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

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Basic information

Entry
Database: PDB / ID: 6zsh
TitleThe mechanism of activation of the actin binding protein EHBP1 by Rab8 family members
Components(EH domain-binding protein 1) x 2
KeywordsENDOCYTOSIS / Rab GTPase / EHBP1 / bMERB domain / CH domain
Function / homology
Function and homology information


endocytosis / protein transport / endosome / 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 / : / Calponin homology domain / Calponin homology (CH) domain ...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 / : / Calponin homology domain / Calponin homology (CH) domain / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile.
Similarity search - Domain/homology
EH domain-binding protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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: EH domain-binding protein 1
B: EH domain-binding protein 1
C: EH domain-binding protein 1
D: EH domain-binding protein 1


Theoretical massNumber of molelcules
Total (without water)51,3634
Polymers51,3634
Non-polymers00
Water2,342130
1
A: EH domain-binding protein 1
B: EH domain-binding protein 1


Theoretical massNumber of molelcules
Total (without water)25,6822
Polymers25,6822
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1180 Å2
ΔGint-6 kcal/mol
Surface area12700 Å2
MethodPISA
2
C: EH domain-binding protein 1
D: EH domain-binding protein 1


Theoretical massNumber of molelcules
Total (without water)25,6822
Polymers25,6822
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1030 Å2
ΔGint-7 kcal/mol
Surface area11810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.060, 48.190, 100.300
Angle α, β, γ (deg.)90.000, 97.480, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein EH domain-binding protein 1


Mass: 12631.514 Da / Num. of mol.: 2
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
#2: Protein EH domain-binding protein 1


Mass: 13050.051 Da / Num. of mol.: 2
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / 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: 2.86 Å3/Da / Density % sol: 56.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M di-Ammonium hydrogen citrate 20% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.00001 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 20, 2016
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00001 Å / Relative weight: 1
ReflectionResolution: 2.2→44.82 Å / Num. obs: 26307 / % possible obs: 99.8 % / Redundancy: 6.6 % / Biso Wilson estimate: 50.832 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.123 / Rrim(I) all: 0.134 / Χ2: 0.876 / Net I/σ(I): 11.15 / Num. measured all: 173618 / Scaling rejects: 8
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
2.2-2.266.741.4622.0413069194019390.7121.58799.9
2.26-2.326.5981.2162.4212365187418740.7431.322100
2.32-2.396.3021.0252.8511394181218080.7621.1299.8
2.39-2.466.8960.8493.6312386179717960.8660.91999.9
2.46-2.5470.6674.5912047171817210.9220.721100
2.54-2.636.9030.5555.311500166716660.9270.60199.9
2.63-2.736.790.4456.0610987162216180.9570.48399.8
2.73-2.846.480.3517.2410147156615660.9620.382100
2.84-2.976.4580.2688.849526147914750.9720.29299.7
2.97-3.116.9720.21110.899887141714180.9870.228100
3.11-3.286.8960.16812.719516137913800.990.182100
3.28-3.486.7030.1216.158707130212990.9930.13199.8
3.48-3.726.1990.08818.977420120111970.9950.09699.7
3.72-4.026.30.07323.057176114311390.9960.0899.7
4.02-4.46.6080.06425.846846104110360.9970.06999.5
4.4-4.926.3110.05827.0559589489440.9970.06499.6
4.92-5.685.8670.05925.2948528328270.9970.06599.4
5.68-6.966.4110.0625.6846807327300.9970.06699.7
6.96-9.846.1330.04131.2834165615570.9970.04599.3
9.84-44.825.4860.03431.3917393273170.9990.03796.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2D89

2d89


Resolution: 2.2→44.82 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.942 / SU B: 6.386 / SU ML: 0.155 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.211 / ESU R Free: 0.188 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2298 1316 5 %RANDOM
Rwork0.177 ---
obs0.1796 24989 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 146.66 Å2 / Biso mean: 53.022 Å2 / Biso min: 26.14 Å2
Baniso -1Baniso -2Baniso -3
1--1.79 Å20 Å2-1.78 Å2
2---1.14 Å2-0 Å2
3---3.28 Å2
Refinement stepCycle: final / Resolution: 2.2→44.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3190 0 0 130 3320
Biso mean---49.82 -
Num. residues----388
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0193244
X-RAY DIFFRACTIONr_bond_other_d0.0010.023179
X-RAY DIFFRACTIONr_angle_refined_deg1.5951.9634366
X-RAY DIFFRACTIONr_angle_other_deg0.96137286
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1595384
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.19624.024164
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.82115626
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4161528
X-RAY DIFFRACTIONr_chiral_restr0.090.2484
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023618
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02766
X-RAY DIFFRACTIONr_mcbond_it3.7234.7941548
X-RAY DIFFRACTIONr_mcbond_other3.6964.7931547
X-RAY DIFFRACTIONr_mcangle_it5.0447.1641928
LS refinement shellResolution: 2.2→2.257 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 98 -
Rwork0.275 1834 -
all-1932 -
obs--99.84 %

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