polymers , 4 types, 10 molecules

#4: Chemical ChemComp-A1E8P / [(2~{Z},6~{E})-3,7,11-trimethyldodeca-2,6,10-trienyl] dihydrogen phosphate


Mass: 302.346 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H27O4P / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Galactan Transporter Complex / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightValue: 0.125 MDa / Experimental value: YES
Source (natural)Organism: Mycobacterium tuberculosis H37Rv (bacteria)
Source (recombinant)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
Buffer solutionpH: 7.5 / Details: 150mM NaCl, 50mM Hepes
SpecimenConc.: 10 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R0.6/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 1200 nm / Alignment procedure: BASIC
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)
EM imaging opticsEnergyfilter name: GIF Bioquantum

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
4cryoSPARCCTF correction
9PHENIXmodel refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 2.61 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 271855 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT

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