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- PDB-4jcj: Crystal structure of Isl1 LIM domains with Ldb1 LIM-interaction domain -

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Basic information

Entry
Database: PDB / ID: 4jcj
TitleCrystal structure of Isl1 LIM domains with Ldb1 LIM-interaction domain
ComponentsInsulin gene enhancer protein ISL-1,LIM domain-binding protein 1
KeywordsPROTEIN BINDING / Zinc finger / Transcriptional complex / Zinc binding / Nucleus
Function / homology
Function and homology information


sensory system development / positive regulation of macrophage colony-stimulating factor production / sinoatrial node cell development / visceral motor neuron differentiation / trigeminal nerve development / peripheral nervous system neuron axonogenesis / positive regulation of granulocyte colony-stimulating factor production / spinal cord motor neuron cell fate specification / regulation of kinase activity / peripheral nervous system neuron development ...sensory system development / positive regulation of macrophage colony-stimulating factor production / sinoatrial node cell development / visceral motor neuron differentiation / trigeminal nerve development / peripheral nervous system neuron axonogenesis / positive regulation of granulocyte colony-stimulating factor production / spinal cord motor neuron cell fate specification / regulation of kinase activity / peripheral nervous system neuron development / cellular component assembly / secondary heart field specification / negative regulation of erythrocyte differentiation / cardiac cell fate determination / negative regulation of mesenchymal cell proliferation / cardiac right ventricle morphogenesis / positive regulation of hemoglobin biosynthetic process / cerebellar Purkinje cell differentiation / regulation of secondary heart field cardioblast proliferation / neuron fate specification / head development / epithelial structure maintenance / atrial septum morphogenesis / primitive erythrocyte differentiation / positive regulation of type B pancreatic cell apoptotic process / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / bHLH transcription factor binding / spinal cord motor neuron differentiation / positive regulation of interleukin-1 alpha production / beta-catenin-TCF complex / pituitary gland development / negative regulation of intracellular estrogen receptor signaling pathway / RUNX1 regulates transcription of genes involved in differentiation of HSCs / LIM domain binding / mesenchymal cell differentiation / neuron fate commitment / cardiac muscle cell myoblast differentiation / pharyngeal system development / innervation / outflow tract septum morphogenesis / positive regulation of smoothened signaling pathway / gastrulation with mouth forming second / pancreas development / retinal ganglion cell axon guidance / positive regulation of granulocyte macrophage colony-stimulating factor production / neural crest cell migration / anterior/posterior axis specification / ventricular cardiac muscle tissue morphogenesis / endocardial cushion morphogenesis / regulation of focal adhesion assembly / positive regulation of calcium ion import / regulation of heart rate by cardiac conduction / outflow tract morphogenesis / cell leading edge / somatic stem cell population maintenance / negative regulation of neuron differentiation / positive regulation of cell adhesion / hair follicle development / canonical Wnt signaling pathway / positive regulation of vascular endothelial growth factor production / positive regulation of epithelial to mesenchymal transition / negative regulation of protein-containing complex assembly / cis-regulatory region sequence-specific DNA binding / heart morphogenesis / core promoter sequence-specific DNA binding / regulation of cell migration / positive regulation of tyrosine phosphorylation of STAT protein / positive regulation of interleukin-12 production / cerebellum development / axonogenesis / positive regulation of interleukin-1 beta production / nuclear estrogen receptor binding / promoter-specific chromatin binding / stem cell differentiation / nuclear receptor binding / positive regulation of transcription elongation by RNA polymerase II / positive regulation of cell differentiation / negative regulation of canonical Wnt signaling pathway / positive regulation of insulin secretion / neuron differentiation / negative regulation of inflammatory response / Wnt signaling pathway / positive regulation of interleukin-6 production / RNA polymerase II transcription regulator complex / positive regulation of angiogenesis / : / negative regulation of epithelial cell proliferation / positive regulation of type II interferon production / sequence-specific double-stranded DNA binding / positive regulation of tumor necrosis factor production / positive regulation of peptidyl-serine phosphorylation / nervous system development / heart development / regulation of gene expression / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor binding / negative regulation of neuron apoptotic process / cell population proliferation / transcription regulator complex / RNA polymerase II-specific DNA-binding transcription factor binding
Similarity search - Function
: / : / LIM-domain binding protein/SEUSS / LIM interaction domain / LIM-domain binding protein / LIM interaction domain (LID) / LIM interaction domain (LID) domain profile. / Cysteine Rich Protein / Cysteine Rich Protein / LIM zinc-binding domain signature. ...: / : / LIM-domain binding protein/SEUSS / LIM interaction domain / LIM-domain binding protein / LIM interaction domain (LID) / LIM interaction domain (LID) domain profile. / Cysteine Rich Protein / Cysteine Rich Protein / LIM zinc-binding domain signature. / LIM domain / Zinc-binding domain present in Lin-11, Isl-1, Mec-3. / Zinc finger, LIM-type / LIM domain profile. / Homeobox, conserved site / 'Homeobox' domain signature. / Homeodomain / 'Homeobox' domain profile. / Homeodomain / Homeobox domain / Homeobox-like domain superfamily / Ribbon / Mainly Beta
Similarity search - Domain/homology
Insulin gene enhancer protein ISL-1 / LIM domain-binding protein 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3 Å
AuthorsGadd, M.S. / Jacques, D.A. / Guss, J.M. / Matthews, J.M.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: A structural basis for the regulation of the LIM-homeodomain protein islet 1 (Isl1) by intra- and intermolecular interactions.
Authors: Gadd, M.S. / Jacques, D.A. / Nisevic, I. / Craig, V.J. / Kwan, A.H. / Guss, J.M. / Matthews, J.M.
History
DepositionFeb 21, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2013Group: Database references
Revision 1.2May 31, 2017Group: Structure summary
Revision 1.3Jun 21, 2017Group: Database references / Category: struct_ref / Item: _struct_ref.pdbx_db_isoform
Revision 1.4Nov 15, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Insulin gene enhancer protein ISL-1,LIM domain-binding protein 1
B: Insulin gene enhancer protein ISL-1,LIM domain-binding protein 1
C: Insulin gene enhancer protein ISL-1,LIM domain-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,84715
Polymers58,0623
Non-polymers78512
Water0
1
A: Insulin gene enhancer protein ISL-1,LIM domain-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6165
Polymers19,3541
Non-polymers2624
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Insulin gene enhancer protein ISL-1,LIM domain-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6165
Polymers19,3541
Non-polymers2624
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Insulin gene enhancer protein ISL-1,LIM domain-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6165
Polymers19,3541
Non-polymers2624
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.310, 56.639, 179.342
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number17
Space group name H-MP2221

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Components

#1: Protein Insulin gene enhancer protein ISL-1,LIM domain-binding protein 1 / Islet-1 / LDB-1 / Carboxyl-terminal LIM domain-binding protein 2 / CLIM-2 / LIM domain-binding ...Islet-1 / LDB-1 / Carboxyl-terminal LIM domain-binding protein 2 / CLIM-2 / LIM domain-binding factor CLIM2 / mLdb1 / Nuclear LIM interactor


Mass: 19354.105 Da / Num. of mol.: 3 / Fragment: UNP RESIDUES 11-138 and unp residues 300-330
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Isl1, Ldb1, Nli / Plasmid: pGEX2T / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P61372, UniProt: P70662
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Zn
Sequence detailsTHE CRYSTALLIZED SEQUENCE CORRESPONDS TO THE ISOFORM 3 OF LIM DOMAIN-BINDING PROTEIN 1.DATABASE ...THE CRYSTALLIZED SEQUENCE CORRESPONDS TO THE ISOFORM 3 OF LIM DOMAIN-BINDING PROTEIN 1.DATABASE REFERENCE UNPROT ENTRY P70662-3

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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: 2.51 Å3/Da / Density % sol: 50.93 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.9
Details: 20% (w/v) PEG 8000, 0.2 M magnesium chloride, 0.1 M Tris, 0.3 mM zinc sulfate, pH 8.9, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 1.2816 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 6, 2011
RadiationMonochromator: Zinc and platinum foils / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2816 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. all: 12362 / Num. obs: 12362 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Biso Wilson estimate: 59.6 Å2 / Rmerge(I) obs: 0.16 / Net I/σ(I): 8.5
Reflection shellResolution: 3→3.05 Å / Redundancy: 7 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 2.8 / Num. unique all: 584 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.5.0109refinement
PDB_EXTRACT3.11data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 3→48.29 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.835 / Occupancy max: 1 / Occupancy min: 1 / SU B: 41.993 / SU ML: 0.401 / Isotropic thermal model: Isotropic with TLS / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.471 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2987 596 4.9 %RANDOM
Rwork0.2536 ---
all0.2556 12218 --
obs0.2556 12218 98.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 161.53 Å2 / Biso mean: 57.864 Å2 / Biso min: 20.62 Å2
Baniso -1Baniso -2Baniso -3
1-7.91 Å20 Å20 Å2
2---6.43 Å20 Å2
3----1.48 Å2
Refinement stepCycle: LAST / Resolution: 3→48.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3083 0 12 0 3095
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0213180
X-RAY DIFFRACTIONr_bond_other_d0.0010.021946
X-RAY DIFFRACTIONr_angle_refined_deg1.3041.9514301
X-RAY DIFFRACTIONr_angle_other_deg0.8953.0154665
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8845433
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.68623.443122
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.15915387
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4861517
X-RAY DIFFRACTIONr_chiral_restr0.0670.2494
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023700
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02680
X-RAY DIFFRACTIONr_mcbond_it1.43122183
X-RAY DIFFRACTIONr_mcbond_other0.2742899
X-RAY DIFFRACTIONr_mcangle_it2.53433366
X-RAY DIFFRACTIONr_scbond_it5.1924997
X-RAY DIFFRACTIONr_scangle_it6.7776935
LS refinement shellResolution: 2.995→3.073 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.376 43 -
Rwork0.358 800 -
all-843 -
obs-43 97.01 %
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)
12.86320.8905-1.09264.3941-0.40866.03350.15820.00180.01930.3192-0.0797-0.3914-0.0110.1545-0.07850.15310.0635-0.09210.06150.00670.1408-17.6687-11.274-23.86
26.69991.79866.1498.62265.004212.4119-0.0587-0.1698-0.31170.4936-0.36090.36530.3965-0.66870.41950.0711-0.06310.10610.1362-0.02330.2729-4.399917.3692-5.5744
32.7179-5.2502-0.366410.61482.013610.45460.1148-0.7861-0.2104-0.11621.1299-0.11320.0691-0.7978-1.24470.4765-0.16550.03910.68470.33210.80521.499420.6346-10.9373
40.99280.2478-3.381817.8156-5.342112.77170.026-0.27480.0351-1.39520.341-0.2264-0.54630.6993-0.3670.64220.15540.11220.27-0.08370.4006-15.8198-6.7876-30.3655
51.98430.46470.1998.8582-1.37565.68780.2089-0.07890.12260.0101-0.31740.22350.0064-0.07710.10850.1483-0.0183-0.02610.03460.02370.0936-31.7971-11.5689-7.5877
65.1179-3.32941.565310.2373-6.089212.70010.3670.3642-0.1951-0.1891-0.28060.10050.05310.7602-0.08640.17540.0974-0.01570.3147-0.02750.3052-48.163416.4693-25.273
729.99572.24171.67820.17430.12220.12260.9567-0.9795-1.78290.1097-0.4213-0.08460.2049-0.0988-0.53531.1432-0.0784-0.31460.56330.18170.8174-52.337918.3379-17.3806
85.44534.7618-0.33698.96187.873714.39030.7887-0.16720.11920.4126-0.2286-0.0085-0.9497-0.499-0.56011.03360.09570.35680.40660.27580.3067-33.9271-7.784-0.5228
92.3327-0.1309-1.19228.51522.08596.5832-0.06410.10390.134-0.1343-0.1064-0.3014-0.004-0.08120.17050.19420.0813-0.06590.0571-0.00630.073-19.684311.3958-39.0654
103.7452-2.65281.08588.60363.43895.23770.1541-0.18540.2536-0.0128-0.0987-0.3133-0.249-0.7216-0.05540.31410.07950.02570.2379-0.12630.228-8.0421-16.859-58.8325
118.04633.8921-14.893719.962213.491852.6902-0.14440.1029-0.16631.25220.0103-1.22871.0566-0.20990.13420.83670.0738-0.66650.4342-0.08531.0012-2.3315-18.2043-52.9596
127.1-0.95984.26853.5819-5.49569.58070.45-0.0045-0.31860.5451-0.19350.1174-0.610.4143-0.25640.4563-0.0322-0.11020.4817-0.1070.3831-14.60877.5185-32.9701
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A14 - 75
2X-RAY DIFFRACTION2A76 - 134
3X-RAY DIFFRACTION3A300 - 310
4X-RAY DIFFRACTION4A316 - 327
5X-RAY DIFFRACTION5B13 - 75
6X-RAY DIFFRACTION6B76 - 136
7X-RAY DIFFRACTION7B301 - 310
8X-RAY DIFFRACTION8B315 - 328
9X-RAY DIFFRACTION9C13 - 75
10X-RAY DIFFRACTION10C76 - 136
11X-RAY DIFFRACTION11C300 - 310
12X-RAY DIFFRACTION12C315 - 328

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