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

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Basic information

Entry
Database: PDB / ID: 5hzj
TitleCrystal structure of photoinhibitable Intersectin1 containing wildtype LOV2 domain
ComponentsIntersectin-1,NPH1-1,Intersectin-1
KeywordsSIGNALING PROTEIN / Photoswitch / Chimera
Function / homology
Function and homology information


clathrin-dependent synaptic vesicle endocytosis / blue light photoreceptor activity / proline-rich region binding / regulation of small GTPase mediated signal transduction / endosomal transport / intracellular vesicle / NRAGE signals death through JNK / RHOQ GTPase cycle / exocytosis / CDC42 GTPase cycle ...clathrin-dependent synaptic vesicle endocytosis / blue light photoreceptor activity / proline-rich region binding / regulation of small GTPase mediated signal transduction / endosomal transport / intracellular vesicle / NRAGE signals death through JNK / RHOQ GTPase cycle / exocytosis / CDC42 GTPase cycle / RHOG GTPase cycle / clathrin-coated pit / EPHB-mediated forward signaling / guanyl-nucleotide exchange factor activity / protein localization / recycling endosome / G alpha (12/13) signalling events / protein transport / Cargo recognition for clathrin-mediated endocytosis / presynaptic membrane / lamellipodium / Clathrin-mediated endocytosis / nuclear envelope / molecular adaptor activity / non-specific serine/threonine protein kinase / neuron projection / protein kinase activity / intracellular signal transduction / phosphorylation / calcium ion binding / ATP binding / metal ion binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Intersectin-1, AP2 binding region / Intersectin and clathrin adaptor AP2 binding region / Pleckstrin homology domain / 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 ...Intersectin-1, AP2 binding region / Intersectin and clathrin adaptor AP2 binding region / Pleckstrin homology domain / 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 / 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 / SH3 domain / PAS domain superfamily / 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 / PH-like domain superfamily / 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
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / non-specific serine/threonine protein kinase / Intersectin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
Avena sativa (oats)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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: Intersectin-1,NPH1-1,Intersectin-1
B: Intersectin-1,NPH1-1,Intersectin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,4754
Polymers116,5622
Non-polymers9132
Water1,35175
1
A: Intersectin-1,NPH1-1,Intersectin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,7372
Polymers58,2811
Non-polymers4561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Intersectin-1,NPH1-1,Intersectin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,7372
Polymers58,2811
Non-polymers4561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.650, 111.170, 88.190
Angle α, β, γ (deg.)90.00, 90.12, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: 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
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 75 / 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: 2.59 Å3/Da / Density % sol: 52.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 0.1 M HEPES pH 7.5, 9% (w/v) PEG 8000, 9% (v/v) ethylene glycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97903 Å
DetectorType: DECTRIS 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: 2.6→50 Å / Num. obs: 35551 / % possible obs: 97 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 12.5
Reflection shellResolution: 2.6→2.7 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.453 / Mean I/σ(I) obs: 2.6 / % possible all: 97.2

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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: 2.6→47.024 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 34.74
RfactorNum. reflection% reflection
Rfree0.2811 1777 5 %
Rwork0.2515 --
obs0.253 35516 96.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.6→47.024 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7778 0 62 75 7915
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0027990
X-RAY DIFFRACTIONf_angle_d0.54710776
X-RAY DIFFRACTIONf_dihedral_angle_d10.1753098
X-RAY DIFFRACTIONf_chiral_restr0.0211204
X-RAY DIFFRACTIONf_plane_restr0.0031368
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.67030.45211370.36882595X-RAY DIFFRACTION97
2.6703-2.74890.34231360.32932577X-RAY DIFFRACTION97
2.7489-2.83760.38261360.30822595X-RAY DIFFRACTION97
2.8376-2.9390.33621370.30422608X-RAY DIFFRACTION98
2.939-3.05670.36281360.28932590X-RAY DIFFRACTION97
3.0567-3.19570.3251380.30482601X-RAY DIFFRACTION98
3.1957-3.36420.33461350.28362575X-RAY DIFFRACTION95
3.3642-3.57490.29651340.27562547X-RAY DIFFRACTION97
3.5749-3.85080.33771390.2572636X-RAY DIFFRACTION97
3.8508-4.23810.26571350.23752556X-RAY DIFFRACTION97
4.2381-4.85080.22281360.20982591X-RAY DIFFRACTION96
4.8508-6.10940.2591380.24052615X-RAY DIFFRACTION97
6.1094-47.03160.21851400.21272653X-RAY DIFFRACTION97
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)
11.9939-0.21840.48861.41280.6921.0232-0.0420.1288-0.00180.17060.0749-0.08980.02320.09860.03130.2873-0.0618-0.01080.1818-0.01580.291316.416929.368716.8757
20.4757-0.3129-0.52380.32530.17941.11960.18710.3865-0.113-0.252-0.15440.1474-0.03890.0003-0.01780.2928-0.1008-0.05370.4804-0.13130.47934.407319.9671-17.814
31.82850.6597-0.38311.21450.12970.8389-0.11380.20360.2467-0.03710.02390.0763-0.2499-0.3134-0.00750.25680.0817-0.00560.33610.04380.301514.4415-8.6428-17.95
40.28040.0120.4976-0.00240.02080.90520.05210.27080.3043-0.0012-0.10130.0833-0.8418-0.08750.01280.74970.02870.07810.63370.09890.586625.94280.3429-52.4736
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 1231:1505)
2X-RAY DIFFRACTION2(chain A and resid 1506:1722)
3X-RAY DIFFRACTION3(chain B and resid 1231:1502)
4X-RAY DIFFRACTION4(chain B and resid 1503:1722)

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