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- PDB-1yhn: Structure basis of RILP recruitment by Rab7 -

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Basic information

Entry
Database: PDB / ID: 1yhn
TitleStructure basis of RILP recruitment by Rab7
Components
  • Rab interacting lysosomal protein
  • Ras-related protein Rab-7
KeywordsPROTEIN TRANSPORT / RILP / Rab7
Function / homology
Function and homology information


synaptic vesicle recycling via endosome / phagosome acidification / lipophagy / protein to membrane docking / positive regulation of viral process / 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 / phagosome acidification / lipophagy / protein to membrane docking / positive regulation of viral process / 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 / intralumenal vesicle formation / establishment of vesicle localization / retromer complex binding / phagosome maturation / presynaptic endosome / endosome transport via multivesicular body sorting pathway / 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 / melanosome membrane / protein targeting to lysosome / RAB GEFs exchange GTP for GDP on RABs / RHOD GTPase cycle / TBC/RABGAPs / RHOF GTPase cycle / retrograde transport, endosome to Golgi / dynein light intermediate chain binding / endosome to lysosome transport / RHOJ GTPase cycle / RHOQ GTPase cycle / CDC42 GTPase cycle / autophagosome membrane / RHOH GTPase cycle / viral release from host cell / RHOG GTPase cycle / cilium assembly / RAC2 GTPase cycle / RAC3 GTPase cycle / autophagosome assembly / bone resorption / intracellular transport / lipid catabolic process / phagocytic vesicle / lipid droplet / RAC1 GTPase cycle / MHC class II antigen presentation / Prevention of phagosomal-lysosomal fusion / secretory granule membrane / small monomeric GTPase / response to bacterium / negative regulation of protein catabolic process / small GTPase binding / mitochondrial membrane / phagocytic vesicle membrane / endocytosis / positive regulation of protein catabolic process / GDP binding / late endosome / late endosome membrane / synaptic vesicle membrane / protein transport / G protein activity / lysosome / protein dimerization activity / endosome membrane / ciliary basal body / intracellular membrane-bounded organelle / lysosomal membrane / GTPase activity / Neutrophil degranulation / GTP binding / glutamatergic synapse / Golgi apparatus / protein-containing complex / mitochondrion / extracellular exosome / plasma membrane / cytoplasm / cytosol
Similarity search - Function
YejL-like / YejL-like - #10 / Rab interacting lysosomal protein, dimerization domain / : / Rab interacting lysosomal protein / RH1 domain / RH2 domain / RILP homology 1 domain / RH1 domain profile. / RH2 domain profile. ...YejL-like / YejL-like - #10 / Rab interacting lysosomal protein, dimerization domain / : / Rab interacting lysosomal protein / RH1 domain / RH2 domain / RILP homology 1 domain / RH1 domain profile. / RH2 domain profile. / Small GTPase Rab domain profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Helix non-globular / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Special / 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'-TRIPHOSPHATE / Ras-related protein Rab-7a / Rab-interacting lysosomal protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsWu, M. / Wang, T. / Hong, W. / Song, H.
CitationJournal: Embo J. / Year: 2005
Title: Structural basis for recruitment of RILP by small GTPase Rab7.
Authors: Wu, M. / Wang, T. / Loh, E. / Hong, W. / Song, H.
History
DepositionJan 10, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 17, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 10, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / diffrn_source ...database_2 / diffrn_source / 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 / _diffrn_source.pdbx_synchrotron_site / _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 1.4Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ras-related protein Rab-7
B: Rab interacting lysosomal protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8354
Polymers31,2882
Non-polymers5472
Water61334
1
A: Ras-related protein Rab-7
B: Rab interacting lysosomal protein
hetero molecules

A: Ras-related protein Rab-7
B: Rab interacting lysosomal protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,6718
Polymers62,5764
Non-polymers1,0954
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_555-x+y,y,-z+1/21
Buried area10810 Å2
ΔGint-90 kcal/mol
Surface area22590 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)93.134, 93.134, 132.826
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
DetailsThe biological assembly is a dimer generated from the monomer in the asymmetric unit by symmetric operation.

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Components

#1: Protein Ras-related protein Rab-7 / Rab7


Mass: 23501.748 Da / Num. of mol.: 1 / Mutation: Q67L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: Rab7 / Plasmid: pGEX-6p-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21* / References: UniProt: P51149
#2: Protein Rab interacting lysosomal protein / RILP


Mass: 7786.252 Da / Num. of mol.: 1 / Fragment: RILP effector domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RILP / Plasmid: pGEX-6p-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21* / References: UniProt: Q96NA2
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / 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: 2.38 Å3/Da / Density % sol: 47.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: ammonium sulfate, polyvinylpyrrolidone K15, HEPS, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.9175 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 29, 2004 / Details: bent mirror
RadiationMonochromator: double crystal focusing / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9175 Å / Relative weight: 1
ReflectionResolution: 3→51 Å / Num. all: 7314 / Num. obs: 7272 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 11.3 % / Biso Wilson estimate: 64 Å2 / Rmerge(I) obs: 0.097 / Rsym value: 0.097 / Net I/σ(I): 6.6
Reflection shellResolution: 3→3.11 Å / Redundancy: 11.4 % / Rmerge(I) obs: 0.426 / Mean I/σ(I) obs: 1.8 / Num. unique all: 690 / Rsym value: 0.426 / % possible all: 100

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
REFMAC5refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1T91

1t91


Resolution: 3→20 Å / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.278 -5 %random
Rwork0.268 ---
all-6904 --
obs-6904 100 %-
Refinement stepCycle: LAST / Resolution: 3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2014 0 33 34 2081
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.009
X-RAY DIFFRACTIONr_bond_other_d0
X-RAY DIFFRACTIONr_angle_refined_deg1.682
X-RAY DIFFRACTIONr_angle_other_deg3.529

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