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- PDB-6hxu: Crystal structure of Human RHOB Q63L in complex with GTP -

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Basic information

Entry
Database: PDB / ID: 6hxu
TitleCrystal structure of Human RHOB Q63L in complex with GTP
ComponentsRho-related GTP-binding protein RhoB
KeywordsIMMUNE SYSTEM / GTPase / RHO / antibody / complex
Function / homology
Function and homology information


RHO GTPases Activate Rhotekin and Rhophilins / endothelial tube morphogenesis / regulation of modification of postsynaptic structure / RHO GTPases Activate ROCKs / RHO GTPases activate CIT / Sema4D induced cell migration and growth-cone collapse / RHOB GTPase cycle / endosome to lysosome transport / cleavage furrow / mitotic cytokinesis ...RHO GTPases Activate Rhotekin and Rhophilins / endothelial tube morphogenesis / regulation of modification of postsynaptic structure / RHO GTPases Activate ROCKs / RHO GTPases activate CIT / Sema4D induced cell migration and growth-cone collapse / RHOB GTPase cycle / endosome to lysosome transport / cleavage furrow / mitotic cytokinesis / Rho protein signal transduction / negative regulation of cell cycle / regulation of cell migration / RHO GTPases activate PKNs / GPVI-mediated activation cascade / negative regulation of cell migration / positive regulation of endothelial cell migration / actin filament organization / RHO GTPases Activate Formins / cellular response to ionizing radiation / intracellular protein transport / Schaffer collateral - CA1 synapse / cellular response to hydrogen peroxide / GDP binding / positive regulation of angiogenesis / G alpha (12/13) signalling events / late endosome membrane / angiogenesis / cell differentiation / early endosome / endosome membrane / cell adhesion / positive regulation of apoptotic process / focal adhesion / GTPase activity / apoptotic process / GTP binding / signal transduction / extracellular exosome / nucleus / 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'-TRIPHOSPHATE / Rho-related GTP-binding protein RhoB
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.19 Å
AuthorsSoulie, S. / Gence, R. / Cabantous, S. / Lajoie-Mazenc, I. / Favre, G. / Pedelacq, J.D.
CitationJournal: Cell Chem Biol / Year: 2019
Title: A Targeted Protein Degradation Cell-Based Screening for Nanobodies Selective toward the Cellular RHOB GTP-Bound Conformation.
Authors: Bery, N. / Keller, L. / Soulie, M. / Gence, R. / Iscache, A.L. / Cherier, J. / Cabantous, S. / Sordet, O. / Lajoie-Mazenc, I. / Pedelacq, J.D. / Favre, G. / Olichon, A.
History
DepositionOct 18, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 25, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2019Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.2Jan 24, 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_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
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.ptnr2_symmetry / _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_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Rho-related GTP-binding protein RhoB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,3874
Polymers20,8151
Non-polymers5723
Water5,278293
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1080 Å2
ΔGint-19 kcal/mol
Surface area9320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.890, 61.460, 76.690
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)

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Components

#1: Protein Rho-related GTP-binding protein RhoB / Rho cDNA clone 6 / h6


Mass: 20814.850 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RHOB, ARH6, ARHB / Production host: Escherichia coli (E. coli) / References: UniProt: P62745
#2: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine triphosphate


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: GTP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 293 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.22 Å3/Da / Density % sol: 44.48 %
Crystal growTemperature: 285 K / Method: vapor diffusion, sitting drop / Details: 100 mM MES pH6 30% v/w PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.969 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 21, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.969 Å / Relative weight: 1
ReflectionResolution: 1.19→47.96 Å / Num. obs: 58942 / % possible obs: 99 % / Redundancy: 2 % / CC1/2: 0.999 / Net I/σ(I): 20
Reflection shellResolution: 1.19→1.23 Å / Num. unique obs: 5349 / CC1/2: 0.966

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2FV8

2fv8


Resolution: 1.19→34.69 Å / Cross valid method: FREE R-VALUE /
Num. reflection% reflection
obs58942 98.65 %
Refinement stepCycle: LAST / Resolution: 1.19→34.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1450 0 34 293 1777

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