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- PDB-9rwf: Solution NMR structure of a peptide encompassing residues 967-991... -

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Basic information

Entry
Database: PDB / ID: 9rwf
TitleSolution NMR structure of a peptide encompassing residues 967-991 of the human formin INF2
ComponentsInverted formin-2
KeywordsCELL ADHESION / formins / actin / microtubules / inherited disease
Function / homology
Function and homology information


regulation of mitochondrial fission / actin filament polymerization / actin filament / small GTPase binding / actin binding / perinuclear region of cytoplasm
Similarity search - Function
Formin, FH3 domain / Formin, GTPase-binding domain / Diaphanous FH3 Domain / Diaphanous GTPase-binding Domain / Diaphanous FH3 Domain / Diaphanous GTPase-binding Domain / Rho GTPase-binding/formin homology 3 (GBD/FH3) domain / Rho GTPase-binding/formin homology 3 (GBD/FH3) domain profile. / Formin, FH2 domain / Formin, FH2 domain superfamily ...Formin, FH3 domain / Formin, GTPase-binding domain / Diaphanous FH3 Domain / Diaphanous GTPase-binding Domain / Diaphanous FH3 Domain / Diaphanous GTPase-binding Domain / Rho GTPase-binding/formin homology 3 (GBD/FH3) domain / Rho GTPase-binding/formin homology 3 (GBD/FH3) domain profile. / Formin, FH2 domain / Formin, FH2 domain superfamily / Formin Homology 2 Domain / Formin homology-2 (FH2) domain profile. / Formin Homology 2 Domain / WH2 motif / WH2 domain profile. / WH2 domain / Armadillo-like helical / Armadillo-type fold
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
AuthorsJimenez, M.A. / Morales, P. / Correas, I. / Alonso, M.A.
Funding support Spain, 3items
OrganizationGrant numberCountry
Autonomous Community of MadridB2017/BMD-3817 Spain
Autonomous Community of MadridS2022/BMD_7232 Spain
Agencia Estatal de Investigacion (AEI)PID2023-146361NB-I00 Spain
CitationJournal: Febs J. / Year: 2025
Title: Structural and functional dissection of the WH2/DAD motif of INF2, a formin linked to human inherited degenerative disorders.
Authors: Labat-de-Hoz, L. / Fernandez-Martin, L. / Morales, P. / Correas, I. / Jimenez, M.A. / Alonso, M.A.
History
DepositionJul 9, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 8, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Inverted formin-2


Theoretical massNumber of molelcules
Total (without water)2,8861
Polymers2,8861
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR Distance Restraints, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1target function

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Components

#1: Protein/peptide Inverted formin-2 / HBEBP2-binding protein C


Mass: 2886.354 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q27J81
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic11D 1H
121isotropic12D 1H-1H COSY
131isotropic12D 1H-1H TOCSY
141isotropic12D 1H-1H NOESY
151isotropic12D 1H-13C HSQC aliphatic
161isotropic12D 1H-13C HSQC aromatic
172isotropic11D 1H
182isotropic12D 1H-1H COSY
192isotropic12D 1H-1H TOCSY
1102isotropic12D 1H-1H NOESY
1112isotropic12D 1H-13C HSQC aliphatic

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.5 mM DAD, 0.1 mM DSS, 10 % v/v [U-2H] D2O, 90 % H2O, 90% H2O/10% D2Osample_190% H2O/10% D2O
solution20.5 mM DAD, 0.1 mM DSS, 100 % [U-2H] D2O, 100% D2Osample_2100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMDADnatural abundance1
0.1 mMDSSnatural abundance1
10 % v/vD2O[U-2H]1
90 %H2Onatural abundance1
0.5 mMDADnatural abundance2
0.1 mMDSSnatural abundance2
100 %D2O[U-2H]2
Sample conditionsIonic strength: 0 M / Label: sample_conditions_1 / pH: 5.5 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
TopSpinBruker Biospinprocessing
NMRFAM-SPARKYLee W, Tonelli M, Markley JLchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
CYANAGuntert, Mumenthaler and Wuthrichrefinement
NMRFAM-SPARKYLee W, Tonelli M, Markley JLpeak picking
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 5
NMR representativeSelection criteria: target function
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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