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- PDB-6zsj: The mechanism of activation of the actin binding protein EHBP1 by... -

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Basic information

Entry
Database: PDB / ID: 6zsj
TitleThe mechanism of activation of the actin binding protein EHBP1 by Rab8 family members.
Components
  • EH domain-binding protein 1
  • Ras-related protein Rab-8A
KeywordsENDOCYTOSIS / Rab GTPase / EHBP1 / bMERB domain / CH domain
Function / homology
Function and homology information


neurotransmitter receptor transport to postsynaptic membrane / Golgi vesicle fusion to target membrane / regulation of protein transport / vesicle-mediated transport in synapse / neurotransmitter receptor transport, endosome to postsynaptic membrane / VxPx cargo-targeting to cilium / myosin V binding / RAB geranylgeranylation / trans-Golgi network transport vesicle / protein localization to cilium ...neurotransmitter receptor transport to postsynaptic membrane / Golgi vesicle fusion to target membrane / regulation of protein transport / vesicle-mediated transport in synapse / neurotransmitter receptor transport, endosome to postsynaptic membrane / VxPx cargo-targeting to cilium / myosin V binding / RAB geranylgeranylation / trans-Golgi network transport vesicle / protein localization to cilium / RAB GEFs exchange GTP for GDP on RABs / endocytic recycling / non-motile cilium / vesicle docking involved in exocytosis / TBC/RABGAPs / ciliary membrane / ciliary base / Golgi organization / exocytosis / cilium assembly / phagocytic vesicle / centriole / Anchoring of the basal body to the plasma membrane / axonogenesis / protein tyrosine kinase binding / small monomeric GTPase / trans-Golgi network membrane / protein localization to plasma membrane / Translocation of SLC2A4 (GLUT4) to the plasma membrane / regulation of long-term neuronal synaptic plasticity / small GTPase binding / autophagy / centriolar satellite / cellular response to insulin stimulus / recycling endosome membrane / phagocytic vesicle membrane / endocytosis / GDP binding / Regulation of PLK1 Activity at G2/M Transition / synaptic vesicle / protein transport / actin cytoskeleton / midbody / lysosome / endosome / regulation of autophagy / endosome membrane / ciliary basal body / cilium / Golgi membrane / neuronal cell body / GTPase activity / centrosome / dendrite / GTP binding / nucleolus / glutamatergic synapse / Golgi apparatus / extracellular exosome / nucleoplasm / plasma membrane / cytosol
Similarity search - Function
NT-type C2 domain / N-terminal C2 in EEIG1 and EHBP1 proteins / C2 NT-type domain profile. / bMERB domain / Bivalent Mical/EHBP Rab binding domain / bMERB domain profile. / DUF3585 / : / : / ARF-like small GTPases; ARF, ADP-ribosylation factor ...NT-type C2 domain / N-terminal C2 in EEIG1 and EHBP1 proteins / C2 NT-type domain profile. / bMERB domain / Bivalent Mical/EHBP Rab binding domain / bMERB domain profile. / DUF3585 / : / : / ARF-like small GTPases; ARF, ADP-ribosylation factor / small GTPase Rab1 family profile. / Calponin homology domain / Calponin homology (CH) domain / Calponin homology domain / CH domain superfamily / Calponin homology (CH) 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 nucleoside triphosphate hydrolase
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Ras-related protein Rab-8A / EH domain-binding protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsRai, A. / Bleimling, N. / Vetter, I.R. / Goody, R.S.
Funding support Germany, 2items
OrganizationGrant numberCountry
Max Planck Society Germany
German Research Foundation (DFG)grant GO 284/10-1 Germany
CitationJournal: Nat Commun / Year: 2020
Title: The mechanism of activation of the actin binding protein EHBP1 by Rab8 family members.
Authors: Rai, A. / Bleimling, N. / Vetter, I.R. / Goody, R.S.
History
DepositionJul 15, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 2, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2020Group: Data collection / Category: reflns_shell / Item: _reflns_shell.percent_possible_all
Revision 1.2Jan 31, 2024Group: 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
A: Ras-related protein Rab-8A
B: Ras-related protein Rab-8A
C: EH domain-binding protein 1
D: EH domain-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,2028
Polymers78,1094
Non-polymers1,0934
Water2,594144
1
A: Ras-related protein Rab-8A
C: EH domain-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,6014
Polymers39,0552
Non-polymers5472
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ras-related protein Rab-8A
D: EH domain-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,6014
Polymers39,0552
Non-polymers5472
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)117.340, 35.660, 168.560
Angle α, β, γ (deg.)90.000, 94.500, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Ras-related protein Rab-8A / Oncogene c-mel


Mass: 20476.572 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAB8A, MEL, RAB8 / Production host: Escherichia coli (E. coli) / References: UniProt: P61006
#2: Protein EH domain-binding protein 1


Mass: 18578.033 Da / Num. of mol.: 2 / Mutation: F1120A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EHBP1, KIAA0903, NACSIN / Production host: Escherichia coli (E. coli) / References: UniProt: Q8NDI1
#3: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O13P3 / Feature type: SUBJECT OF INVESTIGATION
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / 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: 2.25 Å3/Da / Density % sol: 45.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M Mes pH 6.5 10 % (w/v) Peg-MME5000 12% (v/v) 1-propanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.91955 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 4, 2019
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91955 Å / Relative weight: 1
ReflectionResolution: 2→42.14 Å / Num. obs: 47563 / % possible obs: 99.2 % / Redundancy: 6.619 % / Biso Wilson estimate: 52.321 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.067 / Rrim(I) all: 0.073 / Χ2: 0.89 / Net I/σ(I): 12.3 / Num. measured all: 314837 / Scaling rejects: 2189
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2-2.056.5391.4481.1222978351435140.5951.575100
2.05-2.116.4771.0821.5322255343334360.691.179100
2.11-2.177.0740.8592.0623096326732650.7850.92799.9
2.17-2.247.0210.6462.5822902327032620.8880.69899.8
2.24-2.316.5760.4983.5218346309727900.9380.54490.1
2.31-2.396.8250.3774.4421027308230810.9440.408100
2.39-2.486.5630.35.3719216292829280.9630.326100
2.48-2.586.4090.2366.5318017281328110.9770.25799.9
2.58-2.77.0260.28.4419026270827080.9840.217100
2.7-2.836.950.15510.7517980259025870.9890.16899.9
2.83-2.986.850.11214.5517132250425010.9940.12299.9
2.98-3.166.60.0911815364233123280.9950.09999.9
3.16-3.386.0380.06722.313284220722000.9970.07399.7
3.38-3.656.7260.0626.713944207620730.9980.06599.9
3.65-46.4450.05230.0412259191219020.9980.05699.5
4-4.476.3140.04433.1310910173917280.9980.04899.4
4.47-5.165.8160.0433.868811153115150.9980.04499
5.16-6.326.5380.04233.878526130713040.9990.04699.8
6.32-8.946.0250.03635.466284105310430.9990.0499.1
8.94-42.145.9280.02739.4234806025870.9990.0397.5

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Processing

Software
NameVersionClassification
PHENIX1.18rc7_3834refinement
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5szi

5szi


Resolution: 2→42.14 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 35.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2908 2383 5.02 %
Rwork0.2475 45095 -
obs0.2497 47478 98.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 175.81 Å2 / Biso mean: 72.3838 Å2 / Biso min: 26.07 Å2
Refinement stepCycle: final / Resolution: 2→42.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4958 0 66 144 5168
Biso mean--36.57 57.02 -
Num. residues----606
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.040.50741270.44122656278399
2.04-2.090.42231400.389326372777100
2.09-2.130.40361520.356826322784100
2.13-2.190.35541520.338526482800100
2.19-2.250.41071310.362482261394
2.25-2.310.41121210.37472433255492
2.31-2.390.29971410.294726972838100
2.39-2.470.34991410.292126392780100
2.47-2.570.35691410.290526872828100
2.57-2.690.32911390.289426372776100
2.69-2.830.35681400.292926642804100
2.83-3.010.31221410.27726842825100
3.01-3.240.34441430.277227122855100
3.24-3.560.2721420.249326742816100
3.57-4.080.28391400.220226922832100
4.08-5.140.25081440.19612715285999
5.14-42.140.22761480.20022806295499
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)
11.8785-0.0841.28641.1014-0.79061.5997-0.55820.13540.16620.1111-0.3830.8424-1.4683-1.9009-0.15830.7530.5812-0.12951.3618-0.49580.799353.189933.701226.4739
27.7242-0.396-0.4296.4527-0.53797.56430.3557-0.0223-1.0381-0.4983-0.35660.49880.1918-0.9652-0.0310.45440.0506-0.1040.5418-0.00280.47765.248623.972330.6911
38.26080.6351.50534.33521.97195.67050.6726-0.3366-1.33340.3336-0.43080.26810.5017-1.2373-0.16740.5384-0.0538-0.08540.7341-0.02440.571661.61122.756227.3998
41.4944-1.0189-1.87114.07050.70682.60540.0469-1.1164-0.25-0.6125-0.56841.0237-0.2575-1.86990.17950.4470.1233-0.09651.3312-0.25690.596952.881130.609728.0721
55.19362.42840.60735.11060.06126.3098-0.39170.7278-0.1608-0.7958-0.043-0.6691-1.84662.25570.16660.7378-0.03080.07981.04580.12810.404572.102732.999818.0125
65.1068-1.30342.23012.9614-2.95793.4666-0.8210.03260.4567-0.8238-0.05990.7198-1.3803-1.12690.74631.01430.3338-0.35470.6513-0.21830.710565.155936.737828.5412
72.6469-1.36763.19195.5372-2.94876.3038-1.5931-0.52711.85690.1511-0.0641-0.5485-2.4334-0.24031.33161.0980.0409-0.41080.43280.01990.76771.465339.088331.4029
85.75631.3447-0.13050.88181.19714.7121-0.3574-0.9874-0.69910.493-0.2382-0.2858-0.15290.11670.74030.46290.0365-0.0790.48410.08430.479976.671325.868343.2625
95.49953.7958-2.60687.0495-2.52977.20130.25130.14331.01150.81630.78870.3442-0.43081.1808-0.90110.8733-0.0557-0.09140.7572-0.26010.966572.223440.250544.4783
107.7933-1.41590.88881.5889-0.20676.9528-0.5649-1.36870.4443-0.09480.50040.6532-1.4653-1.56160.07840.76220.086-0.18180.78460.01520.494565.655131.16240.5041
113.573-1.3831-0.67671.35481.35422.1286-0.1072-0.6398-0.4455-0.0665-0.37050.9752-1.5173-1.66520.28520.87230.4689-0.03021.6179-0.29170.588353.295835.799436.3394
125.67930.72480.11031.91310.38362.86960.10230.1298-0.5455-0.0966-0.0608-0.323-0.11630.5085-0.01920.3722-0.0080.03860.36120.04440.396149.52844.335555.1833
135.61691.7730.12983.5502-0.91784.12380.147-0.3241-0.49050.0514-0.1861-0.038-0.12260.1016-0.02850.29660.01670.02570.30490.02080.367946.830343.623259.1128
143.37970.54281.41795.11960.74132.4254-0.24120.06260.7026-0.02880.06070.2465-0.35710.09950.17050.46620.0465-0.02370.32650.00980.518138.376354.22454.7859
155.411.44770.51432.62880.6772.3721-0.31320.72690.5897-0.60140.17230.3649-0.26010.34130.15870.513-0.0196-0.00560.40080.07430.374141.654349.68244.6864
168.5452-0.59790.91050.73440.65651.59050.0330.72-1.2918-0.0484-0.12710.5352-0.0556-0.47250.03060.75750.1832-0.04931.0878-0.30960.940233.133521.86058.25
176.96340.4682-0.95354.44510.23085.6677-0.54961.21470.0317-0.4617-0.0269-0.1913-0.0639-0.12950.51360.60940.0424-0.05240.9625-0.04690.423764.556126.339710.6153
182.69-1.95460.60742.2753-1.37523.2274-0.417-2.1709-0.4259-0.00060.20190.1544-0.4887-0.86520.08520.77030.02340.10741.41980.14610.99989.569337.511781.0006
192.45270.41191.26460.4985-0.10051.14970.18810.136-0.97610.070.0606-0.3393-0.13080.1824-0.30090.6739-0.0977-0.04160.60680.10850.736870.504737.249472.2941
203.5605-0.35551.88116.72252.11977.11570.4371-1.5275-0.16440.9269-0.4878-0.15740.06530.38760.11970.5481-0.0373-0.06480.62090.05140.411647.595842.163673.0412
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 7 through 18 )A7 - 18
2X-RAY DIFFRACTION2chain 'A' and (resid 19 through 33 )A19 - 33
3X-RAY DIFFRACTION3chain 'A' and (resid 34 through 55 )A34 - 55
4X-RAY DIFFRACTION4chain 'A' and (resid 56 through 67 )A56 - 67
5X-RAY DIFFRACTION5chain 'A' and (resid 68 through 80 )A68 - 80
6X-RAY DIFFRACTION6chain 'A' and (resid 81 through 92 )A81 - 92
7X-RAY DIFFRACTION7chain 'A' and (resid 93 through 124 )A93 - 124
8X-RAY DIFFRACTION8chain 'A' and (resid 125 through 135 )A125 - 135
9X-RAY DIFFRACTION9chain 'A' and (resid 136 through 145 )A136 - 145
10X-RAY DIFFRACTION10chain 'A' and (resid 146 through 160 )A146 - 160
11X-RAY DIFFRACTION11chain 'A' and (resid 161 through 177 )A161 - 177
12X-RAY DIFFRACTION12chain 'B' and (resid 6 through 33 )B6 - 33
13X-RAY DIFFRACTION13chain 'B' and (resid 34 through 80 )B34 - 80
14X-RAY DIFFRACTION14chain 'B' and (resid 81 through 124 )B81 - 124
15X-RAY DIFFRACTION15chain 'B' and (resid 125 through 178 )B125 - 178
16X-RAY DIFFRACTION16chain 'C' and (resid 18 through 105 )C18 - 105
17X-RAY DIFFRACTION17chain 'C' and (resid 106 through 147 )C106 - 147
18X-RAY DIFFRACTION18chain 'D' and (resid 18 through 52 )D18 - 52
19X-RAY DIFFRACTION19chain 'D' and (resid 53 through 104 )D53 - 104
20X-RAY DIFFRACTION20chain 'D' and (resid 105 through 149 )D105 - 149

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