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- PDB-2p2l: Rac1-GDP-Zinc Complex -

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Basic information

Entry
Database: PDB / ID: 2p2l
TitleRac1-GDP-Zinc Complex
ComponentsRas-related C3 botulinum toxin substrate 1
KeywordsUNKNOWN FUNCTION / Rho Family GTPase
Function / homology
Function and homology information


regulation of respiratory burst / negative regulation of interleukin-23 production / regulation of neutrophil migration / localization within membrane / Activated NTRK2 signals through CDK5 / NADPH oxidase complex / negative regulation of receptor-mediated endocytosis / regulation of hydrogen peroxide metabolic process / ruffle assembly / NTRK2 activates RAC1 ...regulation of respiratory burst / negative regulation of interleukin-23 production / regulation of neutrophil migration / localization within membrane / Activated NTRK2 signals through CDK5 / NADPH oxidase complex / negative regulation of receptor-mediated endocytosis / regulation of hydrogen peroxide metabolic process / ruffle assembly / NTRK2 activates RAC1 / engulfment of apoptotic cell / Inactivation of CDC42 and RAC1 / WNT5:FZD7-mediated leishmania damping / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / cortical cytoskeleton organization / respiratory burst / hepatocyte growth factor receptor signaling pathway / ruffle organization / cell projection assembly / negative regulation of fibroblast migration / thioesterase binding / regulation of stress fiber assembly / RHO GTPases activate CIT / Nef and signal transduction / sphingosine-1-phosphate receptor signaling pathway / regulation of nitric oxide biosynthetic process / PCP/CE pathway / Azathioprine ADME / motor neuron axon guidance / RHO GTPases activate KTN1 / positive regulation of neutrophil chemotaxis / regulation of lamellipodium assembly / Activation of RAC1 / DCC mediated attractive signaling / positive regulation of cell-substrate adhesion / MET activates RAP1 and RAC1 / Wnt signaling pathway, planar cell polarity pathway / Sema4D mediated inhibition of cell attachment and migration / CD28 dependent Vav1 pathway / Ephrin signaling / lamellipodium assembly / positive regulation of Rho protein signal transduction / establishment or maintenance of cell polarity / regulation of cell size / DSCAM interactions / Activation of RAC1 downstream of NMDARs / Rho GDP-dissociation inhibitor binding / small GTPase-mediated signal transduction / NRAGE signals death through JNK / Rac protein signal transduction / RHO GTPases activate PAKs / positive regulation of focal adhesion assembly / semaphorin-plexin signaling pathway / Sema3A PAK dependent Axon repulsion / ficolin-1-rich granule membrane / EPH-ephrin mediated repulsion of cells / RHO GTPases Activate NADPH Oxidases / anatomical structure morphogenesis / RHO GTPases Activate WASPs and WAVEs / RHO GTPases activate IQGAPs / localization / positive regulation of lamellipodium assembly / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / positive regulation of substrate adhesion-dependent cell spreading / regulation of cell migration / RHO GTPases activate PKNs / positive regulation of stress fiber assembly / GPVI-mediated activation cascade / RAC1 GTPase cycle / EPHB-mediated forward signaling / actin filament polymerization / positive regulation of microtubule polymerization / cell-matrix adhesion / cell chemotaxis / substrate adhesion-dependent cell spreading / small monomeric GTPase / G protein activity / positive regulation of endothelial cell migration / secretory granule membrane / VEGFR2 mediated vascular permeability / Signal transduction by L1 / cell motility / actin filament organization / Translocation of SLC2A4 (GLUT4) to the plasma membrane / RHO GTPases Activate Formins / regulation of actin cytoskeleton organization / FCGR3A-mediated phagocytosis / FCERI mediated MAPK activation / neuron migration / MAPK6/MAPK4 signaling / trans-Golgi network / Signaling by SCF-KIT / response to wounding / Regulation of actin dynamics for phagocytic cup formation / cytoplasmic ribonucleoprotein granule / VEGFA-VEGFR2 Pathway / ruffle membrane / recycling endosome membrane / Constitutive Signaling by Aberrant PI3K in Cancer / melanosome
Similarity search - Function
Small GTPase Rho / small GTPase Rho family profile. / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase ...Small GTPase Rho / small GTPase Rho family profile. / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / Ras-related C3 botulinum toxin substrate 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / and molecular replacement / SAD / Resolution: 1.9 Å
AuthorsPrehna, G. / Stebbins, C.E.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2007
Title: A Rac1-GDP trimer complex binds zinc with tetrahedral and octahedral coordination, displacing magnesium.
Authors: Prehna, G. / Stebbins, C.E.
History
DepositionMar 7, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 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 1.4Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ras-related C3 botulinum toxin substrate 1
B: Ras-related C3 botulinum toxin substrate 1
C: Ras-related C3 botulinum toxin substrate 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,22014
Polymers62,3673
Non-polymers1,85311
Water14,484804
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5710 Å2
ΔGint-269 kcal/mol
Surface area24850 Å2
MethodPISA
2
A: Ras-related C3 botulinum toxin substrate 1
B: Ras-related C3 botulinum toxin substrate 1
C: Ras-related C3 botulinum toxin substrate 1
hetero molecules

A: Ras-related C3 botulinum toxin substrate 1
B: Ras-related C3 botulinum toxin substrate 1
C: Ras-related C3 botulinum toxin substrate 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,44028
Polymers124,7356
Non-polymers3,70622
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-1/31
Buried area14140 Å2
ΔGint-604 kcal/mol
Surface area46980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.727, 89.727, 190.618
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-931-

HOH

21A-1057-

HOH

31A-1075-

HOH

DetailsNormally a monomer. In this crystal structure zinc induces a trimer.

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Components

#1: Protein Ras-related C3 botulinum toxin substrate 1 / p21-Rac1 / Ras- like protein TC25 / Cell migration-inducing gene 5 protein


Mass: 20789.117 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAC1 / Plasmid: pGEX4T3 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P63000
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 804 / 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: 3.55 Å3/Da / Density % sol: 65.34 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 100mM MES pH6.0, 15mM ZnSO4, 10% PEGMME 550., VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X3A / Wavelength: 1.284 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jan 30, 2007
Details: Double crystal monochromator. Si(111) or Si(220) options. Sagitall focusing. Cylindrically bent ULE mirror with Pt and Rh coating.
RadiationMonochromator: Double flat crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.284 Å / Relative weight: 1
ReflectionRedundancy: 4.1 % / Av σ(I) over netI: 8.6 / Number: 555099 / Rmerge(I) obs: 0.085 / Χ2: 1.01 / D res high: 1.9 Å / D res low: 50 Å / Num. obs: 135270 / % possible obs: 99.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.095099.110.051.1474.2
3.254.0910010.0671.0454.2
2.843.2510010.0851.14.2
2.582.8410010.1061.2514.1
2.392.5810010.1271.1184.1
2.252.3910010.1641.1134.1
2.142.2510010.2181.2654.1
2.052.1410010.230.7744
1.972.0510010.3040.6254
1.91.9710010.4720.6684
ReflectionResolution: 1.9→77.62 Å / Num. obs: 70803 / % possible obs: 99.9 % / Redundancy: 7.7 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 10
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.512 / Mean I/σ(I) obs: 3.7 / % possible all: 100

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Phasing

PhasingMethod: SAD
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Zn23.4480.1910.9390.0661.199
2Zn22.0840.4280.9240.0641.151
3Zn19.4490.4410.1740.071.05
4Zn20.7020.3540.0120.0680.74
5Zn27.2470.540.2090.1560.779
6Zn26.2870.3750.8140.1490.763
7Zn24.9140.1370.980.1520.792
8Zn35.3530.6890.8670.0010.605
Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å43.67 Å
Translation2.5 Å43.67 Å
Phasing dmFOM : 0.78 / FOM acentric: 0.8 / FOM centric: 0.67 / Reflection: 30529 / Reflection acentric: 27245 / Reflection centric: 3284
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
7.1-29.4070.860.910.6913951025370
4.5-7.10.880.90.7642463570676
3.6-4.50.880.890.7951854590595
3.1-3.60.840.850.7351814690491
2.7-3.10.740.750.5890398291748
2.5-2.70.620.630.4554835079404

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
SOLVE2.12phasing
RESOLVE2.12phasing
REFMAC5.2.0005refinement
PDB_EXTRACT2data extraction
MAR345CCDdata collection
HKL-2000data reduction
RefinementMethod to determine structure: and molecular replacement
Starting model: 1MH1
Resolution: 1.9→77.62 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.948 / SU B: 3.917 / SU ML: 0.071 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.111 / ESU R Free: 0.11 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20808 3560 5 %RANDOM
Rwork0.17568 ---
obs0.17733 67009 99.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.003 Å2
Baniso -1Baniso -2Baniso -3
1-0.63 Å20.31 Å20 Å2
2--0.63 Å20 Å2
3----0.94 Å2
Refinement stepCycle: LAST / Resolution: 1.9→77.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4141 0 92 804 5037
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0224319
X-RAY DIFFRACTIONr_bond_other_d0.0010.023943
X-RAY DIFFRACTIONr_angle_refined_deg1.6272.0095894
X-RAY DIFFRACTIONr_angle_other_deg0.91139211
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6975528
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.03624.431167
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.68515723
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.0191521
X-RAY DIFFRACTIONr_chiral_restr0.1050.2682
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024651
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02808
X-RAY DIFFRACTIONr_nbd_refined0.2250.2946
X-RAY DIFFRACTIONr_nbd_other0.1920.24042
X-RAY DIFFRACTIONr_nbtor_refined0.1780.22137
X-RAY DIFFRACTIONr_nbtor_other0.0890.22263
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1930.2626
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1150.21
X-RAY DIFFRACTIONr_metal_ion_refined0.0520.29
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1470.216
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3110.240
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2640.247
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0890.22
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2781.53437
X-RAY DIFFRACTIONr_mcbond_other0.2231.51069
X-RAY DIFFRACTIONr_mcangle_it1.47424334
X-RAY DIFFRACTIONr_scbond_it2.41231963
X-RAY DIFFRACTIONr_scangle_it3.4474.51560
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 285 -
Rwork0.238 4859 -
obs--99.34 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.3431-0.623-0.27461.8347-0.28041.71990.0874-0.07940.04450.0526-0.0488-0.1221-0.05140.1365-0.0387-0.1076-0.0239-0.0238-0.09020.0011-0.1122-4.35539.8709-12.4509
21.31850.68370.06142.10680.16841.6632-0.0127-0.05730.1280.03910.0470.071-0.00690.1505-0.0343-0.09980.00680.0117-0.094-0.0366-0.1034-4.72845.2761-13.1626
32.175-0.0149-0.32640.78240.09621.2968-0.02130.0363-0.0870.05730.00240.05210.0239-0.03740.0189-0.0614-0.01060.0236-0.13570.0098-0.1002-35.155726.9882-11.4688
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 445 - 48
2X-RAY DIFFRACTION1AA49 - 17953 - 183
3X-RAY DIFFRACTION2BB1 - 485 - 52
4X-RAY DIFFRACTION2BB50 - 17954 - 183
5X-RAY DIFFRACTION3CC1 - 1795 - 183

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