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- PDB-2bmd: high resolution structure of GDP-bound human Rab4a -

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Basic information

Entry
Database: PDB / ID: 2bmd
Titlehigh resolution structure of GDP-bound human Rab4a
ComponentsRAS-RELATED PROTEIN RAB4A
KeywordsPROTEIN TRANSPORT / GTP-BINDING PROTEIN / VESICULAR TRANSPORT / ENDOCYTOSIS / PRENYLATION / TRANSPORT
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 Rab1 family 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 Rab1 family 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
GUANOSINE-5'-DIPHOSPHATE / Ras-related protein Rab-4A
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsScheidig, A.J. / Huber, S.K.
CitationJournal: FEBS Lett. / Year: 2005
Title: High Resolution Crystal Structures of Human Rab4A in its Active and Inactive Conformations.
Authors: Huber, S.K. / Scheidig, A.J.
History
DepositionMar 13, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 25, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.4May 22, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.5May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RAS-RELATED PROTEIN RAB4A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6184
Polymers20,9911
Non-polymers6273
Water3,747208
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)71.140, 63.750, 38.280
Angle α, β, γ (deg.)90.00, 100.03, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein RAS-RELATED PROTEIN RAB4A / RAB4A


Mass: 20990.775 Da / Num. of mol.: 1 / Fragment: NUCLEOTIDE-BINDING DOMAIN, RESIDUES 1-184
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET19TEV / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P20338, small monomeric GTPase
#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 208 / 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: 1.79 Å3/Da / Density % sol: 30.68 %
Description: PARTIALLY REFINED GPPNHP-BOUND RAB4A STRUCTURE WAS USED FOR MOLECULAR REPLACEMENT, SOLVED BY SAME AUTHORS
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 30% (W/V) PEG 8000, 200MM AMMONIUM SULPHATE, 100MM SODIUM CACODYLATE PH6.5 HANGING DROP 20 DEGREE CELSIUS

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 1.0721
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 3, 2003 / Details: MIRROR
RadiationMonochromator: MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0721 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. obs: 15669 / % possible obs: 99.8 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 14.44
Reflection shellResolution: 1.8→1.86 Å / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 7.5 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.1.19refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→18.29 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.933 / SU B: 2.388 / SU ML: 0.076 / Cross valid method: THROUGHOUT / ESU R: 0.13 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DISORDERED REGIONS WERE MODELED STEREOCHEMICALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.205 783 5 %RANDOM
Rwork0.16 ---
obs0.162 14883 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 10.48 Å2
Baniso -1Baniso -2Baniso -3
1-1.09 Å20 Å20.72 Å2
2---0.56 Å20 Å2
3----0.29 Å2
Refinement stepCycle: LAST / Resolution: 1.8→18.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1367 0 40 208 1615
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0211446
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4851.9781947
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4025171
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1060.2214
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021065
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2210.2751
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.170.2179
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2350.261
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1950.218
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7171.5851
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.36821363
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.2043595
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.6374.5584
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.85 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.266 58
Rwork0.186 1104
Refinement TLS params.Method: refined / Origin x: 16.0847 Å / Origin y: 0.8627 Å / Origin z: 10.4003 Å
111213212223313233
T0.0104 Å20.0069 Å2-0.0029 Å2-0.0072 Å2-0.0012 Å2--0.001 Å2
L2.0117 °20.61 °2-0.563 °2-1.5674 °20.0144 °2--1.7407 °2
S-0.0405 Å °0.1609 Å °0.0171 Å °-0.1605 Å °0.0741 Å °-0.1219 Å °-0.0467 Å °0.0904 Å °-0.0336 Å °

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