[English] 日本語
Yorodumi
- PDB-5hzk: Crystal structure of photoinhibitable Intersectin1 containing wil... -

+
Open data


ID or keywords:

Loading...

-
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 / Cdc42 protein signal transduction / positive regulation of synapse structural plasticity / dendritic cell migration ...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 / Cdc42 protein signal transduction / positive regulation of synapse structural plasticity / dendritic cell migration / endothelin receptor signaling pathway involved in heart process / cardiac neural crest cell migration involved in outflow tract morphogenesis / storage vacuole / positive regulation of epithelial cell proliferation involved in lung morphogenesis / apolipoprotein A-I receptor binding / neuron fate determination / GTP-dependent protein binding / modulation by host of viral process / organelle transport along microtubule / regulation of attachment of spindle microtubules to kinetochore / positive regulation of pseudopodium assembly / blue light photoreceptor activity / cardiac conduction system development / Inactivation of CDC42 and RAC1 / establishment of Golgi localization / regulation of filopodium assembly / leading edge membrane / positive regulation of intracellular protein transport / neuropilin signaling pathway / cell junction assembly / filopodium assembly / establishment of epithelial cell apical/basal polarity / mitogen-activated protein kinase kinase kinase binding / dendritic spine morphogenesis / regulation of modification of postsynaptic structure / regulation of stress fiber assembly / thioesterase binding / embryonic heart tube development / proline-rich region binding / RHO GTPases activate KTN1 / regulation of lamellipodium assembly / nuclear migration / adherens junction organization / DCC mediated attractive signaling / regulation of small GTPase mediated signal transduction / sprouting angiogenesis / CD28 dependent Vav1 pathway / Wnt signaling pathway, planar cell polarity pathway / positive regulation of filopodium assembly / endosomal transport / regulation of postsynapse organization / regulation of mitotic nuclear division / RHOV GTPase cycle / phagocytosis, engulfment / intracellular vesicle / establishment or maintenance of cell polarity / NRAGE signals death through JNK / heart contraction / Myogenesis / RHOJ GTPase cycle / Golgi organization / positive regulation of cytokinesis / RHOQ GTPase cycle / RHO GTPases activate PAKs / exocytosis / RHOU GTPase cycle / CDC42 GTPase cycle / macrophage differentiation / RHOG GTPase cycle / RAC2 GTPase cycle / RHO GTPases Activate WASPs and WAVEs / RAC3 GTPase cycle / spindle midzone / RHO GTPases activate IQGAPs / negative regulation of protein-containing complex assembly / positive regulation of lamellipodium assembly / phagocytic vesicle / positive regulation of substrate adhesion-dependent cell spreading / clathrin-coated pit / positive regulation of stress fiber assembly / GPVI-mediated activation cascade / EPHB-mediated forward signaling / substantia nigra development / RAC1 GTPase cycle / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / small monomeric GTPase / positive regulation of DNA replication / secretory granule / guanyl-nucleotide exchange factor activity / filopodium / actin filament organization / integrin-mediated signaling pathway / RHO GTPases Activate Formins / regulation of actin cytoskeleton organization / FCGR3A-mediated phagocytosis / positive regulation of JNK cascade / EGFR downregulation / MAPK6/MAPK4 signaling / Schaffer collateral - CA1 synapse / recycling endosome
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 ...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. / Variant SH3 domain / Variant SH3 domain / Small GTPase Rho / PAS domain / PAS-associated, C-terminal / PAC domain profile. / small GTPase Rho family profile. / Dbl homology (DH) domain superfamily / RhoGEF domain / Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain) / Dbl homology (DH) domain / Dbl homology (DH) domain profile. / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain / C2 domain profile. / C2 domain superfamily / PAS domain / PH domain profile. / Pleckstrin homology domain. / PAS repeat profile. / Pleckstrin homology domain / PAS domain / SH3 domain / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / PAS domain superfamily / 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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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
Water00
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

-
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


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


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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more