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- PDB-2atx: Crystal Structure of the TC10 GppNHp complex -

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Basic information

Entry
Database: PDB / ID: 2atx
TitleCrystal Structure of the TC10 GppNHp complex
Componentssmall GTP binding protein TC10
KeywordsHYDROLASE / TC10 / GTPase / P-loop / alpha-beta
Function / homology
Function and homology information


GBD domain binding / RHO GTPases regulate CFTR trafficking / profilin binding / Golgi-associated vesicle membrane / GTP metabolic process / positive regulation of filopodium assembly / cortical actin cytoskeleton organization / small GTPase-mediated signal transduction / establishment or maintenance of cell polarity / RHOQ GTPase cycle ...GBD domain binding / RHO GTPases regulate CFTR trafficking / profilin binding / Golgi-associated vesicle membrane / GTP metabolic process / positive regulation of filopodium assembly / cortical actin cytoskeleton organization / small GTPase-mediated signal transduction / establishment or maintenance of cell polarity / RHOQ GTPase cycle / negative regulation of protein localization to plasma membrane / actin filament organization / Translocation of SLC2A4 (GLUT4) to the plasma membrane / positive regulation of D-glucose import / actin filament / regulation of actin cytoskeleton organization / cellular response to insulin stimulus / endocytosis / insulin receptor signaling pathway / regulation of cell shape / membrane raft / GTPase activity / GTP binding / protein kinase binding / signal transduction / positive regulation of transcription by RNA polymerase II / extracellular exosome / plasma membrane
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 / Rossmann fold ...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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Rho-related GTP-binding protein RhoQ
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsHemsath, L. / Dvorsky, R. / Fiegen, D. / Carlier, M.F. / Ahmadian, M.R.
CitationJournal: Mol.Cell / Year: 2005
Title: An electrostatic steering mechanism of Cdc42 recognition by Wiskott-Aldrich syndrome proteins
Authors: Hemsath, L. / Dvorsky, R. / Fiegen, D. / Carlier, M.F. / Ahmadian, M.R.
History
DepositionAug 26, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 13, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Mar 13, 2024Group: 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_struct_conn_angle / struct_conn / struct_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_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 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: small GTP binding protein TC10
B: small GTP binding protein TC10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,3966
Polymers42,3032
Non-polymers1,0934
Water23413
1
A: small GTP binding protein TC10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6983
Polymers21,1511
Non-polymers5472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: small GTP binding protein TC10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6983
Polymers21,1511
Non-polymers5472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4360 Å2
ΔGint-49 kcal/mol
Surface area18350 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)43.690, 82.200, 114.310
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
51A
61B

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALAASPASP4AA10 - 13511 - 136
21ALAALAASPASP4BB10 - 13511 - 136
32ASPASPPROPRO6AA136 - 150137 - 151
42ASPASPPROPRO6BB136 - 150137 - 151
53ILEILEPROPRO4AA151 - 193152 - 194
63ILEILEPROPRO4BB151 - 193152 - 194

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Components

#1: Protein small GTP binding protein TC10 / Ras-related GTP-binding protein TC10


Mass: 21151.344 Da / Num. of mol.: 2 / Fragment: TC10 (0-193)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TC10 / Plasmid: pGEX4T / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P17081, small monomeric GTPase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 2.6 Å3/Da / Density % sol: 51.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: MES, PEG 3350, NaCl, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 26, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.65→20 Å / Num. all: 12449 / Num. obs: 12449 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.7 % / Biso Wilson estimate: 58 Å2 / Rsym value: 0.047 / Net I/σ(I): 23.34
Reflection shellResolution: 2.65→2.7 Å / Mean I/σ(I) obs: 5.95 / Rsym value: 0.317 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
ProDCdata collection
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: TC10 GDP (unpublished)

Resolution: 2.65→19.84 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.914 / SU B: 13.468 / SU ML: 0.282 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 3.309 / ESU R Free: 0.349 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25994 623 5 %RANDOM
Rwork0.21013 ---
all0.2127 11826 --
obs0.21279 11826 100 %-
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: 32.466 Å2
Baniso -1Baniso -2Baniso -3
1-2.81 Å20 Å20 Å2
2---1.79 Å20 Å2
3----1.01 Å2
Refinement stepCycle: LAST / Resolution: 2.65→19.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2856 0 66 13 2935
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0222984
X-RAY DIFFRACTIONr_bond_other_d0.0020.022682
X-RAY DIFFRACTIONr_angle_refined_deg1.7552.014070
X-RAY DIFFRACTIONr_angle_other_deg0.95136276
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5185370
X-RAY DIFFRACTIONr_chiral_restr0.0960.2462
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023258
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02540
X-RAY DIFFRACTIONr_nbd_refined0.2230.2598
X-RAY DIFFRACTIONr_nbd_other0.2270.22925
X-RAY DIFFRACTIONr_nbtor_other0.0910.21720
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.255
X-RAY DIFFRACTIONr_metal_ion_refined0.0840.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2270.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2510.256
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1580.22
X-RAY DIFFRACTIONr_mcbond_it0.6491.51854
X-RAY DIFFRACTIONr_mcangle_it1.18522990
X-RAY DIFFRACTIONr_scbond_it1.61631130
X-RAY DIFFRACTIONr_scangle_it2.5414.51080
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
2538medium positional0.330.5
238loose positional15
2538medium thermal0.552
238loose thermal3.7510
LS refinement shellResolution: 2.65→2.718 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.348 46
Rwork0.28 866
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)
13.7993-3.2995-0.137.08610.15832.126-0.5598-0.3895-0.06861.28480.51180.4718-0.2448-0.1040.0480.24520.05170.12520.29150.05260.066412.6718.88642.433
22.4153-1.1880.230310.55470.36752.34220.1025-0.1581-0.3341.56140.2543-0.12460.3155-0.0101-0.35680.1524-0.0715-0.05780.22980.07010.093130.051-20.39343.234
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA8 - 1939 - 194
2X-RAY DIFFRACTION2BB8 - 1939 - 194

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