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- PDB-2d1l: Structure of F-actin binding domain IMD of MIM (Missing In Metastasis) -

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Basic information

Entry
Database: PDB / ID: 2d1l
TitleStructure of F-actin binding domain IMD of MIM (Missing In Metastasis)
ComponentsMetastasis suppressor protein 1
KeywordsPROTEIN BINDING / irsp53 / actin binding / IMD
Function / homology
Function and homology information


metanephric tubule development / nephron tubule epithelial cell differentiation / glomerulus morphogenesis / epithelial cell proliferation involved in renal tubule morphogenesis / adherens junction maintenance / renal tubule morphogenesis / magnesium ion homeostasis / plasma membrane organization / positive regulation of actin filament bundle assembly / cellular response to fluid shear stress ...metanephric tubule development / nephron tubule epithelial cell differentiation / glomerulus morphogenesis / epithelial cell proliferation involved in renal tubule morphogenesis / adherens junction maintenance / renal tubule morphogenesis / magnesium ion homeostasis / plasma membrane organization / positive regulation of actin filament bundle assembly / cellular response to fluid shear stress / muscle organ development / bone mineralization / actin monomer binding / actin filament polymerization / actin filament organization / adherens junction / negative regulation of epithelial cell proliferation / actin filament binding / actin cytoskeleton / nervous system development / actin binding / in utero embryonic development / signaling receptor binding / identical protein binding / cytoplasm
Similarity search - Function
I-BAR domain containing protein MTSS1 / I-BAR domain containing protein MTSS1/MTSS2 / IMD/I-BAR domain / IRSp53/MIM homology domain / IMD domain profile. / WH2 motif / Arfaptin homology (AH) domain/BAR domain / WH2 domain / WH2 domain profile. / AH/BAR domain superfamily ...I-BAR domain containing protein MTSS1 / I-BAR domain containing protein MTSS1/MTSS2 / IMD/I-BAR domain / IRSp53/MIM homology domain / IMD domain profile. / WH2 motif / Arfaptin homology (AH) domain/BAR domain / WH2 domain / WH2 domain profile. / AH/BAR domain superfamily / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.85 Å
AuthorsLee, S.H. / Kerff, F. / Chereau, D. / Ferron, F. / Dominguez, R.
CitationJournal: Structure / Year: 2007
Title: Structural basis for the actin-binding function of missing-in-metastasis
Authors: Lee, S.H. / Kerff, F. / Chereau, D. / Ferron, F. / Klug, A. / Dominguez, R.
History
DepositionAug 27, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 12, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Metastasis suppressor protein 1
B: Metastasis suppressor protein 1


Theoretical massNumber of molelcules
Total (without water)57,9782
Polymers57,9782
Non-polymers00
Water7,062392
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6350 Å2
ΔGint-60 kcal/mol
Surface area24690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.503, 37.319, 129.016
Angle α, β, γ (deg.)90.00, 94.07, 90.00
Int Tables number4
Space group name H-MP1211
Detailsthe biological assembly is the dimer found in the asymetric unit

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Components

#1: Protein Metastasis suppressor protein 1 / MIM / Missing in metastasis protein


Mass: 28988.959 Da / Num. of mol.: 2 / Fragment: IMD domain (residues 1-250)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Mtss1 / Plasmid: pTYB12 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q8R1S4
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 392 / Source method: isolated from a natural source / Formula: H2O

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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: 2.43 Å3/Da / Density % sol: 40.6 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: lithium chloride, PEG2000 MME, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-D / Wavelength: 0.97908, 1.0
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 27, 2005
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979081
211
ReflectionResolution: 1.85→48.1 Å / Num. all: 43473 / Num. obs: 43473 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.7 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 30.4
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 3.6 / Num. unique all: 3873 / % possible all: 88.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
SnBphasing
SOLVEphasing
DMphasing
RefinementMethod to determine structure: SAD / Resolution: 1.85→48.1 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.942 / SU B: 6.292 / SU ML: 0.097 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.149 / ESU R Free: 0.141 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22829 2197 5.1 %RANDOM
Rwork0.18344 ---
obs0.18577 41282 98.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.804 Å2
Baniso -1Baniso -2Baniso -3
1--0.42 Å20 Å2-0.55 Å2
2--1.32 Å20 Å2
3----0.99 Å2
Refinement stepCycle: LAST / Resolution: 1.85→48.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3792 0 0 392 4184
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0224083
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1271.9775521
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.0865544
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.68524.894188
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.27915876
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4931531
X-RAY DIFFRACTIONr_chiral_restr0.0820.2624
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023001
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2250.32092
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3120.52877
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2710.5541
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2160.342
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2330.537
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.2722584
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.01434067
X-RAY DIFFRACTIONr_scbond_it3.10821650
X-RAY DIFFRACTIONr_scangle_it4.51431415
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 155 -
Rwork0.249 2619 -
obs-2774 86.69 %
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)
110.40146.15439.407622.23810.167527.2535-2.33382.3244-0.4015-1.2947-0.5783-0.13250.7767-0.12452.91210.2408-0.05840.6210.5907-0.1130.25682.1216.162-7.779
23.9279-0.50064.00670.1115-1.066710.56750.01110.93210.1331-0.1267-0.0918-0.09760.03920.4550.0807-0.0241-0.00140.00180.4064-0.0108-0.194913.7996.97714.806
31.2250.6590.96090.46160.67022.67160.050.1782-0.0050.0754-0.0344-0.0250.0505-0.0377-0.0156-0.05990.0090-0.0268-0.0257-0.030723.9266.44144.016
40.9477-0.04640.43280.32530.54741.50760.016-0.04880.027-0.0360.0042-0.0062-0.02-0.0878-0.0201-0.0476-0.00950.0082-0.07280.0048-0.01133.68318.41973.275
59.79380.85951.46880.76871.79865.34490.1022-0.60661.1393-0.20780.07960.1792-0.54450.3758-0.18180.0314-0.07430.04530.1095-0.16350.057245.32829.31392.483
627.8026-4.3742-5.471974.3715-26.952689.4629-0.7001-0.4398-1.3305-1.5686-0.5108-0.84310.30812.65251.21090.2691-0.0307-0.01340.3254-0.07610.388264.3925.361134.473
74.25181.3581-1.41033.6204-2.03799.15320.4161-1.71960.20190.8762-0.5551-0.0921-0.78011.12990.1390.1426-0.3017-0.04170.8078-0.0876-0.152757.63922.009112.977
81.36670.3301-0.12360.0801-0.00761.27920.0811-0.2603-0.0919-0.023-0.0321-0.00080.06540.1571-0.0491-0.0356-0.0046-0.0226-0.0150.01150.026149.94115.90983.852
91.05490.32451.16410.38880.49081.70780.02120.16590.0627-0.0437-0.0065-0.0833-0.11530.1135-0.0147-0.04390.00350.0182-0.04990.0170.00136.71317.53553.762
108.00741.2411.95622.91223.17535.5614-0.03710.41250.4589-0.6898-0.19920.2746-0.92380.08120.23630.06580.0863-0.0611-0.00590.0746-0.054522.44818.63135.148
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA142 - 172145 - 175
2X-RAY DIFFRACTION2AA-2 - 181 - 21
3X-RAY DIFFRACTION2AA173 - 191176 - 194
4X-RAY DIFFRACTION2AA122 - 141125 - 144
5X-RAY DIFFRACTION3AA19 - 4122 - 44
6X-RAY DIFFRACTION3AA100 - 121103 - 124
7X-RAY DIFFRACTION3AA192 - 211195 - 214
8X-RAY DIFFRACTION4AA42 - 6445 - 67
9X-RAY DIFFRACTION4AA76 - 9979 - 102
10X-RAY DIFFRACTION4AA212 - 232215 - 235
11X-RAY DIFFRACTION5AA233 - 246236 - 249
12X-RAY DIFFRACTION5AA65 - 7568 - 78
13X-RAY DIFFRACTION6BB142 - 172145 - 175
14X-RAY DIFFRACTION7BB-2 - 181 - 21
15X-RAY DIFFRACTION7BB173 - 191176 - 194
16X-RAY DIFFRACTION7BB122 - 141125 - 144
17X-RAY DIFFRACTION8BB19 - 4122 - 44
18X-RAY DIFFRACTION8BB100 - 121103 - 124
19X-RAY DIFFRACTION8BB192 - 211195 - 214
20X-RAY DIFFRACTION9BB42 - 6445 - 67
21X-RAY DIFFRACTION9BB76 - 9979 - 102
22X-RAY DIFFRACTION9BB212 - 232215 - 235
23X-RAY DIFFRACTION10BB233 - 242236 - 245
24X-RAY DIFFRACTION10BB65 - 7568 - 78

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