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- PDB-1z0k: Structure of GTP-Bound Rab4Q67L GTPase in complex with the centra... -

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Basic information

Entry
Database: PDB / ID: 1z0k
TitleStructure of GTP-Bound Rab4Q67L GTPase in complex with the central Rab binding domain of Rabenosyn-5
Components
  • FYVE-finger-containing Rab5 effector protein rabenosyn-5
  • GTP-binding protein
KeywordsPROTEIN TRANSPORT / Rab GTPases / Rab4 / Rabenosyn / effector complex / vesicular trafficking
Function / homology
Function and homology information


Toll Like Receptor 9 (TLR9) Cascade / Golgi to lysosome transport / postsynaptic recycling endosome / regulation of Golgi organization / Rab protein signal transduction / early endosome to Golgi transport / insulin-responsive compartment / RAB geranylgeranylation / MET receptor recycling / TBC/RABGAPs ...Toll Like Receptor 9 (TLR9) Cascade / Golgi to lysosome transport / postsynaptic recycling endosome / regulation of Golgi organization / Rab protein signal transduction / early endosome to Golgi transport / insulin-responsive compartment / RAB geranylgeranylation / MET receptor recycling / TBC/RABGAPs / endosomal transport / Synthesis of PIPs at the plasma membrane / antigen processing and presentation / regulation of endocytosis / vesicle-mediated transport / small monomeric GTPase / Translocation of SLC2A4 (GLUT4) to the plasma membrane / cytoplasmic vesicle membrane / G protein activity / small GTPase binding / recycling endosome membrane / GDP binding / protein transport / Factors involved in megakaryocyte development and platelet production / early endosome membrane / vesicle / endosome membrane / endosome / intracellular membrane-bounded organelle / GTPase activity / GTP binding / perinuclear region of cytoplasm / 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 / Rab4 / Rabenosyn, Rab binding domain / DNA Excision Repair, Uvrb; Chain A / FYVE zinc finger / FYVE zinc finger ...Rabenosyn, Rab binding domain / Rabenosyn, Rab binding domain superfamily / : / Rabenosyn Rab binding domain / Rabosyn-5 repeating NPF sequence-motif / Rab4 / 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. / ARF-like small GTPases; ARF, ADP-ribosylation factor / 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-4A / Rabenosyn-5 / Rabenosyn-5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.92 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_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 1.4Feb 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: GTP-binding protein
B: FYVE-finger-containing Rab5 effector protein rabenosyn-5
C: GTP-binding protein
D: FYVE-finger-containing Rab5 effector protein rabenosyn-5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,5079
Polymers54,2174
Non-polymers1,2905
Water8,233457
1
A: GTP-binding protein
B: FYVE-finger-containing Rab5 effector protein rabenosyn-5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6564
Polymers27,1082
Non-polymers5472
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2720 Å2
ΔGint-21 kcal/mol
Surface area10570 Å2
MethodPISA
2
C: GTP-binding protein
D: FYVE-finger-containing Rab5 effector protein rabenosyn-5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8515
Polymers27,1082
Non-polymers7433
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3010 Å2
ΔGint-22 kcal/mol
Surface area10470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.440, 81.440, 137.639
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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Protein , 2 types, 4 molecules ACBD

#1: Protein GTP-binding protein


Mass: 19392.014 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAB4 / Plasmid: modified pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) Codon Plus-RIL Cells / References: UniProt: P20338
#2: Protein FYVE-finger-containing Rab5 effector protein rabenosyn-5


Mass: 7716.377 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGEX6P1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q59EY8, UniProt: Q9H1K0*PLUS

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Non-polymers , 4 types, 462 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#5: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 457 / 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: 2.58 Å3/Da / Density % sol: 51.91 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 20% PEG 4000, 200mM ammonium fluoride, 50mM MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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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: May 11, 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: 1.9→50 Å / Num. obs: 42193 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 41.7 Å2 / Rsym value: 0.054 / Net I/σ(I): 27.29
Reflection shellResolution: 1.9→1.96 Å / Redundancy: 5 % / Mean I/σ(I) obs: 4 / Num. unique all: 3439 / Rsym value: 0.379 / % possible all: 98.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Rab4 GTPase

Resolution: 1.92→15 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.934 / SU B: 4.5 / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.188 / ESU R Free: 0.165 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25889 2072 5.1 %RANDOM
Rwork0.22356 ---
all0.24 42214 --
obs0.22538 38744 99.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.045 Å2
Baniso -1Baniso -2Baniso -3
1-1.2 Å20.6 Å20 Å2
2--1.2 Å20 Å2
3----1.8 Å2
Refinement stepCycle: LAST / Resolution: 1.92→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3573 0 78 457 4108
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0223708
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3021.975023
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3415455
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.91824.833180
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.88615622
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7571522
X-RAY DIFFRACTIONr_chiral_restr0.1140.2560
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022780
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1920.21891
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2970.22570
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.2487
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1260.22
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1860.248
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1480.241
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6261.52340
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.05323592
X-RAY DIFFRACTIONr_scbond_it1.24331590
X-RAY DIFFRACTIONr_scangle_it1.9534.51431
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.92→1.969 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 144 -
Rwork0.288 2770 -
obs--99.01 %

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