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- PDB-1z08: GppNHp-Bound Rab21 Q53G mutant GTPase -

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Basic information

Entry
Database: PDB / ID: 1z08
TitleGppNHp-Bound Rab21 Q53G mutant GTPase
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: 1.8 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
DepositionMar 1, 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 1.3Oct 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_asym_id / _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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_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_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
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: Ras-related protein Rab-21
B: Ras-related protein Rab-21
C: Ras-related protein Rab-21
D: Ras-related protein Rab-21
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,34016
Polymers77,0574
Non-polymers2,28312
Water18,1051005
1
A: Ras-related protein Rab-21
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,8113
Polymers19,2641
Non-polymers5472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Ras-related protein Rab-21
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,8113
Polymers19,2641
Non-polymers5472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Ras-related protein Rab-21
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,8354
Polymers19,2641
Non-polymers5713
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Ras-related protein Rab-21
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,8846
Polymers19,2641
Non-polymers6195
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
D: Ras-related protein Rab-21
hetero molecules

C: Ras-related protein Rab-21
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,71810
Polymers38,5282
Non-polymers1,1908
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area3740 Å2
ΔGint-60 kcal/mol
Surface area15090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.200, 77.425, 107.965
Angle α, β, γ (deg.)90.00, 89.86, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Ras-related protein Rab-21


Mass: 19264.133 Da / Num. of mol.: 4 / Fragment: GTPase domain / Mutation: Q53G
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.: 8 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 4 / 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.: 1005 / 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: 2.67 Å3/Da / Density % sol: 53.51 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20% PEG 4000, 200mM Magnesium acetate, 50mM HEPES, pH 7.0, 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: Dec 31, 2003 / Details: Osmic mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 68656 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2 % / Biso Wilson estimate: 26.5 Å2 / Rsym value: 0.064 / Net I/σ(I): 14.4
Reflection shellResolution: 1.8→1.85 Å / Redundancy: 3 % / Mean I/σ(I) obs: 3.4 / Num. unique all: 5610 / Rsym value: 0.311 / % possible all: 97.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Polyalanine Rab3A GTPase

Resolution: 1.8→8 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.93 / SU B: 2.446 / SU ML: 0.078 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.135 / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22512 3448 5.1 %RANDOM
Rwork0.18837 ---
all0.195 68520 --
obs0.1902 64433 97.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.077 Å2
Baniso -1Baniso -2Baniso -3
1-0.34 Å20 Å2-0.59 Å2
2---0.29 Å20 Å2
3----0.05 Å2
Refinement stepCycle: LAST / Resolution: 1.8→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4969 0 136 1005 6110
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0225180
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0261.987019
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9765645
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.29324.67212
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.24515887
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.3621521
X-RAY DIFFRACTIONr_chiral_restr0.0640.2801
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023749
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1740.22517
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2940.23453
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0960.2914
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0560.214
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1460.2118
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0970.2152
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4141.53317
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.74125077
X-RAY DIFFRACTIONr_scbond_it0.88732197
X-RAY DIFFRACTIONr_scangle_it1.4144.51942
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.796→1.84 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 208 -
Rwork0.245 4276 -
obs--91.25 %

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