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- PDB-3law: Structure of GTP-bound L129F mutant Rab7 -

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Basic information

Entry
Database: PDB / ID: 3law
TitleStructure of GTP-bound L129F mutant Rab7
ComponentsRas-related protein Rab-7a
KeywordsPROTON TRANSPORT / Protein - Nucleotide complex / Protein Mutant / Charcot-Marie-Tooth disease / Cytoplasmic vesicle / Disease mutation / Endosome / GTP-binding / Lipoprotein / Lysosome / Methylation / Neuropathy / Nucleotide-binding / Phosphoprotein / Prenylation / Protein transport
Function / homology
Function and homology information


synaptic vesicle recycling via endosome / lipophagy / positive regulation of viral process / phagosome acidification / protein to membrane docking / neurotransmitter receptor transport, postsynaptic endosome to lysosome / epidermal growth factor catabolic process / alveolar lamellar body / negative regulation of intralumenal vesicle formation / Suppression of autophagy ...synaptic vesicle recycling via endosome / lipophagy / positive regulation of viral process / phagosome acidification / protein to membrane docking / neurotransmitter receptor transport, postsynaptic endosome to lysosome / epidermal growth factor catabolic process / alveolar lamellar body / negative regulation of intralumenal vesicle formation / Suppression of autophagy / phagosome-lysosome fusion / negative regulation of exosomal secretion / establishment of vesicle localization / retromer complex binding / phagosome maturation / presynaptic endosome / protein localization to lysosome / endosome to plasma membrane protein transport / early endosome to late endosome transport / phagophore assembly site membrane / positive regulation of exosomal secretion / RAB geranylgeranylation / protein targeting to lysosome / melanosome membrane / RAB GEFs exchange GTP for GDP on RABs / RHOD GTPase cycle / RHOF GTPase cycle / retrograde transport, endosome to Golgi / TBC/RABGAPs / endosome to lysosome transport / RHOJ GTPase cycle / RHOQ GTPase cycle / autophagosome membrane / CDC42 GTPase cycle / viral release from host cell / RHOH GTPase cycle / RHOG GTPase cycle / autophagosome assembly / RAC2 GTPase cycle / RAC3 GTPase cycle / bone resorption / intracellular transport / lipid catabolic process / phagocytic vesicle / lipid droplet / RAC1 GTPase cycle / Prevention of phagosomal-lysosomal fusion / MHC class II antigen presentation / secretory granule membrane / small monomeric GTPase / response to bacterium / mitochondrial membrane / small GTPase binding / phagocytic vesicle membrane / endocytosis / positive regulation of protein catabolic process / GDP binding / synaptic vesicle membrane / late endosome membrane / late endosome / protein transport / G protein activity / lysosome / endosome membrane / lysosomal membrane / intracellular membrane-bounded organelle / GTPase activity / Neutrophil degranulation / GTP binding / glutamatergic synapse / Golgi apparatus / mitochondrion / extracellular exosome / plasma membrane / cytosol
Similarity search - Function
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 ...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-7a
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsMcCray, B.A. / Skordalakes, E. / Taylor, J.P.
CitationJournal: Hum.Mol.Genet. / Year: 2010
Title: Disease mutations in Rab7 result in unregulated nucleotide exchange and inappropriate activation.
Authors: McCray, B.A. / Skordalakes, E. / Taylor, J.P.
History
DepositionJan 7, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 26, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 13, 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_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_asym_id / _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_asym_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ras-related protein Rab-7a
B: Ras-related protein Rab-7a
C: Ras-related protein Rab-7a
D: Ras-related protein Rab-7a
E: Ras-related protein Rab-7a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,48615
Polymers117,7545
Non-polymers2,73310
Water75742
1
A: Ras-related protein Rab-7a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0973
Polymers23,5511
Non-polymers5472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Ras-related protein Rab-7a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0973
Polymers23,5511
Non-polymers5472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Ras-related protein Rab-7a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0973
Polymers23,5511
Non-polymers5472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Ras-related protein Rab-7a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0973
Polymers23,5511
Non-polymers5472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Ras-related protein Rab-7a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0973
Polymers23,5511
Non-polymers5472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)35.554, 89.335, 89.378
Angle α, β, γ (deg.)71.24, 85.97, 85.91
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Ras-related protein Rab-7a


Mass: 23550.734 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAB7A, RAB7 / Production host: Escherichia coli (E. coli) / References: UniProt: P51149
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


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


Mass: 18.015 Da / Num. of mol.: 42 / 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: 2.27 Å3/Da / Density % sol: 45.91 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: 0.2 M sodium formate, 10mM trimethylamine hydrochloride, and 20% polyethylene glycol 3,350, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1 Å
RadiationScattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. all: 24170 / Num. obs: 23869 / % possible obs: 98.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2 % / Rsym value: 0.1 / Net I/σ(I): 7.7
Reflection shellResolution: 2.8→2.871 Å / Redundancy: 2 % / Mean I/σ(I) obs: 1.7 / Rsym value: 0.417 / % possible all: 98.2

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→19.88 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.838 / SU B: 35.857 / SU ML: 0.364 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.452 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.27265 1277 5.1 %RANDOM
Rwork0.22036 ---
obs0.23678 23869 98.7 %-
all-24300 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 29.888 Å2
Baniso -1Baniso -2Baniso -3
1--2.02 Å20.35 Å20.09 Å2
2--0.75 Å2-1.21 Å2
3---1.98 Å2
Refinement stepCycle: LAST / Resolution: 2.8→19.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7044 0 165 42 7251
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0227349
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1751.9689982
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6365875
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.85324.958357
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.314151264
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4121540
X-RAY DIFFRACTIONr_chiral_restr0.0810.21106
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025498
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2450.23431
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3210.25010
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1630.2289
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0880.25
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2430.258
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2950.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7221.54469
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.26927090
X-RAY DIFFRACTIONr_scbond_it1.46633305
X-RAY DIFFRACTIONr_scangle_it2.4234.52892
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.871 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.382 91 -
Rwork0.309 1710 -
obs--98.2 %
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)
12.4007-0.17570.66574.84461.05351.75490.01090.0259-0.0788-0.05720.0604-0.25320.04660.154-0.0713-0.09330.00750.0058-0.0281-0.0181-0.094716.355112.188732.0531
22.6658-1.0072-0.08812.65730.693.3959-0.0544-0.07190.24160.0030.0581-0.1401-0.06630.0817-0.0037-0.084-0.01760.0134-0.1065-0.0028-0.019823.6769-11.84778.6827
32.04860.90610.52332.9725-1.84743.3491-0.06560.1387-0.07980.0933-0.0845-0.25990.00890.11580.1501-0.07410.0260.0201-0.0763-0.0341-0.03529.216941.902315.9532
42.79720.4189-0.92812.3522-0.68422.11740.0391-0.3263-0.0797-0.0315-0.0884-0.0246-0.01730.24560.0493-0.035-0.0032-0.00210.017-0.0078-0.12230.74922.7593-21.6196
52.75461.2824-0.22253.36671.65864.05370.02780.1002-0.2089-0.00070.0469-0.2287-0.11270.3126-0.0748-0.07580.0037-0.0414-0.06830.0282-0.04212.29636.1486-17.4153
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 180
2X-RAY DIFFRACTION2B8 - 180
3X-RAY DIFFRACTION3C8 - 180
4X-RAY DIFFRACTION4D8 - 180
5X-RAY DIFFRACTION5E8 - 180

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