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- PDB-2pz1: Crystal Structure of Auto-inhibited Asef -

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Basic information

Entry
Database: PDB / ID: 2pz1
TitleCrystal Structure of Auto-inhibited Asef
ComponentsRho guanine nucleotide exchange factor 4
KeywordsSIGNALING PROTEIN / Helical Bundle / Beta Barrel / Beta Sandwich
Function / homology
Function and homology information


filopodium assembly / regulation of small GTPase mediated signal transduction / lamellipodium assembly / NRAGE signals death through JNK / CDC42 GTPase cycle / RHOA GTPase cycle / RAC1 GTPase cycle / guanyl-nucleotide exchange factor activity / ruffle membrane / G alpha (12/13) signalling events ...filopodium assembly / regulation of small GTPase mediated signal transduction / lamellipodium assembly / NRAGE signals death through JNK / CDC42 GTPase cycle / RHOA GTPase cycle / RAC1 GTPase cycle / guanyl-nucleotide exchange factor activity / ruffle membrane / G alpha (12/13) signalling events / intracellular signal transduction / protein domain specific binding / cytosol
Similarity search - Function
Dbl Homology Domain; Chain A / Dbl homology (DH) domain / Guanine-nucleotide dissociation stimulator, CDC24, conserved site / Dbl homology (DH) domain signature. / SOS1/NGEF-like PH 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. ...Dbl Homology Domain; Chain A / Dbl homology (DH) domain / Guanine-nucleotide dissociation stimulator, CDC24, conserved site / Dbl homology (DH) domain signature. / SOS1/NGEF-like PH 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. / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / SH3 Domains / PH-domain like / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / SH3 domain / SH3 type barrels. / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / PH-like domain superfamily / Roll / Up-down Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Rho guanine nucleotide exchange factor 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD, MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsBetts, L. / Sondek, J. / Rossman, K.L.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2007
Title: Release of autoinhibition of ASEF by APC leads to CDC42 activation and tumor suppression.
Authors: Mitin, N. / Betts, L. / Yohe, M.E. / Der, C.J. / Sondek, J. / Rossman, K.L.
History
DepositionMay 17, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Feb 21, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Rho guanine nucleotide exchange factor 4


Theoretical massNumber of molelcules
Total (without water)53,9381
Polymers53,9381
Non-polymers00
Water1,802100
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)100.418, 79.883, 67.407
Angle α, β, γ (deg.)90.00, 122.99, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Rho guanine nucleotide exchange factor 4 / APC-stimulated guanine nucleotide exchange factor / Asef


Mass: 53937.777 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ARHGEF4, KIAA1112 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Rosetta / References: UniProt: Q9NR80
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 100 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.1 Å3/Da / Density % sol: 41.48 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 100 mM HEPES pH 7, 20 % PEG 3350, 200 mM magnesium acetate, 10% glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
SYNCHROTRONAPS 22-ID1.97925, .97936, .97164
ROTATING ANODERIGAKU RU30021.5418
Detector
TypeIDDetectorDateDetails
MARMOSAIC 300 mm CCD1CCDFeb 12, 2005Rosenbaum-Rock vertical focusing mirror
RIGAKU RAXIS IV2IMAGE PLATEFeb 15, 2006Osmic Confocal Blue multi-layer mirrors
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Rosenbaum-Rock double Si(220) crystal cryogenically cooled monochromatorMADMx-ray1
2GraphiteSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.979251
20.979361
30.971641
41.54181
ReflectionResolution: 2.25→50 Å / Num. all: 21205 / Num. obs: 20993 / % possible obs: 99.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.8 % / Biso Wilson estimate: 49.6 Å2 / Rsym value: 0.041 / Net I/σ(I): 30.2
Reflection shellResolution: 2.25→2.34 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 3.23 / Num. unique all: 2069 / Rsym value: 0.412 / % possible all: 97.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SHELXDphasing
MLPHAREphasing
PHASERphasing
RefinementMethod to determine structure: MAD, MOLECULAR REPLACEMENT / Resolution: 2.25→15 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.911 / SU B: 16.619 / SU ML: 0.208 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.374 / ESU R Free: 0.267 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27925 1071 5.1 %RANDOM
Rwork0.2174 ---
all0.22063 20075 --
obs0.22063 19854 98.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 51.173 Å2
Baniso -1Baniso -2Baniso -3
1-1.92 Å20 Å20.14 Å2
2---1.35 Å20 Å2
3----0.42 Å2
Refinement stepCycle: LAST / Resolution: 2.25→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3330 0 0 100 3430
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0213394
X-RAY DIFFRACTIONr_angle_refined_deg1.0631.9464565
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8185406
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.48323.797187
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.58215622
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3361533
X-RAY DIFFRACTIONr_chiral_restr0.0760.2477
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022613
X-RAY DIFFRACTIONr_nbd_refined0.2480.31577
X-RAY DIFFRACTIONr_nbtor_refined0.320.52298
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2270.5265
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2980.350
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2250.54
X-RAY DIFFRACTIONr_mcbond_it0.58422068
X-RAY DIFFRACTIONr_mcangle_it1.00533224
X-RAY DIFFRACTIONr_scbond_it0.48821493
X-RAY DIFFRACTIONr_scangle_it0.78631341
LS refinement shellResolution: 2.25→2.31 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 85 -
Rwork0.268 1366 -
obs--93.55 %
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)
123.02011.519-5.211110.04579.881447.0624-0.7146-2.5-3.32081.50450.5967-1.9194-1.3423-2.18250.11790.32350.2395-0.10590.35150.07350.010919.024515.277740.221
23.7626-0.94760.9394.23220.27283.13310.1084-0.17280.2024-0.2575-0.082-0.5459-0.08370.2205-0.0265-0.2392-0.01940.0503-0.2495-0.0352-0.159817.644816.332923.8018
32.4601-0.65090.47541.9369-0.52241.5893-0.00660.0194-0.1464-0.0227-0.029-0.0613-0.0324-0.07620.0356-0.1728-0.0360.0182-0.19460.0465-0.20480.7459-0.752424.75
426.7788-1.9206-14.26641.9133.194210.25541.2966-2.70431.14710.5223-0.0803-0.829-0.15841.3554-1.21630.0136-0.1374-0.07070.1929-0.05330.0197-8.320910.236629.9004
52.370.6771-0.73023.03270.03472.0168-0.03210.2145-0.383-0.20290.027-0.4571-0.05370.19430.0051-0.23080.01260.1073-0.2111-0.018-0.111515.3279-0.403720.7993
65.1660.32781.65537.67760.37956.5055-0.30020.10430.17490.06460.17260.473-0.82880.05320.12760.0511-0.05910.0367-0.19590.0065-0.280614.966124.33542.0345
710.35489.1564-6.942634.61472.386425.3340.8003-0.61840.8274-0.7662-0.0113-2.0371-1.65210.5894-0.78910.2131-0.14050.12020.09070.04550.133631.026537.7192-0.1163
85.0041.4206-1.72271.4597-1.92977.1826-0.12710.12430.14680.56660.1978-0.0066-0.42410.4106-0.07070.0496-0.0968-0.0085-0.11040.0397-0.17821.468726.17872.1749
918.2657-14.174-12.503116.727335.6154125.77850.1289-1.68880.79680.91161.431-0.36591.02212.642-1.560.29450.0106-0.01860.1671-0.02960.269515.051937.297912.6268
1011.1628-2.5795-1.93693.6891-0.71728.6895-0.10470.54130.50870.1101-0.2106-0.0302-1.12640.2120.31520.1272-0.2193-0.0225-0.17090.0413-0.25920.332628.2507-2.644
1174.27564.90413.83944.5784-8.715219.10450.3728-0.6687-0.81070.9811-0.9627-0.46270.69510.29920.5899-0.1071-0.1284-0.077-0.01020.01250.015738.179522.9333-0.2285
1218.0502-1.46488.554711.6956-4.58446.5476-0.83410.90710.4792-0.4189-0.0442-0.6852-1.46591.33790.8782-0.0668-0.36100.54470.08440.285834.577127.43270.022
138.50742.56294.998610.5574-0.209812.3213-0.27930.4326-1.34960.60450.5255-0.4640.66852.1335-0.2462-0.07570.03260.00910.2794-0.00030.143629.484615.81074.5444
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA182 - 19616 - 30
2X-RAY DIFFRACTION2AA197 - 25431 - 88
3X-RAY DIFFRACTION3AA278 - 404112 - 238
4X-RAY DIFFRACTION4AA405 - 416239 - 250
5X-RAY DIFFRACTION5AA417 - 477251 - 311
6X-RAY DIFFRACTION6AA478 - 506312 - 340
7X-RAY DIFFRACTION7AA507 - 518341 - 352
8X-RAY DIFFRACTION8AA519 - 532353 - 366
9X-RAY DIFFRACTION9AA533 - 541367 - 375
10X-RAY DIFFRACTION10AA542 - 550376 - 384
11X-RAY DIFFRACTION11AA551 - 559385 - 393
12X-RAY DIFFRACTION12AA569 - 591403 - 425
13X-RAY DIFFRACTION13AA592 - 611426 - 445

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