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- PDB-1yzt: GppNHp-Bound Rab21 GTPase at 2.05 A Resolution -

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Basic information

Entry
Database: PDB / ID: 1yzt
TitleGppNHp-Bound Rab21 GTPase at 2.05 A Resolution
ComponentsRas-related protein Rab-21
KeywordsPROTEIN TRANSPORT / Rab GTPase / Rab21 / Vesicular Trafficking
Function / homology
Function and homology information


cytoplasmic side of early endosome membrane / Rab protein signal transduction / positive regulation of early endosome to late endosome transport / regulation of exocytosis / RAB geranylgeranylation / positive regulation of dendrite morphogenesis / anterograde axonal transport / RAB GEFs exchange GTP for GDP on RABs / vesicle membrane / regulation of axon extension ...cytoplasmic side of early endosome membrane / Rab protein signal transduction / positive regulation of early endosome to late endosome transport / regulation of exocytosis / RAB geranylgeranylation / positive regulation of dendrite morphogenesis / anterograde axonal transport / RAB GEFs exchange GTP for GDP on RABs / vesicle membrane / regulation of axon extension / Golgi cisterna membrane / cleavage furrow / endomembrane system / axon cytoplasm / small monomeric GTPase / intracellular protein transport / trans-Golgi network / positive regulation of receptor-mediated endocytosis / cytoplasmic side of plasma membrane / GDP binding / early endosome membrane / early endosome / endosome / protein stabilization / Golgi membrane / focal adhesion / GTPase activity / synapse / endoplasmic reticulum membrane / GTP binding / extracellular exosome / cytosol
Similarity search - Function
Rab21 / Small GTPase Rab domain profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / 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 ...Rab21 / Small GTPase Rab domain profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / 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 / Ras-related protein Rab-21
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsEathiraj, S. / Pan, X. / Ritacco, C. / Lambright, D.G.
CitationJournal: Nature / Year: 2005
Title: Structural basis of family-wide Rab GTPase recognition by rabenosyn-5.
Authors: Eathiraj, S. / Pan, X. / Ritacco, C. / Lambright, D.G.
History
DepositionFeb 28, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 26, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ras-related protein Rab-21
B: Ras-related protein Rab-21
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,0196
Polymers41,9262
Non-polymers1,0934
Water8,557475
1
A: Ras-related protein Rab-21
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,5103
Polymers20,9631
Non-polymers5472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ras-related protein Rab-21
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,5103
Polymers20,9631
Non-polymers5472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)130.357, 36.567, 86.666
Angle α, β, γ (deg.)90.00, 113.40, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Ras-related protein Rab-21


Mass: 20963.070 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAB21, KIAA0118 / Plasmid: pGEX4T1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) Codon Plus-RIL Cells / References: UniProt: Q9UL25
#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.: 475 / 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: 2.75 Å3/Da / Density % sol: 54.98 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 18% PEG 6000, 200mM Lithium sufate, 50mM Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Apr 14, 2004 / Details: Osmic mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 23946 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 35.1 Å2 / Rsym value: 0.08 / Net I/σ(I): 15.8
Reflection shellResolution: 2.05→2.11 Å / Redundancy: 4 % / Mean I/σ(I) obs: 3.8 / Num. unique all: 1952 / Rsym value: 0.368 / % possible all: 98.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Polyalanine Rab3a GTPase

Resolution: 2.05→12 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.873 / SU B: 6.231 / SU ML: 0.168 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.228 / ESU R Free: 0.215 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28586 1219 5.1 %RANDOM
Rwork0.21041 ---
all0.232 24116 --
obs0.21425 22613 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 23.139 Å2
Baniso -1Baniso -2Baniso -3
1--0.84 Å20 Å2-0.9 Å2
2--0.66 Å20 Å2
3----0.54 Å2
Refinement stepCycle: LAST / Resolution: 2.05→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2395 0 66 475 2936
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222493
X-RAY DIFFRACTIONr_bond_other_d0.0060.022255
X-RAY DIFFRACTIONr_angle_refined_deg1.261.9873371
X-RAY DIFFRACTIONr_angle_other_deg0.75535253
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1375305
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.77225104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.69115450
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9421510
X-RAY DIFFRACTIONr_chiral_restr0.0690.2386
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022699
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02471
X-RAY DIFFRACTIONr_nbd_refined0.2090.2561
X-RAY DIFFRACTIONr_nbd_other0.1960.22271
X-RAY DIFFRACTIONr_nbtor_refined0.1750.21161
X-RAY DIFFRACTIONr_nbtor_other0.0820.21321
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2110.2402
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0420.21
X-RAY DIFFRACTIONr_metal_ion_refined0.0420.22
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1540.218
X-RAY DIFFRACTIONr_symmetry_vdw_other0.180.248
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.20.242
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1051.51997
X-RAY DIFFRACTIONr_mcbond_other0.1051.5643
X-RAY DIFFRACTIONr_mcangle_it1.02822423
X-RAY DIFFRACTIONr_scbond_it1.831166
X-RAY DIFFRACTIONr_scangle_it2.434.5948
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.05→2.102 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 100 -
Rwork0.255 1581 -
obs--99.7 %

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