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- PDB-6if2: Complex structure of Rab35 and its effector RUSC2 -

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Basic information

Entry
Database: PDB / ID: 6if2
TitleComplex structure of Rab35 and its effector RUSC2
Components
  • Iporin
  • Ras-related protein Rab-35
KeywordsENDOCYTOSIS / Rab35 / RUSC2 / complex
Function / homology
Function and homology information


Rab protein signal transduction / plasma membrane to endosome transport / protein localization to endosome / cell projection membrane / clathrin-coated endocytic vesicle / RAB geranylgeranylation / RAB GEFs exchange GTP for GDP on RABs / endocytic recycling / TBC/RABGAPs / endosomal transport ...Rab protein signal transduction / plasma membrane to endosome transport / protein localization to endosome / cell projection membrane / clathrin-coated endocytic vesicle / RAB geranylgeranylation / RAB GEFs exchange GTP for GDP on RABs / endocytic recycling / TBC/RABGAPs / endosomal transport / intercellular bridge / mitotic cytokinesis / antigen processing and presentation / clathrin-coated pit / phosphatidylinositol-4,5-bisphosphate binding / cellular response to nerve growth factor stimulus / clathrin-coated endocytic vesicle membrane / protein localization / small GTPase binding / recycling endosome membrane / neuron projection development / GDP binding / melanosome / protein transport / cytoplasmic vesicle / endosome membrane / GTPase activity / GTP binding / extracellular exosome / plasma membrane / cytosol
Similarity search - Function
Rab35 / RUN domain / RUN / RUN domain / RUN domain superfamily / RUN domain / RUN domain profile. / ARF-like small GTPases; ARF, ADP-ribosylation factor / small GTPase Rab1 family profile. / Variant SH3 domain ...Rab35 / RUN domain / RUN / RUN domain / RUN domain superfamily / RUN domain / RUN domain profile. / ARF-like small GTPases; ARF, ADP-ribosylation factor / small GTPase Rab1 family profile. / Variant SH3 domain / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / Up-down Bundle / 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-35 / AP-4 complex accessory subunit RUSC2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsLin, L. / Zhu, J. / Zhang, R.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31600607 China
CitationJournal: Structure / Year: 2019
Title: Rab35/ACAP2 and Rab35/RUSC2 Complex Structures Reveal Molecular Basis for Effector Recognition by Rab35 GTPase.
Authors: Lin, L. / Shi, Y. / Wang, M. / Wang, C. / Zhu, J. / Zhang, R.
History
DepositionSep 18, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 3, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2May 22, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first
Revision 1.3Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Ras-related protein Rab-35
A: Iporin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,4034
Polymers43,8552
Non-polymers5472
Water4,161231
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2660 Å2
ΔGint-19 kcal/mol
Surface area17310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)188.213, 188.213, 37.185
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Ras-related protein Rab-35 / GTP-binding protein RAY / Ras-related protein Rab-1C


Mass: 21095.869 Da / Num. of mol.: 1 / Mutation: Q67L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAB35, RAB1C, RAY / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q15286
#2: Protein Iporin / Interacting protein of Rab1 / RUN and SH3 domain-containing protein 2


Mass: 22759.436 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RUSC2, KIAA0375 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8N2Y8
#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 / Guanosine 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 / Water


Mass: 18.015 Da / Num. of mol.: 231 / 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: 4.34 Å3/Da / Density % sol: 71.63 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: HEPES, PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 30173 / % possible obs: 99.9 % / Redundancy: 9.9 % / Rmerge(I) obs: 0.145 / Rpim(I) all: 0.048 / Rrim(I) all: 0.153 / Χ2: 0.927 / Net I/σ(I): 3.9 / Num. measured all: 299834
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.4-2.449.50.76114980.80.2590.8050.937100
2.44-2.499.40.66914990.8380.2290.7080.93198.9
2.49-2.5310.40.66314520.880.2160.6971.063100
2.53-2.59100.53514730.9070.1770.5630.938100
2.59-2.649.50.48415190.910.1640.5110.931100
2.64-2.710.10.51814830.9020.1710.5461.20899.3
2.7-2.7710.40.414770.9540.1290.420.917100
2.77-2.8510.10.35815260.9580.1160.3770.94699.8
2.85-2.9310.40.29814670.9730.0960.3130.9299.5
2.93-3.0210.30.24714860.9840.0810.260.917100
3.02-3.139.60.21615180.9790.0730.2280.92699.8
3.13-3.269.90.18514900.9880.0620.1950.954100
3.26-3.41100.14515080.9910.0480.1530.91999.9
3.41-3.589.90.13815000.9910.0470.1461.036100
3.58-3.8110.40.12615190.9960.040.1321.06699.9
3.81-4.110.30.10415270.9950.0340.111.027100
4.1-4.529.70.07115120.9980.0240.0750.811100
4.52-5.179.70.06415290.9980.0220.0680.757100
5.17-6.519.70.07715580.9970.0260.0820.757100
6.51-509.40.04216320.9990.0140.0440.575100

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
SCALEPACKdata scaling
PDB_EXTRACT3.24data extraction
d*TREKdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TW8, 4GIW

3tw8

4giw


Resolution: 2.4→47.053 Å / FOM work R set: 0.8685 / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2044 1518 5.07 %
Rwork0.1672 28441 -
obs0.1691 29959 99.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 119 Å2 / Biso mean: 42.43 Å2 / Biso min: 18.43 Å2
Refinement stepCycle: final / Resolution: 2.4→47.053 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2921 0 33 231 3185
Biso mean--35.52 48.35 -
Num. residues----373
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083036
X-RAY DIFFRACTIONf_angle_d1.1344134
X-RAY DIFFRACTIONf_chiral_restr0.048478
X-RAY DIFFRACTIONf_plane_restr0.005522
X-RAY DIFFRACTIONf_dihedral_angle_d18.6071086
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4001-2.47750.26921450.22712564270999
2.4775-2.56610.27141160.2152521263799
2.5661-2.66880.27331520.21132588274099
2.6688-2.79030.2671330.20462525265899
2.7903-2.93740.21431440.188125772721100
2.9374-3.12140.22341320.18642591272399
3.1214-3.36230.22431250.179526152740100
3.3623-3.70050.21821460.167325862732100
3.7005-4.23570.17281310.142725972728100
4.2357-5.33540.15071420.13152645278799
5.3354-47.06230.18241520.15362632278497
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)
12.5539-1.04530.93492.82540.86830.98980.1189-0.4790.16940.5881-0.11390.26630.1259-0.164900.3424-0.08120.07480.372-0.01130.3053161.5183106.68738.6927
23.5741.73231.04483.8003-0.50161.803-0.0699-0.281-0.18390.55-0.1609-0.3175-0.1644-0.0520.22720.3271-0.0417-0.02750.28180.03080.3133169.0627107.480910.6059
31.1778-0.33360.87670.3396-0.11930.7154-0.04470.8201-0.1437-0.32240.0452-0.23640.20160.0556-0.01120.3386-0.02620.01590.574-0.05190.4267169.1783103.4089-4.8329
40.8926-0.7439-0.69432.39850.06492.66770.22030.37530.2575-0.3322-0.25030.11810.0441-0.36060.02730.29760.0186-0.01580.38580.06910.2861166.3248116.1366-4.3464
51.17790.1621-0.01692.6913-0.92352.4143-0.03780.13680.35370.3329-0.04050.1147-0.4012-0.17280.0180.29880.01870.01280.22060.03890.3069164.5597121.61225.4826
62.7486-0.9082-1.20761.96810.42790.69660.2076-0.10750.5630.1368-0.1043-0.07410.0505-0.1008-0.0180.3027-0.1037-0.01020.43150.04970.2081153.88591.14813.563
72.68830.35980.37760.8150.02340.3810.1858-0.0965-0.38130.1093-0.0794-0.2190.1411-0.0104-0.09810.2893-0.0794-0.04290.35860.02670.2705161.627580.36647.6101
83.8450.97021.04453.4987-0.51695.85410.07740.9967-0.3088-0.87370.12220.00540.0953-0.0661-0.14180.3769-0.01750.00680.6042-0.07980.2832163.745575.9084-6.2452
92.68620.7311-0.30351.15710.12010.9797-0.00430.3001-0.04460.025-0.00460.02720.1459-0.09230.00740.2256-0.0847-0.01480.33240.01210.1773155.058581.22982.0938
101.429-0.0497-1.00611.4043-0.15491.28520.1392-0.01610.09020.0158-0.1052-0.13620.0140.0703-0.00490.2481-0.0874-0.05960.35420.01850.3239164.567287.02896.9908
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 1 through 20 )B1 - 20
2X-RAY DIFFRACTION2chain 'B' and (resid 21 through 64 )B21 - 64
3X-RAY DIFFRACTION3chain 'B' and (resid 65 through 82 )B65 - 82
4X-RAY DIFFRACTION4chain 'B' and (resid 83 through 120 )B83 - 120
5X-RAY DIFFRACTION5chain 'B' and (resid 121 through 178 )B121 - 178
6X-RAY DIFFRACTION6chain 'A' and (resid 984 through 1011 )A984 - 1011
7X-RAY DIFFRACTION7chain 'A' and (resid 1012 through 1076 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 1077 through 1094 )A0
9X-RAY DIFFRACTION9chain 'A' and (resid 1095 through 1149 )A0
10X-RAY DIFFRACTION10chain 'A' and (resid 1150 through 1178 )A0

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