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- PDB-1z0j: Structure of GTP-Bound Rab22Q64L GTPase in complex with the minim... -

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Basic information

Entry
Database: PDB / ID: 1z0j
TitleStructure of GTP-Bound Rab22Q64L GTPase in complex with the minimal Rab binding domain of Rabenosyn-5
Components
  • FYVE-finger-containing Rab5 effector protein rabenosyn-5
  • Ras-related protein Rab-22A
KeywordsPROTEIN TRANSPORT / Rab Effector / Rab GTPase / Rab22 GTPase / Rabenosyn / Endosomal trafficking
Function / homology
Function and homology information


RAB geranylgeranylation / Toll Like Receptor 9 (TLR9) Cascade / Golgi to lysosome transport / regulation of Golgi organization / early endosome to Golgi transport / regulation of vesicle size / endosome organization / endosomal transport / endomembrane system / phagocytic vesicle ...RAB geranylgeranylation / Toll Like Receptor 9 (TLR9) Cascade / Golgi to lysosome transport / regulation of Golgi organization / early endosome to Golgi transport / regulation of vesicle size / endosome organization / endosomal transport / endomembrane system / phagocytic vesicle / ruffle / intracellular protein transport / small GTPase binding / endocytosis / phagocytic vesicle membrane / GDP binding / late endosome / protein transport / actin cytoskeleton / Factors involved in megakaryocyte development and platelet production / early endosome membrane / early endosome / endosome membrane / endosome / intracellular membrane-bounded organelle / GTPase activity / GTP binding / extracellular exosome / zinc ion binding / plasma membrane / cytosol
Similarity search - Function
Rabenosyn, Rab binding domain / Rabenosyn, Rab binding domain superfamily / : / Rabenosyn Rab binding domain / Rabosyn-5 repeating NPF sequence-motif / Rabenosyn, Rab binding domain / DNA Excision Repair, Uvrb; Chain A / FYVE zinc finger / FYVE zinc finger / Protein present in Fab1, YOTB, Vac1, and EEA1 ...Rabenosyn, Rab binding domain / Rabenosyn, Rab binding domain superfamily / : / Rabenosyn Rab binding domain / Rabosyn-5 repeating NPF sequence-motif / Rabenosyn, Rab binding domain / DNA Excision Repair, Uvrb; Chain A / FYVE zinc finger / FYVE zinc finger / Protein present in Fab1, YOTB, Vac1, and EEA1 / : / Zinc finger, FYVE-related / Zinc finger FYVE/FYVE-related type profile. / small GTPase Rab1 family profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Zinc finger, FYVE/PHD-type / Few Secondary Structures / Irregular / Small GTP-binding protein domain / Zinc finger, RING/FYVE/PHD-type / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / : / Ras-related protein Rab-22A / Rabenosyn-5
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.32 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: Non-polymer description / 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_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.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.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 1.4Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Remark 999SEQUENCE CONSTRUCT USED FOR THE CRYSTALLIZATION CONTAINS PCR INDUCED V22M MUTATION

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ras-related protein Rab-22A
B: FYVE-finger-containing Rab5 effector protein rabenosyn-5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6206
Polymers25,8582
Non-polymers7624
Water5,423301
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2790 Å2
ΔGint-19 kcal/mol
Surface area10650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.075, 55.897, 85.960
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Ras-related protein Rab-22A / Rab-22


Mass: 19182.889 Da / Num. of mol.: 1 / Mutation: V22M,Q64L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Rab22a, Rab22 / Plasmid: modified pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) Codon Plus-RIL Cells / References: UniProt: P35285
#2: Protein FYVE-finger-containing Rab5 effector protein rabenosyn-5


Mass: 6675.441 Da / Num. of mol.: 1 / Fragment: minimal Rab binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: modified pET15b / Production host: Escherichia coli (E. coli) / References: GenBank: 11641241, UniProt: Q9H1K0*PLUS

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Non-polymers , 5 types, 305 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#5: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 301 / 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: 2.19 Å3/Da / Density % sol: 43.39 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 10% PEG 6000, 50mM Na acetate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 25, 2004
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.3→50 Å / Num. obs: 46168 / % possible obs: 85.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10 % / Biso Wilson estimate: 21.5 Å2 / Rsym value: 0.038 / Net I/σ(I): 54.1
Reflection shellResolution: 1.3→1.34 Å / Redundancy: 10 % / Mean I/σ(I) obs: 3.8 / Num. unique all: 2217 / Rsym value: 0.381 / % possible all: 49.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Rab22 GTPase

Resolution: 1.32→15 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.927 / SU B: 0.803 / SU ML: 0.035 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.072 / ESU R Free: 0.073 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23481 2264 5 %RANDOM
Rwork0.21436 ---
all0.206 46206 --
obs0.21536 42797 87.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.034 Å2
Baniso -1Baniso -2Baniso -3
1--0.2 Å20 Å20 Å2
2--0.3 Å20 Å2
3----0.1 Å2
Refinement stepCycle: LAST / Resolution: 1.32→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1716 0 47 301 2064
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0221793
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.191.9872432
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4145218
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.38924.23178
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.25715310
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.0941512
X-RAY DIFFRACTIONr_chiral_restr0.0750.2278
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021310
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1930.2849
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3020.21231
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1220.2265
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1940.260
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1320.253
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.32→1.354 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.574 108 -
Rwork0.515 2021 -
obs--56.77 %

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