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Basic information

Entry
Database: PDB / ID: 3o4x
TitleCrystal structure of complex between amino and carboxy terminal fragments of mDia1
Components(Protein diaphanous homolog 1) x 2
KeywordsPROTEIN BINDING / autoinhibition / actin nucleator / actin binding
Function / homology
Function and homology information


negative regulation of neuron projection regeneration / multicellular organismal locomotion / ERBB2 Regulates Cell Motility / RHOF GTPase cycle / RHOC GTPase cycle / RHOD GTPase cycle / actin nucleation / neuron projection retraction / RHOB GTPase cycle / RHO GTPases Activate Formins ...negative regulation of neuron projection regeneration / multicellular organismal locomotion / ERBB2 Regulates Cell Motility / RHOF GTPase cycle / RHOC GTPase cycle / RHOD GTPase cycle / actin nucleation / neuron projection retraction / RHOB GTPase cycle / RHO GTPases Activate Formins / RHOA GTPase cycle / profilin binding / regulation of microtubule-based process / axon midline choice point recognition / brush border / synaptic vesicle endocytosis / ephrin receptor signaling pathway / actin filament polymerization / cytoskeleton organization / Neutrophil degranulation / sensory perception of sound / brain development / small GTPase binding / spindle / ruffle membrane / neuron projection development / intracellular protein localization / regulation of cell shape / presynapse / actin binding / actin cytoskeleton organization / gene expression / transmembrane transporter binding / neuron projection / centrosome / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Lyase 2-enoyl-coa Hydratase; Chain A, domain 2 - #30 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #630 / Formin, FH3 diaphanous domain / Lyase 2-enoyl-coa Hydratase; Chain A, domain 2 / Formin, FH2 domain / DRF autoregulatory / DRF Autoregulatory Domain / Formin Homology Region 1 / Diaphanous, GTPase-binding domain superfamily / : ...Lyase 2-enoyl-coa Hydratase; Chain A, domain 2 - #30 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #630 / Formin, FH3 diaphanous domain / Lyase 2-enoyl-coa Hydratase; Chain A, domain 2 / Formin, FH2 domain / DRF autoregulatory / DRF Autoregulatory Domain / Formin Homology Region 1 / Diaphanous, GTPase-binding domain superfamily / : / Diaphanous autoregulatory (DAD) domain / Diaphanous autoregulatory domain (DAD) profile. / 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 / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Recoverin; domain 1 / Helix non-globular / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Special / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Protein diaphanous homolog 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsEck, M.J. / Nezami, A. / Toms, A.V.
CitationJournal: Plos One / Year: 2010
Title: Crystal structure of a complex between amino and carboxy terminal fragments of mDia1: insights into autoinhibition of diaphanous-related formins.
Authors: Nezami, A. / Poy, F. / Toms, A. / Zheng, W. / Eck, M.J.
History
DepositionJul 27, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 13, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 17, 2011Group: Database references
Revision 1.3Oct 5, 2011Group: Database references
Revision 1.4Apr 11, 2012Group: Database references
Revision 1.5Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein diaphanous homolog 1
B: Protein diaphanous homolog 1
C: Protein diaphanous homolog 1
D: Protein diaphanous homolog 1
E: Protein diaphanous homolog 1
H: Protein diaphanous homolog 1
G: Protein diaphanous homolog 1
F: Protein diaphanous homolog 1


Theoretical massNumber of molelcules
Total (without water)367,4658
Polymers367,4658
Non-polymers00
Water86548
1
A: Protein diaphanous homolog 1
D: Protein diaphanous homolog 1
E: Protein diaphanous homolog 1
H: Protein diaphanous homolog 1


Theoretical massNumber of molelcules
Total (without water)183,7334
Polymers183,7334
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21460 Å2
ΔGint-155 kcal/mol
Surface area78740 Å2
MethodPISA
2
B: Protein diaphanous homolog 1
C: Protein diaphanous homolog 1
G: Protein diaphanous homolog 1
F: Protein diaphanous homolog 1


Theoretical massNumber of molelcules
Total (without water)183,7334
Polymers183,7334
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21580 Å2
ΔGint-156 kcal/mol
Surface area77580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.762, 206.832, 131.065
Angle α, β, γ (deg.)90.00, 105.94, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
12E
22F
32G
42H

NCS domain segments:

Refine code: 4

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ARGARGHISHISAA134 - 1906 - 62
211ARGARGHISHISBB134 - 1906 - 62
311ARGARGHISHISCC134 - 1906 - 62
411ARGARGHISHISDD134 - 1906 - 62
121GLNGLNGLUGLUAA205 - 42777 - 299
221GLNGLNGLUGLUBB205 - 42777 - 299
321GLNGLNGLUGLUCC205 - 42777 - 299
421GLNGLNGLUGLUDD205 - 42777 - 299
131VALVALLYSLYSAA429 - 444301 - 316
231VALVALLYSLYSBB429 - 444301 - 316
331VALVALLYSLYSCC429 - 444301 - 316
431VALVALLYSLYSDD429 - 444301 - 316
112VALVALASNASNEE829 - 95596 - 222
212VALVALASNASNFH829 - 95596 - 222
312VALVALASNASNGG829 - 95596 - 222
412VALVALASNASNHF829 - 95596 - 222
122PHEPHEASNASNEE956 - 971223 - 238
222PHEPHEASNASNFH956 - 971223 - 238
322PHEPHEASNASNGG956 - 971223 - 238
422PHEPHEASNASNHF956 - 971223 - 238
132LEULEULEULEUEE1006 - 1129273 - 396
232LEULEULEULEUFH1006 - 1129273 - 396
332LEULEULEULEUGG1006 - 1129273 - 396
432LEULEULEULEUHF1006 - 1129273 - 396
142LYSLYSVALVALEE753 - 78420 - 51
242LYSLYSVALVALFH753 - 78420 - 51
342LYSLYSVALVALGG753 - 78420 - 51
442LYSLYSVALVALHF753 - 78420 - 51
152ALAALAGLNGLNEE1131 - 1168398 - 435
252ALAALAGLNGLNFH1131 - 1168398 - 435
352ALAALAGLNGLNGG1131 - 1168398 - 435
452ALAALAGLNGLNHF1131 - 1168398 - 435
162LYSLYSTHRTHREE785 - 80652 - 73
262LYSLYSTHRTHRFH785 - 80652 - 73
362LYSLYSTHRTHRGG785 - 80652 - 73
462LYSLYSTHRTHRHF785 - 80652 - 73

NCS ensembles :
ID
1
2

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Components

#1: Protein
Protein diaphanous homolog 1 / Diaphanous-related formin-1 / DRF1 / p140mDIA / mDIA1


Mass: 37993.582 Da / Num. of mol.: 4
Fragment: mDia1 N-terminal regulatory domain (unp residues 131-458)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Diaph1, Diap1 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O08808
#2: Protein
Protein diaphanous homolog 1 / Diaphanous-related formin-1 / DRF1 / p140mDIA / mDIA1


Mass: 53872.695 Da / Num. of mol.: 4
Fragment: mDia1 C-terminal FH2-DAD domain (unp residues 736-1200)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Diaph1, Diap1 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O08808
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.4 Å3/Da / Density % sol: 63.79 %
Crystal growTemperature: 313 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Peg 4000, sodium malonate, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 313K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 18, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 3.2→25 Å / Num. all: 76970 / Num. obs: 75584 / % possible obs: 98.2 % / Observed criterion σ(F): 0.1 / Observed criterion σ(I): 1 / Redundancy: 3.8 % / Rsym value: 0.114 / Net I/σ(I): 13.5

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.5.0109refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→20.12 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.828 / SU B: 68.667 / SU ML: 0.512 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.551 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2983 3981 5 %RANDOM
Rwork0.23265 ---
all0.23589 75584 --
obs0.23589 75584 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 107.401 Å2
Baniso -1Baniso -2Baniso -3
1-0.66 Å20 Å2-2.87 Å2
2--0.03 Å20 Å2
3----2.26 Å2
Refinement stepCycle: LAST / Resolution: 3.2→20.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24287 0 0 48 24335
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.02224662
X-RAY DIFFRACTIONr_angle_refined_deg1.0591.98133125
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.76652982
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.33525.141251
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.921154906
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.43115168
X-RAY DIFFRACTIONr_chiral_restr0.0730.23687
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02118360
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: MEDIUM POSITIONAL / Weight position: 0.5

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A23800.32
12B23800.33
13C23800.33
14D23800.4
21E29620.43
22F29620.43
23G29620.41
24H29620.38
LS refinement shellResolution: 3.2→3.281 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.398 256 -
Rwork0.362 4922 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.38-0.3670.87031.2786-1.59672.5432-0.14090.05210.0271-0.00130.1222-0.0526-0.07850.07780.01870.17710.0253-0.03980.1552-0.03960.18418.395-29.19616.813
20.3233-0.41250.20470.6734-0.30330.20340.06650.1230.0207-0.11550.07190.0380.11950.0001-0.13840.1334-0.0598-0.0150.25430.02560.2053-8.7726.502-23.031
30.4275-0.527-0.02141.2694-0.1673-0.18050.07110.1819-0.0518-0.52220.0693-0.2361-0.0684-0.0751-0.14040.3822-0.15610.10890.3673-0.11250.307714.817-7.967-19.922
40.1480.0759-0.06791.5116-1.1370.95770.059-0.05250.1301-0.02890.40310.4807-0.0055-0.1468-0.46210.1583-0.0364-0.11810.22820.0280.3119-14.785-3.253-1.984
50.1636-0.2161-0.09130.5976-0.05150.5839-0.1396-0.0887-0.0410.14610.1996-0.06950.22730.0343-0.060.14170.00690.02820.2872-0.05280.193815.43522.4581.732
60.7957-0.6985-1.00881.22731.07742.06470.01520.0716-0.00880.19750.13780.0244-0.0716-0.2058-0.15310.14730.09970.10710.17170.10040.1866-12.18947.83113.972
71.08060.3276-1.12280.5907-0.76541.77980.08530.03120.0021-0.0291-0.00380.0128-0.08540.1888-0.08150.0652-0.04350.08350.3063-0.02640.158324.05345.188-34.154
80.54150.44730.851.11451.22321.8725-0.1662-0.03710.0783-0.48380.05890.3032-0.2127-0.10740.10730.5896-0.2521-0.31760.18180.10650.1998-15.331-25.863-38.572
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A132 - 452
2X-RAY DIFFRACTION2E745 - 1198
3X-RAY DIFFRACTION3F745 - 1198
4X-RAY DIFFRACTION4G745 - 1198
5X-RAY DIFFRACTION5H745 - 1198
6X-RAY DIFFRACTION6B132 - 452
7X-RAY DIFFRACTION7C132 - 452
8X-RAY DIFFRACTION8D132 - 452

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