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- PDB-2bme: high resolution structure of GppNHp-bound human Rab4a -

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Basic information

Entry
Database: PDB / ID: 2bme
Titlehigh resolution structure of GppNHp-bound human Rab4a
ComponentsRAS-RELATED PROTEIN RAB4A
KeywordsPROTEIN TRANSPORT / GTP-BINDING PROTEIN / VESICULAR TRANSPORT / ENDOCYTOSIS / PRENYLATION / TRANSPORT
Function / homology
Function and homology information


Rab protein signal transduction / postsynaptic recycling endosome / insulin-responsive compartment / RAB geranylgeranylation / MET receptor recycling / TBC/RABGAPs / Synthesis of PIPs at the plasma membrane / regulation of endocytosis / antigen processing and presentation / vesicle-mediated transport ...Rab protein signal transduction / postsynaptic recycling endosome / insulin-responsive compartment / RAB geranylgeranylation / MET receptor recycling / TBC/RABGAPs / Synthesis of PIPs at the plasma membrane / regulation of endocytosis / antigen processing and presentation / vesicle-mediated transport / small monomeric GTPase / G protein activity / Translocation of SLC2A4 (GLUT4) to the plasma membrane / cytoplasmic vesicle membrane / recycling endosome membrane / GDP binding / protein transport / early endosome membrane / vesicle / GTPase activity / GTP binding / perinuclear region of cytoplasm / 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 / Small GTP-binding protein domain ...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 / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Ras-related protein Rab-4A
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 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: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_biol
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RAS-RELATED PROTEIN RAB4A
B: RAS-RELATED PROTEIN RAB4A
C: RAS-RELATED PROTEIN RAB4A
D: RAS-RELATED PROTEIN RAB4A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,79418
Polymers83,9634
Non-polymers2,83114
Water12,322684
1
A: RAS-RELATED PROTEIN RAB4A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8606
Polymers20,9911
Non-polymers8695
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: RAS-RELATED PROTEIN RAB4A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,5373
Polymers20,9911
Non-polymers5472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: RAS-RELATED PROTEIN RAB4A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7385
Polymers20,9911
Non-polymers7474
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
D: RAS-RELATED PROTEIN RAB4A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6594
Polymers20,9911
Non-polymers6693
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)99.790, 99.790, 95.540
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
RAS-RELATED PROTEIN RAB4A / RAB4A


Mass: 20990.775 Da / Num. of mol.: 4 / 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

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Non-polymers , 5 types, 698 molecules

#2: Chemical
ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / 5'-Guanylyl imidodiphosphate


Mass: 522.196 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#3: Chemical
ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL / 2-Mercaptoethanol


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 684 / 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: 2.65 Å3/Da / Density % sol: 53.24 %
Description: USED MODEL WITHOUT NUCLEOTIDE, MAGNESIUM AND WATER
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 8% (W/V) PEG 4000, 100MM SODIUM ACETATE PH 4.0 HANGING DROP 25 DEGREE CELSIUS

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 1.008
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 23, 2002 / Details: MIRROR
RadiationMonochromator: MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.008 Å / Relative weight: 1
ReflectionResolution: 1.6→20 Å / Num. obs: 128819 / % possible obs: 99.5 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 20.9
Reflection shellResolution: 1.6→1.75 Å / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 6.7 / % possible all: 97.4

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Processing

Software
NameVersionClassification
REFMAC5.1.19refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HUQ

1huq


Resolution: 1.57→19.54 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.93 / SU B: 1.634 / SU ML: 0.06 / Cross valid method: THROUGHOUT / ESU R: 0.078 / ESU R Free: 0.083 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DISORDERED REGIONS WERE MODELED STEREOCHEMICALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.229 6441 5 %RANDOM
Rwork0.192 ---
obs0.194 122377 100 %-
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: 15.9 Å2
Baniso -1Baniso -2Baniso -3
1-0.45 Å20 Å20 Å2
2--0.45 Å20 Å2
3----0.89 Å2
Refinement stepCycle: LAST / Resolution: 1.57→19.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5532 0 172 684 6388
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0215726
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8211.9787728
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0385678
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_restr0.1240.2861
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024180
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.210.22504
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1490.2445
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2420.295
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1480.243
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0221.53390
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.65825426
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.70932336
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.2054.52302
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: 1.56→1.61 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.269 377
Rwork0.228 7178
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.16630.12160.03241.6168-0.34982.6802-0.03460.00890.0278-0.05350.010.0007-0.15290.0330.02460.0420.0045-0.0220.06680.02160.0565.65382.27420.354
21.5719-0.0573-0.01081.60370.63791.90270.00740.0711-0.0507-0.0298-0.0280.0523-0.02850.00290.02060.0206-0.0109-0.01240.0224-0.01720.041484.1533.17328.5431
31.559-0.10450.50681.61770.02642.19960.0075-0.08070.10350.10530.0182-0.10750.00710.1271-0.02570.0211-0.0127-0.01230.059-0.0090.068946.807614.5741-22.3992
42.2890.5663-1.33871.5725-0.28473.4396-0.07180.0212-0.1851-0.05440.0367-0.12120.16570.06820.03510.10010.0181-0.00540.0549-0.01610.092944.661935.0966.437
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 179
2X-RAY DIFFRACTION2B5 - 177
3X-RAY DIFFRACTION3C4 - 177
4X-RAY DIFFRACTION4D4 - 177

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