[English] 日本語
Yorodumi
- PDB-4eza: Crystal structure of the atypical phosphoinositide (aPI) binding ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4eza
TitleCrystal structure of the atypical phosphoinositide (aPI) binding domain of IQGAP2
ComponentsRas GTPase-activating-like protein IQGAP2
KeywordsSIGNALING PROTEIN / gap / structural genomics consortium / sgc
Function / homology
Function and homology information


mitotic actomyosin contractile ring assembly actin filament organization / thrombin-activated receptor signaling pathway / Arp2/3 complex-mediated actin nucleation / Arp2/3 complex binding / GTPase inhibitor activity / microvillus / phosphatidylinositol-3,4,5-trisphosphate binding / CDC42 GTPase cycle / RHOG GTPase cycle / RHO GTPases activate IQGAPs ...mitotic actomyosin contractile ring assembly actin filament organization / thrombin-activated receptor signaling pathway / Arp2/3 complex-mediated actin nucleation / Arp2/3 complex binding / GTPase inhibitor activity / microvillus / phosphatidylinositol-3,4,5-trisphosphate binding / CDC42 GTPase cycle / RHOG GTPase cycle / RHO GTPases activate IQGAPs / RAC1 GTPase cycle / GTPase activator activity / secretory granule membrane / filopodium / regulation of actin cytoskeleton organization / small GTPase binding / actin filament binding / actin cytoskeleton / lamellipodium / actin binding / cell cortex / microtubule / calmodulin binding / Neutrophil degranulation / cell surface / signal transduction / extracellular exosome / plasma membrane / cytosol / cytoplasm
Similarity search - Function
RasGAP protein, C-terminal / RasGAP C-terminus / Ras GTPase-activating protein, conserved site / Ras GTPase-activating proteins domain signature. / GTPase-activator protein for Ras-like GTPase / Ras GTPase-activating proteins profile. / GTPase-activator protein for Ras-like GTPases / Ras GTPase-activating domain / IQ calmodulin-binding motif / Calponin homology domain ...RasGAP protein, C-terminal / RasGAP C-terminus / Ras GTPase-activating protein, conserved site / Ras GTPase-activating proteins domain signature. / GTPase-activator protein for Ras-like GTPase / Ras GTPase-activating proteins profile. / GTPase-activator protein for Ras-like GTPases / Ras GTPase-activating domain / IQ calmodulin-binding motif / Calponin homology domain / Calponin homology (CH) domain / Rho GTPase activation protein / Short calmodulin-binding motif containing conserved Ile and Gln residues. / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. / IQ motif profile. / WW/rsp5/WWP domain signature. / WW/rsp5/WWP domain profile. / IQ motif, EF-hand binding site / WW domain
Similarity search - Domain/homology
Ras GTPase-activating-like protein IQGAP2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.5 Å
AuthorsVan Aalten, D.M.F. / Dixon, M.J. / Gray, A. / Schenning, M. / Agacan, M. / Leslie, N.R. / Downes, C.P. / Batty, I.H. / Nedyalkova, L. / Tempel, W. ...Van Aalten, D.M.F. / Dixon, M.J. / Gray, A. / Schenning, M. / Agacan, M. / Leslie, N.R. / Downes, C.P. / Batty, I.H. / Nedyalkova, L. / Tempel, W. / Tong, Y. / Zhong, N. / Crombet, L. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Bochkarev, A. / Park, H. / Structural Genomics Consortium (SGC)
CitationJournal: J.Biol.Chem. / Year: 2012
Title: IQGAP Proteins Reveal an Atypical Phosphoinositide (aPI) Binding Domain with a Pseudo C2 Domain Fold.
Authors: Dixon, M.J. / Gray, A. / Schenning, M. / Agacan, M. / Tempel, W. / Tong, Y. / Nedyalkova, L. / Park, H.W. / Leslie, N.R. / van Aalten, D.M. / Downes, C.P. / Batty, I.H.
History
DepositionMay 2, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 18, 2012Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ras GTPase-activating-like protein IQGAP2
B: Ras GTPase-activating-like protein IQGAP2


Theoretical massNumber of molelcules
Total (without water)26,4652
Polymers26,4652
Non-polymers00
Water2,810156
1
A: Ras GTPase-activating-like protein IQGAP2


Theoretical massNumber of molelcules
Total (without water)13,2321
Polymers13,2321
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ras GTPase-activating-like protein IQGAP2


Theoretical massNumber of molelcules
Total (without water)13,2321
Polymers13,2321
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.067, 47.234, 46.631
Angle α, β, γ (deg.)90.00, 95.51, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Ras GTPase-activating-like protein IQGAP2


Mass: 13232.346 Da / Num. of mol.: 2 / Fragment: UNP residues 1476-1571
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IQGAP2 / Plasmid: pET28-mhl / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-V2R-pRARE2 / References: UniProt: Q13576
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 156 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.87 Å3/Da / Density % sol: 34.11 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 30% PEG-MME, 0.2M ammonium sulfate, 0.1M MES, 1:100 (w/w) chymotrypsin, pH 6.5, vapor diffusion, sitting drop, temperature 291K

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 23-ID-B10.97946
SYNCHROTRONAPS 23-ID-B21.07205
Detector
TypeIDDetectorDate
MAR scanner 300 mm plate1IMAGE PLATEJun 20, 2009
MAR scanner 300 mm plate2IMAGE PLATEJun 20, 2009
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.979461
21.072051
ReflectionResolution: 1.5→50 Å / Num. obs: 31375 / % possible obs: 98.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
REFMACrefmac_5.5.0109refinement
PDB_EXTRACT3.006data extraction
RefinementResolution: 1.5→46.42 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.935 / Occupancy max: 1 / Occupancy min: 1 / SU B: 3.248 / SU ML: 0.055 / Cross valid method: THROUGHOUT / ESU R: 0.085 / ESU R Free: 0.086 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23932 461 1.5 %RANDOM
Rwork0.20977 ---
obs0.21024 30080 97.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.828 Å2
Baniso -1Baniso -2Baniso -3
1-0.13 Å20 Å2-0.41 Å2
2---0.25 Å20 Å2
3---0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.5→46.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1518 0 0 156 1674
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221536
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.31.9792066
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1395186
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.62926.85770
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.97815314
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.281152
X-RAY DIFFRACTIONr_chiral_restr0.0840.2248
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021092
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7861.5932
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.53221516
X-RAY DIFFRACTIONr_scbond_it2.693604
X-RAY DIFFRACTIONr_scangle_it4.4014.5550
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.241 29 -
Rwork0.262 1829 -
obs--80.68 %
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)
10.4742-0.42460.30191.42150.23620.8985-0.0265-0.0130.01650.03320.0568-0.0603-0.03190.0163-0.03020.05950.00320.00110.0572-0.00630.065620.3838.86139.448
21.46590.43081.35991.81160.25461.9560.02230.0204-0.02010.00180.04390.08390.02980.0133-0.06620.0979-0.00910.01190.09470.00410.11284.7129.04421.146
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 95
2X-RAY DIFFRACTION2B2 - 95

+
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