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- PDB-5hzk: Crystal structure of photoinhibitable Intersectin1 containing wil... -

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Basic information

Entry
Database: PDB / ID: 5hzk
TitleCrystal structure of photoinhibitable Intersectin1 containing wildtype LOV2 domain in complex with Cdc42
Components
  • Cell division control protein 42 homolog
  • Intersectin-1,NPH1-1,Intersectin-1
KeywordsSIGNALING PROTEIN / Photoswitch / Chimera / Complex
Function / homology
Function and homology information


clathrin-dependent synaptic vesicle endocytosis / GBD domain binding / submandibular salivary gland formation / actin filament branching / Golgi transport complex / positive regulation of pinocytosis / modification of synaptic structure / endothelin receptor signaling pathway involved in heart process / Cdc42 protein signal transduction / cardiac neural crest cell migration involved in outflow tract morphogenesis ...clathrin-dependent synaptic vesicle endocytosis / GBD domain binding / submandibular salivary gland formation / actin filament branching / Golgi transport complex / positive regulation of pinocytosis / modification of synaptic structure / endothelin receptor signaling pathway involved in heart process / Cdc42 protein signal transduction / cardiac neural crest cell migration involved in outflow tract morphogenesis / positive regulation of synapse structural plasticity / dendritic cell migration / storage vacuole / apolipoprotein A-I receptor binding / positive regulation of epithelial cell proliferation involved in lung morphogenesis / neuron fate determination / modulation by host of viral process / blue light photoreceptor activity / organelle transport along microtubule / regulation of attachment of spindle microtubules to kinetochore / positive regulation of pseudopodium assembly / Inactivation of CDC42 and RAC1 / cardiac conduction system development / GTP-dependent protein binding / regulation of filopodium assembly / establishment of Golgi localization / leading edge membrane / neuropilin signaling pathway / positive regulation of intracellular protein transport / cell junction assembly / filopodium assembly / establishment of epithelial cell apical/basal polarity / regulation of modification of postsynaptic structure / dendritic spine morphogenesis / mitogen-activated protein kinase kinase kinase binding / embryonic heart tube development / thioesterase binding / regulation of stress fiber assembly / RHO GTPases activate KTN1 / regulation of lamellipodium assembly / proline-rich region binding / nuclear migration / DCC mediated attractive signaling / adherens junction organization / sprouting angiogenesis / Wnt signaling pathway, planar cell polarity pathway / regulation of small GTPase mediated signal transduction / CD28 dependent Vav1 pathway / regulation of postsynapse organization / positive regulation of filopodium assembly / endosomal transport / regulation of mitotic nuclear division / establishment or maintenance of cell polarity / phagocytosis, engulfment / RHOV GTPase cycle / intracellular vesicle / NRAGE signals death through JNK / heart contraction / Myogenesis / RHOJ GTPase cycle / Golgi organization / RHOQ GTPase cycle / exocytosis / positive regulation of cytokinesis / RHO GTPases activate PAKs / CDC42 GTPase cycle / RHOU GTPase cycle / macrophage differentiation / RHOG GTPase cycle / RHO GTPases Activate WASPs and WAVEs / RAC3 GTPase cycle / RAC2 GTPase cycle / RHO GTPases activate IQGAPs / spindle midzone / positive regulation of DNA replication / negative regulation of protein-containing complex assembly / phagocytic vesicle / positive regulation of lamellipodium assembly / positive regulation of substrate adhesion-dependent cell spreading / clathrin-coated pit / positive regulation of stress fiber assembly / GPVI-mediated activation cascade / RAC1 GTPase cycle / EPHB-mediated forward signaling / substantia nigra development / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / guanyl-nucleotide exchange factor activity / small monomeric GTPase / G protein activity / filopodium / secretory granule / actin filament organization / integrin-mediated signaling pathway / RHO GTPases Activate Formins / regulation of actin cytoskeleton organization / FCGR3A-mediated phagocytosis / EGFR downregulation / positive regulation of JNK cascade / MAPK6/MAPK4 signaling / Schaffer collateral - CA1 synapse
Similarity search - Function
Intersectin-1, AP2 binding region / Intersectin and clathrin adaptor AP2 binding region / Pleckstrin homology domain / Cdc42 / Cytoskeletal-regulatory complex EF hand / EH domain profile. / Eps15 homology domain / EH domain / Guanine-nucleotide dissociation stimulator, CDC24, conserved site / Dbl homology (DH) domain signature. ...Intersectin-1, AP2 binding region / Intersectin and clathrin adaptor AP2 binding region / Pleckstrin homology domain / Cdc42 / Cytoskeletal-regulatory complex EF hand / EH domain profile. / Eps15 homology domain / EH domain / Guanine-nucleotide dissociation stimulator, CDC24, conserved site / Dbl homology (DH) domain signature. / PAS-associated, C-terminal / PAC domain profile. / PAS domain / Variant SH3 domain / Variant SH3 domain / Small GTPase Rho / small GTPase Rho family profile. / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain) / Dbl homology (DH) domain superfamily / RhoGEF domain / Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases / Dbl homology (DH) domain / Dbl homology (DH) domain profile. / C2 domain / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain profile. / C2 domain superfamily / PAS domain / PH domain profile. / PAS repeat profile. / Pleckstrin homology domain. / Pleckstrin homology domain / PAS domain / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / SH3 domain / PAS domain superfamily / Small GTPase / Ras family / Rab subfamily of small GTPases / EF-hand, calcium binding motif / Src homology 3 domains / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / EF-hand domain / EF-hand domain pair / Small GTP-binding protein domain / PH-like domain superfamily / P-loop containing nucleotide triphosphate hydrolases / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / GUANOSINE-5'-DIPHOSPHATE / non-specific serine/threonine protein kinase / Cell division control protein 42 homolog / Intersectin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
Avena sativa (oats)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsTarnawski, M. / Dagliyan, O. / Chu, P.H. / Shirvanyants, D. / Dokholyan, N.V. / Hahn, K.M. / Schlichting, I.
CitationJournal: Science / Year: 2016
Title: Engineering extrinsic disorder to control protein activity in living cells.
Authors: Dagliyan, O. / Tarnawski, M. / Chu, P.H. / Shirvanyants, D. / Schlichting, I. / Dokholyan, N.V. / Hahn, K.M.
History
DepositionFeb 2, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 21, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cell division control protein 42 homolog
B: Intersectin-1,NPH1-1,Intersectin-1
C: Cell division control protein 42 homolog
D: Intersectin-1,NPH1-1,Intersectin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)160,5288
Polymers158,7294
Non-polymers1,7994
Water0
1
A: Cell division control protein 42 homolog
B: Intersectin-1,NPH1-1,Intersectin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,2644
Polymers79,3642
Non-polymers9002
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4200 Å2
ΔGint-26 kcal/mol
Surface area31870 Å2
MethodPISA
2
C: Cell division control protein 42 homolog
D: Intersectin-1,NPH1-1,Intersectin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,2644
Polymers79,3642
Non-polymers9002
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4210 Å2
ΔGint-25 kcal/mol
Surface area32580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.370, 119.080, 131.080
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Cell division control protein 42 homolog / G25K GTP-binding protein


Mass: 21083.172 Da / Num. of mol.: 2 / Mutation: C188S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDC42 / Production host: Escherichia coli (E. coli) / References: UniProt: P60953
#2: Protein Intersectin-1,NPH1-1,Intersectin-1 / SH3 domain-containing protein 1A / SH3P17


Mass: 58281.121 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Avena sativa (oats)
Gene: ITSN1, ITSN, SH3D1A, NPH1-1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15811, UniProt: O49003
#3: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#4: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P

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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: 2.76 Å3/Da / Density % sol: 55.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6 / Details: 0.1 M MES, 20% (w/v) PEG 6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97903 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 27, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97903 Å / Relative weight: 1
ReflectionResolution: 3.3→50 Å / Num. obs: 27085 / % possible obs: 99.9 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 23.3
Reflection shellResolution: 3.3→3.4 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.524 / Mean I/σ(I) obs: 3.8 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KI1, 2WKQ

1ki1

2wkq


Resolution: 3.3→47.378 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.03
RfactorNum. reflection% reflection
Rfree0.2573 1353 5 %
Rwork0.2069 --
obs0.2094 27076 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.3→47.378 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10359 0 118 0 10477
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00210685
X-RAY DIFFRACTIONf_angle_d0.61914460
X-RAY DIFFRACTIONf_dihedral_angle_d10.384085
X-RAY DIFFRACTIONf_chiral_restr0.0241636
X-RAY DIFFRACTIONf_plane_restr0.0041829
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3001-3.4180.34491330.27212529X-RAY DIFFRACTION100
3.418-3.55480.29851340.25682544X-RAY DIFFRACTION100
3.5548-3.71650.31061340.23582540X-RAY DIFFRACTION100
3.7165-3.91240.26321320.22052515X-RAY DIFFRACTION100
3.9124-4.15740.25651340.20992545X-RAY DIFFRACTION100
4.1574-4.47810.23271340.18192564X-RAY DIFFRACTION100
4.4781-4.92840.24351360.16692576X-RAY DIFFRACTION100
4.9284-5.64050.22471360.18682581X-RAY DIFFRACTION100
5.6405-7.10260.2731370.23952602X-RAY DIFFRACTION100
7.1026-47.38260.24451430.19712727X-RAY DIFFRACTION100
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)
11.76730.0471.18930.5040.56751.95740.07220.3921-0.0753-0.03770.05960.16320.16550.472200.58630.0897-0.02220.48720.00460.4148-26.296-16.565115.9524
20.5606-0.2825-0.47110.59580.11060.17380.0649-0.290.0845-0.0712-0.04880.4063-0.5161-0.1964-0.10030.69560.11640.03190.71830.14280.542-48.84940.327916.6522
31.2055-1.44940.59981.57330.19551.9738-0.1192-0.33630.1328-0.00370.1228-0.1108-0.02990.0889-00.4645-0.03220.12170.6805-0.00960.9513-57.2765-3.500756.3323
41.8042-1.407-0.09613.04610.10711.8305-0.0734-0.289-0.229-0.6063-0.06080.25670.21060.1277-0.05370.64330.0411-0.09730.46630.00970.4389-47.3364-8.68911.025
51.01420.26010.18940.95970.39430.86140.36010.0055-0.1977-2.5924-0.31-0.3105-0.5491-1.204-0.1541.9967-0.15740.0079-0.4078-0.14010.6788-44.1671-31.5454-15.8326
61.8271-0.7240.90031.60340.07451.7072-0.02130.0164-0.17050.0630.01710.16260.3548-0.245700.3309-0.0369-0.01980.49610.04710.5449-43.0462-30.842557.1493
71.06771.1053-0.42870.7133-0.2440.1148-0.07970.07990.30540.20410.53620.03030.22940.07910.46930.4930.0196-0.07420.44350.02940.3233-17.0176-24.837565.9674
80.78980.570.03630.7559-0.80550.8787-0.04750.4416-0.26940.1640.00960.3249-0.29340.4687-0.00210.6148-0.26450.00111.0128-0.06270.7973-4.2497-3.845732.9563
92.04021.38980.09621.97520.19430.8734-0.13160.18920.05990.40140.3789-0.25670.55720.16270.14590.65890.0715-0.07460.44820.03710.4267-21.9047-34.427264.2684
100.8177-0.3147-0.44090.5280.11470.6370.25130.2096-0.53780.24040.18930.0778-0.1404-0.39670.36530.5765-0.0671-0.31970.5410.2811.095-31.2559-68.333168.4778
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 3:178)
2X-RAY DIFFRACTION2(chain B and resid 1231:1308)
3X-RAY DIFFRACTION3(chain B and resid 1309:1451)
4X-RAY DIFFRACTION4(chain B and resid 1452:1582)
5X-RAY DIFFRACTION5(chain B and resid 1583:1722)
6X-RAY DIFFRACTION6(chain C and resid 3:178)
7X-RAY DIFFRACTION7(chain D and resid 1231:1308)
8X-RAY DIFFRACTION8(chain D and resid 1309:1451)
9X-RAY DIFFRACTION9(chain D and resid 1452:1582)
10X-RAY DIFFRACTION10(chain D and resid 1583:1722)

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