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- PDB-5hzi: Crystal structure of photoinhibitable Intersectin1 containing C45... -

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Basic information

Entry
Database: PDB / ID: 5hzi
TitleCrystal structure of photoinhibitable Intersectin1 containing C450M mutant LOV2 domain
ComponentsIntersectin-1,NPH1-1,Intersectin-1
KeywordsSIGNALING PROTEIN / Photoswitch / Chimera
Function / homology
Function and homology information


clathrin-dependent synaptic vesicle endocytosis / positive regulation of caveolin-mediated endocytosis / positive regulation of growth hormone secretion / postsynaptic endocytic zone / blue light photoreceptor activity / regulation of modification of postsynaptic actin cytoskeleton / apical dendrite / postsynaptic actin cytoskeleton / proline-rich region binding / regulation of postsynapse organization ...clathrin-dependent synaptic vesicle endocytosis / positive regulation of caveolin-mediated endocytosis / positive regulation of growth hormone secretion / postsynaptic endocytic zone / blue light photoreceptor activity / regulation of modification of postsynaptic actin cytoskeleton / apical dendrite / postsynaptic actin cytoskeleton / proline-rich region binding / regulation of postsynapse organization / regulation of small GTPase mediated signal transduction / endosomal transport / NRAGE signals death through JNK / positive regulation of dendritic spine development / intracellular vesicle / RHOQ GTPase cycle / exocytosis / CDC42 GTPase cycle / RHOG GTPase cycle / clathrin-coated pit / EPHB-mediated forward signaling / guanyl-nucleotide exchange factor activity / recycling endosome / intracellular protein localization / nuclear envelope / Cargo recognition for clathrin-mediated endocytosis / G alpha (12/13) signalling events / protein transport / lamellipodium / Clathrin-mediated endocytosis / presynaptic membrane / molecular adaptor activity / dendritic spine / non-specific serine/threonine protein kinase / intracellular signal transduction / neuronal cell body / protein serine/threonine kinase activity / calcium ion binding / glutamatergic synapse / ATP binding / metal ion binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Intersectin-1, AP2 binding region / Intersectin and clathrin adaptor AP2 binding region / Pleckstrin homology domain / : / EH domain / EH domain profile. / Eps15 homology domain / EH domain / Dbl Homology Domain; Chain A / Dbl homology (DH) domain ...Intersectin-1, AP2 binding region / Intersectin and clathrin adaptor AP2 binding region / Pleckstrin homology domain / : / EH domain / EH domain profile. / Eps15 homology domain / EH domain / Dbl Homology Domain; Chain A / Dbl homology (DH) domain / Guanine-nucleotide dissociation stimulator, CDC24, conserved site / Dbl homology (DH) domain signature. / Variant SH3 domain / Variant SH3 domain / PAS domain / PAS-associated, C-terminal / PAC domain profile. / 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. / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain) / PAS domain / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain / C2 domain profile. / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / Beta-Lactamase / PAS domain / C2 domain superfamily / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / PAS repeat profile. / PAS domain / SH3 domain / PAS domain superfamily / EF-hand, calcium binding motif / Src homology 3 domains / SH3-like domain superfamily / EF-Hand 1, calcium-binding site / Src homology 3 (SH3) domain profile. / SH3 domain / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / PH-like domain superfamily / Roll / 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 / Up-down Bundle / 2-Layer Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
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)117,5314
Polymers116,6182
Non-polymers9132
Water77543
1
A: Intersectin-1,NPH1-1,Intersectin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,7662
Polymers58,3091
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)58,7662
Polymers58,3091
Non-polymers4561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.060, 111.530, 88.330
Angle α, β, γ (deg.)90.00, 90.63, 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: 58309.168 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


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


Mass: 18.015 Da / Num. of mol.: 43 / 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: 2.62 Å3/Da / Density % sol: 53.07 %
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: 0.99998 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 21, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99998 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 36823 / % possible obs: 99.4 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 17.9
Reflection shellResolution: 2.6→2.7 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.548 / Mean I/σ(I) obs: 3.6 / % possible all: 99.2

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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→47.153 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 34.43
RfactorNum. reflection% reflection
Rfree0.2846 1841 5 %
Rwork0.2379 --
obs0.2403 36785 99.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.6→47.153 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7782 0 62 43 7887
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0027994
X-RAY DIFFRACTIONf_angle_d0.5110780
X-RAY DIFFRACTIONf_dihedral_angle_d9.6333102
X-RAY DIFFRACTIONf_chiral_restr0.021204
X-RAY DIFFRACTIONf_plane_restr0.0031368
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6001-2.67030.42061400.33692647X-RAY DIFFRACTION99
2.6703-2.74890.35041390.31172658X-RAY DIFFRACTION99
2.7489-2.83760.40841420.30322695X-RAY DIFFRACTION99
2.8376-2.9390.31761410.2862661X-RAY DIFFRACTION99
2.939-3.05670.37071410.29382671X-RAY DIFFRACTION99
3.0567-3.19580.37311400.30052677X-RAY DIFFRACTION99
3.1958-3.36420.32861420.27692688X-RAY DIFFRACTION100
3.3642-3.57490.32981410.27792673X-RAY DIFFRACTION99
3.5749-3.85080.2831420.25372704X-RAY DIFFRACTION99
3.8508-4.23810.23691410.2272679X-RAY DIFFRACTION100
4.2381-4.85090.24321440.19222731X-RAY DIFFRACTION100
4.8509-6.10950.25751420.21972705X-RAY DIFFRACTION100
6.1095-47.1610.23791460.18392755X-RAY DIFFRACTION99
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)
12.16970.66980.74281.39370.93392.2702-0.19720.168-0.06110.08920.1039-0.0415-0.27780.0864-0.06330.3129-0.0744-0.00630.13760.01290.333516.21729.402616.9638
20.4697-0.1868-1.25790.1640.49233.2309-0.00640.2345-0.0663-0.1342-0.20820.158-0.0645-0.3504-0.00020.3944-0.0418-0.0270.5231-0.1130.48844.511119.917-17.9722
32.8590.904-0.68081.4338-0.31031.3643-0.1438-0.09040.1071-0.04670.03570.06550.11320.0775-0.00280.23660.0568-0.01340.1720.01530.288514.8457-8.773-18.1239
41.0024-0.08620.58080.4367-0.222.25550.09790.32440.1988-0.2823-0.146-0.0715-0.22390.00870.00020.61330.05770.05240.50310.07020.454926.59030.0734-52.7122
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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