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- PDB-9nm2: Dimeric Structure of full-length CrgA, a Cell Division Protein fr... -

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Basic information

Entry
Database: PDB / ID: 9nm2
TitleDimeric Structure of full-length CrgA, a Cell Division Protein from Mycobacterium tuberculosis, in Lipid Bilayers
ComponentsCell division protein CrgA
KeywordsMEMBRANE PROTEIN / Cell division proteins / Transmembrane proteins
Function / homologyCell division protein CrgA / Cell division protein CrgA / regulation of cell shape / cell division / plasma membrane / Cell division protein CrgA
Function and homology information
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodSOLID-STATE NMR / molecular dynamics
AuthorsShin, Y. / Prasad, R. / Das, N. / Taylor, J.A. / Qin, H. / Hu, W. / Hu, Y.-Y. / Fu, R. / Zhang, R. / Zhou, H.-X. / Cross, T.A.
Funding support United States, 6items
OrganizationGrant numberCountry
National Institutes of Health/Office of the DirectorAI119178 United States
National Institutes of Health/Office of the DirectorGM122698 United States
National Institutes of Health/Office of the DirectorGM148766 United States
National Institutes of Health/Office of the DirectorGM118091 United States
National Science Foundation (NSF, United States)DMR1644779 United States
National Science Foundation (NSF, United States)DMR2128556 United States
Citation
Journal: J.Am.Chem.Soc. / Year: 2025
Title: Mycobacterium tuberculosis CrgA Forms a Dimeric Structure with Its Transmembrane Domain Sandwiched between Cytoplasmic and Periplasmic beta-Sheets, Enabling Multiple Interactions with Other Divisome Proteins.
Authors: Shin, Y. / Prasad, R. / Das, N. / Taylor, J.A. / Qin, H. / Hu, W. / Hu, Y.Y. / Fu, R. / Zhang, R. / Zhou, H.X. / Cross, T.A.
#1: Journal: Proc Natl Acad Sci U S A / Year: 2015
Title: Structure of CrgA, a cell division structural and regulatory protein from Mycobacterium tuberculosis, in lipid bilayers.
Authors: Das, N. / Dai, J. / Hung, I. / Rajagopalan, M.R. / Zhou, H.X. / Cross, T.A.
History
DepositionMar 3, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 2, 2025Provider: repository / Type: Initial release
Revision 1.1Apr 9, 2025Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cell division protein CrgA
B: Cell division protein CrgA


Theoretical massNumber of molelcules
Total (without water)23,2842
Polymers23,2842
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 13structures with the least restraint violations
RepresentativeModel #1closest to the average

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Components

#1: Protein Cell division protein CrgA


Mass: 11641.963 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: crgA, Rv0011c, MTCY10H4.11c / Production host: Escherichia coli (E. coli) / References: UniProt: P9WP57
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: SOLID-STATE NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111anisotropic12D 1H-15N PISEMA
122anisotropic12D 1H-15N PISEMA
233isotropic22D 13C-13C DARR

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
oriented membrane film1200 mg/L [U-15N]-Ala CrgA-Ala, 200 mg/L [U-15N]-Val CrgA-Val, 200 mg/L [U-15N]-Leu, [U-15N]-Thr CrgA-Leu,Thr, 200 mg/L [U-15N]-Met CrgA-Met, 200 mg/L [U-15N]-Phe CrgA-Phe, 200 mg/L [U-15N]-Trp CrgA-Trp, 200 mg/L [U-15N]-Gly CrgA-Gly, 200 mg/L [U-15N]-Ile CrgA-Ile, 200 mg/L [U-15N]-Tyr CrgA-Tyr, Aqueous solutionCrgA incorporated into POPC/POPG (4/1) at a protein (monomer) to lipid ratio of 1/80.15N_samplesAqueous solution
liposome3200 mg/L [U-13C]-Met,[U-13C]-Ala CrgA-Met,Ala, 200 mg/L [U-13C]-Leu,[U-13C]-Tyr CrgA-Leu,Tyr, 200 mg/L [U-13C]-Phe CrgA-Phe, 200 mg/L [U-13C]-Met CrgA-Met, 200 mg/L [U-13C]-Val CrgA-Val, 200 mg/L [U-13C]-Lys CrgA-Lys, Aqueous solutionCrgA incorporated into POPC/POPG (4/1) at a protein (monomer) to lipid ratio of 1/40.13C_samplesAqueous solution
oriented membrane film21 g/L [U-15N]-NH4Cl CrgA-Arg, 1 g/L [U-15N]-NH4Cl CrgA-Asn,Lys,Ser, Aqueous solutionCrgA incorporated into POPC/POPG (4/1) at a protein (monomer) to lipid ratio of 1/80.15N_reverse_samplesAqueous solution
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
200 mg/LCrgA-Ala[U-15N]-Ala1
200 mg/LCrgA-Val[U-15N]-Val1
200 mg/LCrgA-Leu,Thr[U-15N]-Leu, [U-15N]-Thr1
200 mg/LCrgA-Met[U-15N]-Met1
200 mg/LCrgA-Phe[U-15N]-Phe1
200 mg/LCrgA-Trp[U-15N]-Trp1
200 mg/LCrgA-Gly[U-15N]-Gly1
200 mg/LCrgA-Ile[U-15N]-Ile1
200 mg/LCrgA-Tyr[U-15N]-Tyr1
200 mg/LCrgA-Met,Ala[U-13C]-Met,[U-13C]-Ala3
200 mg/LCrgA-Leu,Tyr[U-13C]-Leu,[U-13C]-Tyr3
200 mg/LCrgA-Phe[U-13C]-Phe3
200 mg/LCrgA-Met[U-13C]-Met3
200 mg/LCrgA-Val[U-13C]-Val3
200 mg/LCrgA-Lys[U-13C]-Lys3
1 g/LCrgA-Arg[U-15N]-NH4Cl2
1 g/LCrgA-Asn,Lys,Ser[U-15N]-NH4Cl2
Sample conditions
Conditions-IDIonic strengthLabelpHPressure (kPa)Temperature (K)
15 mMConditions_181 atm289 K
25 mMConditions_281 atm265 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE6001
Bruker AVANCEBrukerAVANCE6002

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Processing

NMR software
NameVersionDeveloperClassification
NAMD2.13Phillips, Braun, Wang, Gumbart, Tajkhorshid, Villa, Chipot, Skeel, Kale and Schultenrefinement
X-PLOR NIH3.4Schwieters, Kuszewski, Tjandra and Clorestructure calculation
TopSpinBruker Biospinchemical shift assignment
TopSpinBruker Biospinpeak picking
TopSpinBruker Biospindata analysis
TopSpinBruker Biospinprocessing
RefinementMethod: molecular dynamics / Software ordinal: 1
Details: The authors state that the N-Ca-C bond angle of Thr20 in chain B is 160 deg, much higher than the ideal 110 deg due to strain at this type-VI turn.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 13 / Conformers submitted total number: 10

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