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- PDB-1yu9: GppNHp-Bound Rab4A -

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Basic information

Entry
Database: PDB / ID: 1yu9
TitleGppNHp-Bound Rab4A
ComponentsGTP-binding protein
KeywordsPROTEIN TRANSPORT / Rab GTPase / Rab4 / vesicular trafficking
Function / homology
Function and homology information


neurotransmitter receptor transport postsynaptic membrane to endosome / Rab protein signal transduction / insulin-responsive compartment / vesicle-mediated transport in synapse / RAB geranylgeranylation / MET receptor recycling / TBC/RABGAPs / antigen processing and presentation / Synthesis of PIPs at the plasma membrane / regulation of endocytosis ...neurotransmitter receptor transport postsynaptic membrane to endosome / Rab protein signal transduction / insulin-responsive compartment / vesicle-mediated transport in synapse / RAB geranylgeranylation / MET receptor recycling / TBC/RABGAPs / antigen processing and presentation / Synthesis of PIPs at the plasma membrane / regulation of endocytosis / vesicle-mediated transport / cytoplasmic vesicle membrane / small monomeric GTPase / Translocation of SLC2A4 (GLUT4) to the plasma membrane / recycling endosome / recycling endosome membrane / GDP binding / protein transport / G protein activity / early endosome membrane / vesicle / GTPase activity / GTP binding / perinuclear region of cytoplasm / glutamatergic synapse / extracellular exosome
Similarity search - Function
Rab4 / : / ARF-like small GTPases; ARF, ADP-ribosylation factor / 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 ...Rab4 / : / ARF-like small GTPases; ARF, ADP-ribosylation factor / 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-4A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.07 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 13, 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: Derived calculations / 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

Downloads & links

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Assembly

Deposited unit
A: GTP-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4135
Polymers19,6741
Non-polymers7394
Water4,270237
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
A: GTP-binding protein
hetero molecules

A: GTP-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,82610
Polymers39,3492
Non-polymers1,4778
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area4020 Å2
ΔGint-87 kcal/mol
Surface area16400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.808, 68.808, 90.920
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein GTP-binding protein


Mass: 19674.312 Da / Num. of mol.: 1 / Fragment: GTPase domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: Rab4a / Plasmid: PGEX-6P1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) Codon Plus-RIL cells / References: UniProt: P20338
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 237 / 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: 2.69 Å3/Da / Density % sol: 54 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: Ammonium sulfate, MES, Glycerol, pH 6.0, 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: Nov 23, 2002
RadiationMonochromator: confocal blue optic device / Protocol: 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: 13803 / % possible obs: 98.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4 % / Rsym value: 0.078 / Net I/σ(I): 15.1
Reflection shellResolution: 2.05→2.11 Å / Redundancy: 4 % / Mean I/σ(I) obs: 4.1 / Num. unique all: 2011 / Rsym value: 0.282 / % possible all: 98.9

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMAC5.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Rab3a polyalanine

Resolution: 2.07→7 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19547 665 -Random
Rwork0.15631 ---
all0.179 25209 --
obs0.1582 12656 98.58 %-
Displacement parametersBiso mean: 16.527 Å2
Baniso -1Baniso -2Baniso -3
1-0.15 Å20 Å20 Å2
2--0.15 Å20 Å2
3----0.3 Å2
Refinement stepCycle: LAST / Resolution: 2.07→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1384 0 43 237 1664
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.008
X-RAY DIFFRACTIONr_bond_other_d0.001
X-RAY DIFFRACTIONr_angle_refined_deg1.222
X-RAY DIFFRACTIONr_angle_other_deg0.795
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.016
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.178
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.098
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.99
X-RAY DIFFRACTIONr_chiral_restr0.071
X-RAY DIFFRACTIONr_gen_planes_refined0.004
X-RAY DIFFRACTIONr_gen_planes_other0.001
X-RAY DIFFRACTIONr_nbd_refined0.204
X-RAY DIFFRACTIONr_nbd_other0.182
X-RAY DIFFRACTIONr_nbtor_refined0.176
X-RAY DIFFRACTIONr_nbtor_other0.081
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.157
X-RAY DIFFRACTIONr_metal_ion_refined0.037
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.136
X-RAY DIFFRACTIONr_symmetry_vdw_other0.186
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.176
X-RAY DIFFRACTIONr_mcbond_it0.876
X-RAY DIFFRACTIONr_mcbond_other0.115
X-RAY DIFFRACTIONr_mcangle_it0.963
X-RAY DIFFRACTIONr_scbond_it1.543
X-RAY DIFFRACTIONr_scangle_it2.425
LS refinement shellResolution: 2.067→2.116 Å
RfactorNum. reflection% reflection
Rfree0.225 52 -
Rwork0.172 --
obs-12780 91.16 %

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