[English] 日本語
Yorodumi
- PDB-2atx: Crystal Structure of the TC10 GppNHp complex -

+
Open data


ID or keywords:

Loading...

-
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 / cortical actin cytoskeleton organization / positive regulation of filopodium assembly / small GTPase-mediated signal transduction / establishment of cell polarity / RHOQ GTPase cycle ...GBD domain binding / RHO GTPases regulate CFTR trafficking / profilin binding / Golgi-associated vesicle membrane / GTP metabolic process / cortical actin cytoskeleton organization / positive regulation of filopodium assembly / small GTPase-mediated signal transduction / establishment of cell polarity / RHOQ GTPase cycle / negative regulation of protein localization to plasma membrane / actin filament organization / positive regulation of D-glucose import / regulation of actin cytoskeleton organization / Translocation of SLC2A4 (GLUT4) to the plasma membrane / actin filament / endocytosis / cellular response to insulin stimulus / insulin receptor signaling pathway / regulation of cell shape / membrane raft / GTPase activity / protein kinase binding / GTP binding / signal transduction / positive regulation of transcription by RNA polymerase II / extracellular exosome / plasma membrane
Similarity search - Function
Small GTPase Rho / Small GTPase Rho domain 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 domain 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
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://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