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- PDB-2ic5: Crystal structure of human RAC3 grown in the presence of Gpp(NH)p. -

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Basic information

Entry
Database: PDB / ID: 2ic5
TitleCrystal structure of human RAC3 grown in the presence of Gpp(NH)p.
ComponentsRas-related C3 botulinum toxin substrate 3
KeywordsSIGNALING PROTEIN / GTPase RAC3 / small GTP binding protein / p21 rac / ras-related C3 botulinum toxin substrate 3 / signalling protein / GppNHp / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


cerebral cortex GABAergic interneuron development / regulation of neuron maturation / regulation of neutrophil migration / postsynaptic actin cytoskeleton organization / NADPH oxidase complex / engulfment of apoptotic cell / cortical cytoskeleton organization / respiratory burst / cell projection assembly / PCP/CE pathway ...cerebral cortex GABAergic interneuron development / regulation of neuron maturation / regulation of neutrophil migration / postsynaptic actin cytoskeleton organization / NADPH oxidase complex / engulfment of apoptotic cell / cortical cytoskeleton organization / respiratory burst / cell projection assembly / PCP/CE pathway / synaptic transmission, GABAergic / motor neuron axon guidance / positive regulation of cell adhesion mediated by integrin / establishment or maintenance of cell polarity / Rac protein signal transduction / filamentous actin / neuromuscular process controlling balance / RAC3 GTPase cycle / endomembrane system / positive regulation of substrate adhesion-dependent cell spreading / homeostasis of number of cells within a tissue / cell chemotaxis / small monomeric GTPase / G protein activity / actin filament organization / cell periphery / regulation of actin cytoskeleton organization / Wnt signaling pathway / calcium-dependent protein binding / lamellipodium / regulation of cell shape / growth cone / cytoplasmic vesicle / actin cytoskeleton organization / cytoskeleton / neuron projection / intracellular signal transduction / GTPase activity / neuronal cell body / glutamatergic synapse / GTP binding / endoplasmic reticulum membrane / protein kinase binding / perinuclear region of cytoplasm / extracellular exosome / plasma membrane / cytosol
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 / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Ras-related C3 botulinum toxin substrate 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsUgochukwu, E. / Yang, X. / Zao, Y. / Elkins, J. / Gileadi, C. / Burgess, N. / Colebrook, S. / Gileadi, O. / Fedorov, O. / Bunkoczi, G. ...Ugochukwu, E. / Yang, X. / Zao, Y. / Elkins, J. / Gileadi, C. / Burgess, N. / Colebrook, S. / Gileadi, O. / Fedorov, O. / Bunkoczi, G. / Sundstrom, M. / Arrowsmith, C. / Weigelt, J. / Edwards, A. / von Delft, F. / Doyle, D. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal structure of human RAC3 grown in the presence of Gpp(NH)p.
Authors: Yang, X. / Ugochukwu, E. / Elkins, J. / Doyle, D.
History
DepositionSep 12, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 10, 2006Provider: 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
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / 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_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.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.value / _struct_conn.pdbx_dist_value / _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.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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_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 3
B: Ras-related C3 botulinum toxin substrate 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,2789
Polymers39,9842
Non-polymers1,2947
Water5,008278
1
A: Ras-related C3 botulinum toxin substrate 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7835
Polymers19,9921
Non-polymers7914
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ras-related C3 botulinum toxin substrate 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4954
Polymers19,9921
Non-polymers5033
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.755, 81.583, 84.381
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31A
41B

NCS domain segments:

Ens-ID: 1 / Refine code: 5

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETPHEPHEAA1 - 282 - 29
21METMETPHEPHEBB1 - 282 - 29
32ASNASNGLYGLYAA39 - 17840 - 179
42ASNASNGLYGLYBB39 - 17840 - 179

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Ras-related C3 botulinum toxin substrate 3 / p21-Rac3


Mass: 19991.979 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAC3 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21 (DE3)R3 / References: UniProt: P60763

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Non-polymers , 6 types, 285 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / 5'-Guanylyl imidodiphosphate


Mass: 522.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#5: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER / Bis-tris methane


Mass: 209.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#6: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 278 / 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: 2.31 Å3/Da / Density % sol: 46.81 %
Crystal growTemperature: 293 K / pH: 6.5
Details: 0.1 M BIS-TRIS, 20% MPEG 5K , pH 6.5, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9998 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 20, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9998 Å / Relative weight: 1
ReflectionResolution: 1.9→45.31 Å / Num. all: 29632 / Num. obs: 29632 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 %
Reflection shellResolution: 1.9→2 Å / % possible all: 92.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2G0N
Resolution: 1.9→45.31 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.942 / SU B: 5.586 / SU ML: 0.09 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.132 / ESU R Free: 0.129 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20026 1501 5.1 %RANDOM
Rwork0.15264 ---
obs0.15505 28080 98.82 %-
all-28080 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 24.712 Å2
Baniso -1Baniso -2Baniso -3
1--0.3 Å20 Å20 Å2
2--1.28 Å20 Å2
3----0.98 Å2
Refinement stepCycle: LAST / Resolution: 1.9→45.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2725 0 78 278 3081
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222889
X-RAY DIFFRACTIONr_bond_other_d0.0010.021909
X-RAY DIFFRACTIONr_angle_refined_deg1.4692.0073957
X-RAY DIFFRACTIONr_angle_other_deg0.93534671
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.35360
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.30423.652115
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.58615452
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2731518
X-RAY DIFFRACTIONr_chiral_restr0.0850.2455
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023162
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02564
X-RAY DIFFRACTIONr_nbd_refined0.2030.2551
X-RAY DIFFRACTIONr_nbd_other0.1980.22040
X-RAY DIFFRACTIONr_nbtor_refined0.1790.21427
X-RAY DIFFRACTIONr_nbtor_other0.0850.21407
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1380.2209
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0460.21
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1360.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2390.249
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2110.221
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.68831925
X-RAY DIFFRACTIONr_mcbond_other1.3623714
X-RAY DIFFRACTIONr_mcangle_it4.59252903
X-RAY DIFFRACTIONr_scbond_it6.75771236
X-RAY DIFFRACTIONr_scangle_it8.427111050
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
979medium positional0.210.5
1132loose positional0.615
979medium thermal1.042
1132loose thermal2.2810
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 107 -
Rwork0.209 1826 -
obs--89.45 %
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)
11.0219-0.0170.16450.9705-0.01231.3765-0.02550.0950.0146-0.04970.0350.0330.07150.0909-0.0095-0.0989-0.0010.0085-0.1127-0.0046-0.06-16.101915.1225-7.469
21.17650.161-0.02361.27920.17582.07030.0079-0.1082-0.02750.1202-0.00640.03590.26550.2537-0.0014-0.05250.04670.0008-0.1080.0007-0.0893-10.4442-13.8672-12.6727
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA0 - 1781 - 179
2X-RAY DIFFRACTION2BB1 - 1782 - 179

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