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- PDB-6iyb: Structure of human ORP1 ANK - Rab7 complex -

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Basic information

Entry
Database: PDB / ID: 6iyb
TitleStructure of human ORP1 ANK - Rab7 complex
Components
  • Oxysterol-binding protein-related protein 1
  • Ras-related protein Rab-7a
KeywordsTRANSPORT PROTEIN / oxysterol-binding protein / ORP1 / membrane contact site / Rab7 / Ankyrin repeat / cholesterol / RILP / Late endosome
Function / homology
Function and homology information


lipophagy / epidermal growth factor catabolic process / positive regulation of viral process / phagosome acidification / protein to membrane docking / organelle membrane contact site / negative regulation of intralumenal vesicle formation / alveolar lamellar body / negative regulation of exosomal secretion / phagosome-lysosome fusion ...lipophagy / epidermal growth factor catabolic process / positive regulation of viral process / phagosome acidification / protein to membrane docking / organelle membrane contact site / negative regulation of intralumenal vesicle formation / alveolar lamellar body / negative regulation of exosomal secretion / phagosome-lysosome fusion / Suppression of autophagy / phagosome maturation / : / establishment of vesicle localization / retromer complex binding / endosome to plasma membrane protein transport / bile acid biosynthetic process / perinuclear endoplasmic reticulum / melanosome membrane / phagophore assembly site membrane / protein targeting to lysosome / RAB geranylgeranylation / early endosome to late endosome transport / positive regulation of exosomal secretion / RAB GEFs exchange GTP for GDP on RABs / RHOF GTPase cycle / RHOD GTPase cycle / retrograde transport, endosome to Golgi / TBC/RABGAPs / cholesterol binding / endosome to lysosome transport / RHOJ GTPase cycle / RHOQ GTPase cycle / autophagosome membrane / RHOH GTPase cycle / autophagosome assembly / CDC42 GTPase cycle / intracellular transport / RHOG GTPase cycle / viral release from host cell / Synthesis of bile acids and bile salts / RAC3 GTPase cycle / RAC2 GTPase cycle / lipid catabolic process / phagocytic vesicle / bone resorption / vesicle-mediated transport / Prevention of phagosomal-lysosomal fusion / cholesterol metabolic process / RAC1 GTPase cycle / MHC class II antigen presentation / lipid droplet / small monomeric GTPase / G protein activity / secretory granule membrane / mitochondrial membrane / response to bacterium / phospholipid binding / synaptic vesicle membrane / small GTPase binding / endocytosis / positive regulation of protein catabolic process / GDP binding / phagocytic vesicle membrane / protein transport / late endosome / late endosome membrane / lysosome / endosome membrane / endosome / lysosomal membrane / intracellular membrane-bounded organelle / GTPase activity / Neutrophil degranulation / GTP binding / Golgi apparatus / mitochondrion / extracellular exosome / plasma membrane / cytosol
Similarity search - Function
Oxysterol-binding protein / Oxysterol-binding protein, conserved site / Oxysterol-binding protein superfamily / Oxysterol-binding protein / Oxysterol-binding protein family signature. / small GTPase Rab1 family profile. / Ankyrin repeat-containing domain / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / PH domain profile. / Pleckstrin homology domain. ...Oxysterol-binding protein / Oxysterol-binding protein, conserved site / Oxysterol-binding protein superfamily / Oxysterol-binding protein / Oxysterol-binding protein family signature. / small GTPase Rab1 family profile. / Ankyrin repeat-containing domain / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Ankyrin repeats (3 copies) / Rab subfamily of small GTPases / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Small GTP-binding protein domain / PH-like domain superfamily / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / Ras-related protein Rab-7a / Oxysterol-binding protein-related protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.091 Å
AuthorsTong, J. / Im, Y.J.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (Korea)NRF-2017R1A2B4004914 Korea, Republic Of
CitationJournal: PLoS ONE / Year: 2019
Title: Structural basis of human ORP1-Rab7 interaction for the late-endosome and lysosome targeting.
Authors: Tong, J. / Tan, L. / Chun, C. / Im, Y.J.
History
DepositionDec 14, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 13, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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.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.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

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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: Oxysterol-binding protein-related protein 1
C: Ras-related protein Rab-7a
D: Oxysterol-binding protein-related protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,1918
Polymers79,0964
Non-polymers1,0954
Water6,017334
1
A: Ras-related protein Rab-7a
B: Oxysterol-binding protein-related protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0954
Polymers39,5482
Non-polymers5472
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Ras-related protein Rab-7a
D: Oxysterol-binding protein-related protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0954
Polymers39,5482
Non-polymers5472
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.136, 117.222, 130.476
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 22536.592 Da / Num. of mol.: 2 / Fragment: UNP residues 2-195 / Mutation: Q67L, Leu73 deletion
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAB7A / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P51149
#2: Protein Oxysterol-binding protein-related protein 1 / OSBP-related protein 1


Mass: 17011.248 Da / Num. of mol.: 2 / Fragment: UNP residues 5-152
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: OSBPL1A / Plasmid: pHIS2-Thr / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9BXW6
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine triphosphate


Mass: 523.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: GTP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 334 / 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: 2.81 Å3/Da / Density % sol: 56.18 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 0.1 M Na3Citrate-HCl, 1 M LiCl, 20% PEG 1000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97949 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Mar 14, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.09→50 Å / Num. obs: 50042 / % possible obs: 99.1 % / Redundancy: 5.7 % / Biso Wilson estimate: 29.7 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 39.3
Reflection shellResolution: 2.09→2.14 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.324 / Mean I/σ(I) obs: 7.3 / Num. unique obs: 2496 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1T91
Resolution: 2.091→26.286 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.37
RfactorNum. reflection% reflection
Rfree0.2318 2545 5.09 %
Rwork0.1948 --
obs0.1967 49988 98.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 41.3 Å2
Refinement stepCycle: LAST / Resolution: 2.091→26.286 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4825 0 66 334 5225
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084971
X-RAY DIFFRACTIONf_angle_d0.9266739
X-RAY DIFFRACTIONf_dihedral_angle_d20.9822991
X-RAY DIFFRACTIONf_chiral_restr0.053761
X-RAY DIFFRACTIONf_plane_restr0.005869
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0915-2.13170.27241160.23892268X-RAY DIFFRACTION86
2.1317-2.17520.26631310.21532638X-RAY DIFFRACTION100
2.1752-2.22240.24981300.22462648X-RAY DIFFRACTION100
2.2224-2.27410.26811570.22572620X-RAY DIFFRACTION100
2.2741-2.3310.28461380.21872639X-RAY DIFFRACTION100
2.331-2.39390.27221480.22422655X-RAY DIFFRACTION100
2.3939-2.46430.24631650.22362599X-RAY DIFFRACTION100
2.4643-2.54380.26751360.22172660X-RAY DIFFRACTION100
2.5438-2.63460.25291350.2162678X-RAY DIFFRACTION100
2.6346-2.740.25421440.22672649X-RAY DIFFRACTION100
2.74-2.86460.28291470.22052641X-RAY DIFFRACTION100
2.8646-3.01540.25781420.2122675X-RAY DIFFRACTION100
3.0154-3.2040.23231310.21122673X-RAY DIFFRACTION100
3.204-3.45090.24151470.19712706X-RAY DIFFRACTION100
3.4509-3.79730.22041540.17392646X-RAY DIFFRACTION100
3.7973-4.34460.20831420.15712716X-RAY DIFFRACTION99
4.3446-5.46570.16941450.162730X-RAY DIFFRACTION99
5.4657-26.28770.2131370.18742602X-RAY DIFFRACTION90

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