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- PDB-7f6j: Crystal structure of the PDZD8 coiled-coil domain - Rab7 complex -

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Basic information

Entry
Database: PDB / ID: 7f6j
TitleCrystal structure of the PDZD8 coiled-coil domain - Rab7 complex
Components
  • PDZ domain-containing protein 8
  • Ras-related protein Rab-7a
KeywordsLIPID TRANSPORT / complex / PDZD8 / Rab7 / GTP / coiled-coil
Function / homology
Function and homology information


synaptic vesicle recycling via endosome / positive regulation of viral process / lipophagy / 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 / negative regulation of exosomal secretion ...synaptic vesicle recycling via endosome / positive regulation of viral process / lipophagy / 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 / negative regulation of exosomal secretion / phagosome-lysosome fusion / Suppression of autophagy / establishment of vesicle localization / mitochondrial calcium ion homeostasis / presynaptic endosome / retromer complex binding / phagosome maturation / mitochondria-associated endoplasmic reticulum membrane contact site / endosome to plasma membrane protein transport / phagophore assembly site membrane / RAB geranylgeranylation / positive regulation of exosomal secretion / melanosome membrane / protein targeting to lysosome / early endosome to late endosome transport / RAB GEFs exchange GTP for GDP on RABs / RHOD GTPase cycle / regulation of cell morphogenesis / RHOF GTPase cycle / retrograde transport, endosome to Golgi / TBC/RABGAPs / lipid transport / mitochondrion-endoplasmic reticulum membrane tethering / endosome to lysosome transport / RHOJ GTPase cycle / RHOQ GTPase cycle / viral release from host cell / CDC42 GTPase cycle / autophagosome membrane / 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 / cytoskeleton organization / 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 / synaptic vesicle membrane / phagocytic vesicle membrane / endocytosis / positive regulation of protein catabolic process / GDP binding / late endosome membrane / late endosome / protein transport / G protein activity / lysosome / endosome membrane / lysosomal membrane / GTPase activity / intracellular membrane-bounded organelle / lipid binding / Neutrophil degranulation / endoplasmic reticulum membrane / GTP binding / glutamatergic synapse / Golgi apparatus / mitochondrion / extracellular exosome / metal ion binding / membrane / plasma membrane / cytosol
Similarity search - Function
PDZ domain-containing protein 8 / Synaptotagmin-like mitochondrial-lipid-binding domain / Synaptotagmin-like mitochondrial lipid-binding proteins (SMP) domain profile. / PDZ domain 6 / PDZ domain / small GTPase Rab1 family profile. / Phorbol esters/diacylglycerol binding domain (C1 domain) / Zinc finger phorbol-ester/DAG-type profile. / Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains) / Protein kinase C-like, phorbol ester/diacylglycerol-binding domain ...PDZ domain-containing protein 8 / Synaptotagmin-like mitochondrial-lipid-binding domain / Synaptotagmin-like mitochondrial lipid-binding proteins (SMP) domain profile. / PDZ domain 6 / PDZ domain / small GTPase Rab1 family profile. / Phorbol esters/diacylglycerol binding domain (C1 domain) / Zinc finger phorbol-ester/DAG-type profile. / Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains) / Protein kinase C-like, phorbol ester/diacylglycerol-binding domain / C1-like domain superfamily / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / PDZ domain profile. / Rho (Ras homology) subfamily of Ras-like small GTPases / Domain present in PSD-95, Dlg, and ZO-1/2. / Ras subfamily of RAS small GTPases / Small GTPase / PDZ domain / Ras family / PDZ superfamily / Rab subfamily of small GTPases / Small GTP-binding protein domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / Ras-related protein Rab-7a / PDZ domain-containing protein 8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsKhan, H. / Chen, L. / Tan, L. / Im, Y.J.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)2019R1A2C1085530 Korea, Republic Of
CitationJournal: Sci Rep / Year: 2021
Title: Structural basis of human PDZD8-Rab7 interaction for the ER-late endosome tethering.
Authors: Khan, H. / Chen, L. / Tan, L. / Im, Y.J.
History
DepositionJun 25, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 23, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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

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Assembly

Deposited unit
A: Ras-related protein Rab-7a
B: Ras-related protein Rab-7a
C: PDZ domain-containing protein 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,4817
Polymers60,3863
Non-polymers1,0954
Water2,774154
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6620 Å2
ΔGint-56 kcal/mol
Surface area20810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.226, 84.226, 154.622
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65
Space group name HallP65
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: -x,-y,z+1/2

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Components

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


Mass: 22649.750 Da / Num. of mol.: 2 / Mutation: Q67L
Source method: isolated from a genetically manipulated source
Details: GTP-bound Rab7 Q67L / Source: (gene. exp.) Homo sapiens (human) / Gene: RAB7A, RAB7 / Plasmid: pHIS-2 / Details (production host): The N-terminal cleavable His-tag / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P51149, small monomeric GTPase
#2: Protein PDZ domain-containing protein 8 / Sarcoma antigen NY-SAR-84/NY-SAR-104


Mass: 15086.063 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The coiled-coil domain of PDZD8 / Source: (gene. exp.) Homo sapiens (human) / Gene: PDZD8, PDZK8 / Plasmid: pHIS-2 / Details (production host): The N-terminal cleavable his-tag / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8NEN9
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GTP / GUANOSINE-5'-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


Mass: 18.015 Da / Num. of mol.: 154 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.62 Å3/Da / Density % sol: 53.09 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.1 M Tris-HCl pH 8.0, 25% PEG 1000, 0.1 M NaCl

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Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 30, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 36020 / % possible obs: 99.7 % / Redundancy: 11 % / Biso Wilson estimate: 34.3 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rrim(I) all: 0.027 / Net I/σ(I): 53.9
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 11.3 % / Mean I/σ(I) obs: 7.8 / Num. unique obs: 1773 / CC1/2: 0.938 / CC star: 0.984 / Rrim(I) all: 0.506 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCdata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PHENIX1.15.2-3472refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1T91

1t91


Resolution: 2.1→29.77 Å / SU ML: 0.248 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.1218
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.253 1990 5.54 %
Rwork0.2069 33960 -
obs0.2094 35950 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.16 Å2
Refinement stepCycle: LAST / Resolution: 2.1→29.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3598 0 66 154 3818
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00793724
X-RAY DIFFRACTIONf_angle_d1.08885044
X-RAY DIFFRACTIONf_chiral_restr0.0596570
X-RAY DIFFRACTIONf_plane_restr0.0056638
X-RAY DIFFRACTIONf_dihedral_angle_d26.93071396
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.150.34931440.27312432X-RAY DIFFRACTION100
2.15-2.210.32961430.26952430X-RAY DIFFRACTION100
2.21-2.280.32931400.24892417X-RAY DIFFRACTION99.96
2.28-2.350.26051460.24792421X-RAY DIFFRACTION99.92
2.35-2.440.31051430.25792400X-RAY DIFFRACTION99.88
2.44-2.530.29481440.26192444X-RAY DIFFRACTION99.96
2.53-2.650.30821430.25142432X-RAY DIFFRACTION99.96
2.65-2.790.32181400.2472416X-RAY DIFFRACTION100
2.79-2.960.26671420.24762423X-RAY DIFFRACTION100
2.96-3.190.27731410.23642447X-RAY DIFFRACTION99.92
3.19-3.510.27061400.20942436X-RAY DIFFRACTION100
3.51-4.020.23031430.18062449X-RAY DIFFRACTION100
4.02-5.060.2021420.15322430X-RAY DIFFRACTION99.92
5.06-29.770.18391390.16592383X-RAY DIFFRACTION96.3

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