[English] 日本語
Yorodumi
- PDB-3qwm: Crystal Structure of GEP100, the plextrin homology domain of IQ m... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3qwm
TitleCrystal Structure of GEP100, the plextrin homology domain of IQ motif and SEC7 domain-containing protein 1 isoform a
ComponentsIQ motif and SEC7 domain-containing protein 1
KeywordsSIGNALING PROTEIN / Structural Genomics / Structural Genomics Consortium / SGC / PH domain / guanine nucleotide exchange factor / ARF1 / ARF5 / ARF6 / alpha-catenin / EGFR
Function / homology
Function and homology information


positive regulation of keratinocyte migration / dendritic spine development / positive regulation of focal adhesion disassembly / regulation of ARF protein signal transduction / guanyl-nucleotide exchange factor activity / synaptic vesicle / actin cytoskeleton organization / postsynaptic density / intracellular membrane-bounded organelle / lipid binding ...positive regulation of keratinocyte migration / dendritic spine development / positive regulation of focal adhesion disassembly / regulation of ARF protein signal transduction / guanyl-nucleotide exchange factor activity / synaptic vesicle / actin cytoskeleton organization / postsynaptic density / intracellular membrane-bounded organelle / lipid binding / nucleolus / membrane
Similarity search - Function
IQ motif and SEC7 domain-containing protein, PH domain / PH domain / Sec7 domain / Sec7, C-terminal domain superfamily / Sec7 domain superfamily / Sec7 domain / SEC7 domain profile. / Sec7 domain / IQ motif profile. / IQ motif, EF-hand binding site ...IQ motif and SEC7 domain-containing protein, PH domain / PH domain / Sec7 domain / Sec7, C-terminal domain superfamily / Sec7 domain superfamily / Sec7 domain / SEC7 domain profile. / Sec7 domain / IQ motif profile. / IQ motif, EF-hand binding site / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / Pleckstrin homology domain. / Pleckstrin homology domain / PH-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
IQ motif and SEC7 domain-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.39 Å
AuthorsFilippakopoulos, P. / Picaud, S. / Felletar, I. / Feller, S. / Janning, M. / Sabe, H. / Krojer, T. / Chaikuad, A. / Allerston, C. / von Delft, F. ...Filippakopoulos, P. / Picaud, S. / Felletar, I. / Feller, S. / Janning, M. / Sabe, H. / Krojer, T. / Chaikuad, A. / Allerston, C. / von Delft, F. / Bountra, C. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. / Knapp, S. / Structural Genomics Consortium (SGC)
CitationJournal: to be published
Title: Crystal Structure of GEP100, the plextrin homology domain of IQ motif and SEC7 domain-containing protein 1 isoform a
Authors: Filippakopoulos, P. / Picaud, S. / Felletar, I. / Feller, S. / Janning, M. / Sabe, H. / Krojer, T. / Chaikuad, A. / Allerston, C. / von Delft, F. / Bountra, C. / Arrowsmith, C.H. / Weigelt, ...Authors: Filippakopoulos, P. / Picaud, S. / Felletar, I. / Feller, S. / Janning, M. / Sabe, H. / Krojer, T. / Chaikuad, A. / Allerston, C. / von Delft, F. / Bountra, C. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. / Knapp, S.
History
DepositionFeb 28, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 13, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 20, 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: IQ motif and SEC7 domain-containing protein 1


Theoretical massNumber of molelcules
Total (without water)16,4331
Polymers16,4331
Non-polymers00
Water28816
1
A: IQ motif and SEC7 domain-containing protein 1

A: IQ motif and SEC7 domain-containing protein 1


Theoretical massNumber of molelcules
Total (without water)32,8662
Polymers32,8662
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/61
Buried area2470 Å2
ΔGint-7 kcal/mol
Surface area14720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.730, 56.730, 234.080
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-1-

HOH

-
Components

#1: Protein IQ motif and SEC7 domain-containing protein 1 / IQSEC1


Mass: 16432.998 Da / Num. of mol.: 1 / Fragment: PH domain, residues in UNP 643-880
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IQSEC1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6DN90
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 3.31 Å3/Da / Density % sol: 62.82 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.25
Details: 17.5%(w/v) PEG 3350, 0.20M Na nitrate, 10.0%(v/v) ethylene glycol, 0.1M Bis-Tris propane, pH 8.25, VAPOR DIFFUSION, SITTING DROP, temperature 277K

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONDiamond I0310.9763
SYNCHROTRONDiamond I0420.984
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDJan 28, 2010
ADSC QUANTUM 3152CCDApr 29, 2010
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97631
20.9841
ReflectionResolution: 2.39→48.07 Å / Num. all: 9658 / Num. obs: 9658 / % possible obs: 99.8 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 5.4 % / Biso Wilson estimate: 72.9 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 10.6
Reflection shellResolution: 2.39→2.52 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.667 / Mean I/σ(I) obs: 2 / Num. unique all: 1343 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
GDAdata collection
SHARPphasing
REFMAC5.6.0066refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SIRAS / Resolution: 2.39→48.07 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.929 / SU B: 16.577 / SU ML: 0.176 / Cross valid method: THROUGHOUT / ESU R Free: 0.225 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.27242 487 5.1 %RANDOM
Rwork0.24228 ---
all0.24369 9587 --
obs0.24369 9587 99.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 59.584 Å2
Baniso -1Baniso -2Baniso -3
1-0.5 Å20.25 Å20 Å2
2--0.5 Å20 Å2
3----0.76 Å2
Refinement stepCycle: LAST / Resolution: 2.39→48.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1035 0 0 16 1051
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221056
X-RAY DIFFRACTIONr_bond_other_d0.0010.02736
X-RAY DIFFRACTIONr_angle_refined_deg1.2881.9661427
X-RAY DIFFRACTIONr_angle_other_deg0.77231783
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8545125
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.68523.92956
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.60115184
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.157159
X-RAY DIFFRACTIONr_chiral_restr0.0740.2157
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211166
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02223
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.39→2.452 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.456 32 -
Rwork0.372 650 -
obs--99.27 %
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)
10.44670.4157-0.00011.0613-0.19580.6111-0.0503-0.1914-0.0758-0.0155-0.13480.2098-0.0340.1780.18510.1397-0.04690.06730.18170.10910.272622.489128.833822.9879
20.1507-0.50480.19232.2507-0.07880.8675-0.01490.0739-0.0178-0.1571-0.06620.1375-0.17730.36770.08120.1286-0.09270.03050.25380.04490.078830.163337.170519.8883
30.07250.0647-0.35631.92920.40092.59140.0246-0.1029-0.0091-0.1218-0.03-0.06520.01120.35870.00540.1042-0.05460.04490.220.05820.090632.72133.954117.0138
42.04780.20433.32593.0018-6.766426.1334-0.3573-0.1212-0.1251-0.2364-0.4313-0.01141.1509-0.51320.78860.492-0.25960.31450.4218-0.32110.302331.551929.2678-5.4461
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A736 - 788
2X-RAY DIFFRACTION2A789 - 812
3X-RAY DIFFRACTION3A813 - 848
4X-RAY DIFFRACTION4A849 - 865

+
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://pdbjlvh1.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