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- PDB-9w46: Complex structure of INF2 DID and Calcium bound CaM -

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Basic information

Entry
Database: PDB / ID: 9w46
TitleComplex structure of INF2 DID and Calcium bound CaM
Components
  • Calmodulin-1
  • Inverted formin-2
KeywordsPROTEIN BINDING / INF2 / DID / formin / calmodulin / calcium / complex
Function / homology
Function and homology information


regulation of cellular component size / actin nucleation / transporter inhibitor activity / : / type 3 metabotropic glutamate receptor binding / establishment of protein localization to membrane / response to corticosterone / negative regulation of ryanodine-sensitive calcium-release channel activity / organelle localization by membrane tethering / : ...regulation of cellular component size / actin nucleation / transporter inhibitor activity / : / type 3 metabotropic glutamate receptor binding / establishment of protein localization to membrane / response to corticosterone / negative regulation of ryanodine-sensitive calcium-release channel activity / organelle localization by membrane tethering / : / autophagosome membrane docking / regulation of mitochondrial fission / regulation of synaptic vesicle exocytosis / negative regulation of calcium ion export across plasma membrane / regulation of ryanodine-sensitive calcium-release channel activity / regulation of cardiac muscle cell action potential / presynaptic endocytosis / calcineurin-mediated signaling / nitric-oxide synthase binding / regulation of cell communication by electrical coupling involved in cardiac conduction / adenylate cyclase binding / protein phosphatase activator activity / regulation of synaptic vesicle endocytosis / detection of calcium ion / postsynaptic cytosol / regulation of cardiac muscle contraction / cell surface receptor signaling pathway via JAK-STAT / catalytic complex / phosphatidylinositol 3-kinase binding / calcium channel inhibitor activity / presynaptic cytosol / cellular response to interferon-beta / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / titin binding / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / regulation of calcium-mediated signaling / voltage-gated potassium channel complex / calcium channel complex / regulation of heart rate / calyx of Held / nitric-oxide synthase regulator activity / adenylate cyclase activator activity / protein serine/threonine kinase activator activity / regulation of cytokinesis / spindle microtubule / positive regulation of receptor signaling pathway via JAK-STAT / response to amphetamine / sarcomere / calcium channel regulator activity / response to calcium ion / cellular response to type II interferon / G2/M transition of mitotic cell cycle / Schaffer collateral - CA1 synapse / small GTPase binding / spindle pole / calcium-dependent protein binding / myelin sheath / synaptic vesicle membrane / growth cone / actin binding / sperm midpiece / gene expression / vesicle / transmembrane transporter binding / protein domain specific binding / calcium ion binding / centrosome / protein kinase binding / chromatin / perinuclear region of cytoplasm / protein-containing complex / mitochondrion / nucleoplasm / membrane / nucleus / cytoplasm / cytosol
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 / WH2 domain profile. / : / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Armadillo-like helical / Armadillo-type fold
Similarity search - Domain/homology
Calmodulin-1 / Inverted formin-2
Similarity search - Component
Biological speciesMus musculus (house mouse)
Rattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.11 Å
AuthorsZhang, B. / Zhang, M. / Lin, L. / Zhu, J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Calcium Directs Actin Assembly via Allosteric Activation of Formin INF2
Authors: Zhang, B. / Zhang, M. / Lin, L. / Zhu, J.
History
DepositionJul 31, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 8, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Inverted formin-2
A: Inverted formin-2
C: Calmodulin-1
D: Calmodulin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,24212
Polymers96,9214
Non-polymers3218
Water4,738263
1
B: Inverted formin-2
D: Calmodulin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6216
Polymers48,4612
Non-polymers1604
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4350 Å2
ΔGint-55 kcal/mol
Surface area21750 Å2
MethodPISA
2
A: Inverted formin-2
C: Calmodulin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6216
Polymers48,4612
Non-polymers1604
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4500 Å2
ΔGint-40 kcal/mol
Surface area20010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.193, 110.924, 113.576
Angle α, β, γ (deg.)90.00, 91.88, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Inverted formin-2


Mass: 31309.791 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: INF2 aa 1-283, with aa 20-25 deleted / Source: (gene. exp.) Mus musculus (house mouse) / Gene: Inf2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q0GNC1
#2: Protein Calmodulin-1


Mass: 17150.842 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Calm1, Calm, Cam, Cam1, CaMI / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0DP29
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 263 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.42 Å3/Da / Density % sol: 49.09 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 100 mM MES pH 6.5, 200 mM Ammonium sulfate, 30% PEG5000 MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97851 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 13, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97851 Å / Relative weight: 1
ReflectionResolution: 2.11→79.34 Å / Num. obs: 53164 / % possible obs: 99.7 % / Redundancy: 6.5 % / CC1/2: 0.997 / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.043 / Rrim(I) all: 0.111 / Χ2: 0.93 / Net I/σ(I): 10.1 / Num. measured all: 343802
Reflection shellResolution: 2.11→2.22 Å / % possible obs: 99.4 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.798 / Num. measured all: 49897 / Num. unique obs: 7721 / CC1/2: 0.793 / Rpim(I) all: 0.337 / Rrim(I) all: 0.868 / Χ2: 0.83 / Net I/σ(I) obs: 2.5

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
xia2data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.11→31.57 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 25.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2439 2570 4.87 %
Rwork0.1923 --
obs0.1948 52807 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.11→31.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6466 0 8 263 6737
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016538
X-RAY DIFFRACTIONf_angle_d1.2938810
X-RAY DIFFRACTIONf_dihedral_angle_d4.709883
X-RAY DIFFRACTIONf_chiral_restr0.0631012
X-RAY DIFFRACTIONf_plane_restr0.0111162
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.11-2.150.31651440.24142786X-RAY DIFFRACTION99
2.15-2.190.26741150.242828X-RAY DIFFRACTION100
2.19-2.240.33191230.23952734X-RAY DIFFRACTION99
2.24-2.290.27661510.22822783X-RAY DIFFRACTION100
2.29-2.350.26541550.21742789X-RAY DIFFRACTION100
2.35-2.410.30171400.222766X-RAY DIFFRACTION99
2.41-2.490.2821190.20752831X-RAY DIFFRACTION100
2.49-2.570.26731170.22062761X-RAY DIFFRACTION100
2.57-2.660.28721580.21152833X-RAY DIFFRACTION100
2.66-2.760.27681300.20642740X-RAY DIFFRACTION100
2.76-2.890.26381420.21842824X-RAY DIFFRACTION100
2.89-3.040.26011340.2172788X-RAY DIFFRACTION100
3.04-3.230.25591740.20862738X-RAY DIFFRACTION100
3.23-3.480.27951580.19492792X-RAY DIFFRACTION100
3.48-3.830.2261800.18392783X-RAY DIFFRACTION100
3.83-4.380.20131600.16252772X-RAY DIFFRACTION100
4.39-5.520.22371390.16882838X-RAY DIFFRACTION100
5.52-31.570.20831310.17262851X-RAY DIFFRACTION99

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