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- PDB-6yig: Crystal structure of the N-terminal EF-hand domain of Arabidopsis... -

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Basic information

Entry
Database: PDB / ID: 6yig
TitleCrystal structure of the N-terminal EF-hand domain of Arabidopsis thaliana AtEH1/Pan1
ComponentsCalcium-binding EF hand family protein
KeywordsENDOCYTOSIS / calcium-binding / clathrin / TPLATE / lipid-binding.
Function / homology
Function and homology information


endosomal transport / endocytosis / protein-macromolecule adaptor activity / calcium ion binding / nucleus / plasma membrane / cytoplasm
Similarity search - Function
EH domain / EH domain profile. / Eps15 homology domain / EH domain / EF hand / EF-hand / Recoverin; domain 1 / EF-hand, calcium binding motif / EF-hand calcium-binding domain profile. / EF-hand domain ...EH domain / EH domain profile. / Eps15 homology domain / EH domain / EF hand / EF-hand / Recoverin; domain 1 / EF-hand, calcium binding motif / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Calcium-binding EF hand family protein
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsYperman, K. / Merceron, R. / De Munck, S. / Bloch, Y. / Savvides, S.N. / Pleskot, R. / Van Damme, D.
Funding supportEuropean Union, Belgium, 2items
OrganizationGrant numberCountry
European Research Council (ERC)682436European Union
Research Foundation - Flanders (FWO)AUGE-11-029 Belgium
CitationJournal: Nat Commun / Year: 2021
Title: Distinct EH domains of the endocytic TPLATE complex confer lipid and protein binding.
Authors: Yperman, K. / Papageorgiou, A.C. / Merceron, R. / De Munck, S. / Bloch, Y. / Eeckhout, D. / Jiang, Q. / Tack, P. / Grigoryan, R. / Evangelidis, T. / Van Leene, J. / Vincze, L. / ...Authors: Yperman, K. / Papageorgiou, A.C. / Merceron, R. / De Munck, S. / Bloch, Y. / Eeckhout, D. / Jiang, Q. / Tack, P. / Grigoryan, R. / Evangelidis, T. / Van Leene, J. / Vincze, L. / Vandenabeele, P. / Vanhaecke, F. / Potocky, M. / De Jaeger, G. / Savvides, S.N. / Tripsianes, K. / Pleskot, R. / Van Damme, D.
History
DepositionApr 1, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 14, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 9, 2021Group: Database references / Refinement description
Category: citation / citation_author / pdbx_refine_tls_group
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.year / _pdbx_refine_tls_group.beg_auth_asym_id / _pdbx_refine_tls_group.beg_auth_seq_id / _pdbx_refine_tls_group.end_auth_asym_id / _pdbx_refine_tls_group.end_auth_seq_id / _pdbx_refine_tls_group.selection_details
Revision 1.2Jan 24, 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: Calcium-binding EF hand family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,7993
Polymers11,7361
Non-polymers632
Water1,71195
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering, domain is a monomer in SEC-MALLS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area220 Å2
ΔGint-24 kcal/mol
Surface area5940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.510, 38.620, 63.520
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Calcium-binding EF hand family protein / F2D10.25


Mass: 11736.118 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The first 21 amino acids encode for an N-terminal 6xHis tag and a TEV cleavage site. The protein was subjected to a TEV digest hence the first 15 amino acids should no longer be present.
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At1g20760, F2D10.25, F2D10_25 / Plasmid: pEt22b / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): NEB C2527 / References: UniProt: Q9LM78
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / 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: 1.97 Å3/Da / Density % sol: 37.44 % / Description: plate like
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.3
Details: 100mM HEPES pH 7.6, 0.8M SodiumMalonate, 0.5% Jeffamine
Temp details: temperature controlled incubator

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 1.033 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 29, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.55→33 Å / Num. obs: 23759 / % possible obs: 97.2 % / Redundancy: 7.47 % / Biso Wilson estimate: 15.68 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.052 / Net I/σ(I): 22.88
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.55-1.593.643.414510.9190.38781.4
1.59-1.634.244.6815480.9480.30388
1.63-1.684.895.6616140.960.26693.4
1.68-1.735.737.0316150.980.23998.5
1.73-1.797.099.1316130.9890.21499.8
1.79-1.858.5411.6415740.9920.186100
1.85-1.928.5313.3215210.9950.15499.9
1.92-28.4516.6114390.9960.122100
2-2.098.4920.814090.9980.09199.9
2.09-2.198.6225.8313180.9980.073100
2.19-2.318.7128.3512640.9980.06599.9
2.31-2.458.7133.5111990.9980.057100
2.45-2.628.6735.8311120.9990.05399.9
2.62-2.8339.510530.9990.04699.9
2.83-3.18.543.659680.9990.041100
3.1-3.478.7149.68670.9990.037100
3.47-48.855.367670.9990.034100
4-4.98.7860.2765410.03100
4.9-6.938.7856.875000.9990.033100
6.93-338.7463.432730.9990.029100

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Processing

Software
NameVersionClassification
ARP/wARPmodel building
PHENIX1.17.1_3660refinement
XDS20180409data reduction
XSCALE20180409data scaling
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2qpt

2qpt


Resolution: 1.55→33 Å / SU ML: 0.1056 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.4594
RfactorNum. reflection% reflection
Rfree0.164 1197 5.04 %
Rwork0.1449 --
obs0.1459 23738 97.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 22.05 Å2
Refinement stepCycle: LAST / Resolution: 1.55→33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms754 0 2 95 851
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082813
X-RAY DIFFRACTIONf_angle_d0.93081111
X-RAY DIFFRACTIONf_chiral_restr0.0483123
X-RAY DIFFRACTIONf_plane_restr0.0067150
X-RAY DIFFRACTIONf_dihedral_angle_d17.3351295
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.610.24371150.19212154X-RAY DIFFRACTION83.91
1.61-1.690.20271250.16822375X-RAY DIFFRACTION91.44
1.69-1.770.18531330.15612519X-RAY DIFFRACTION98.84
1.77-1.890.18611320.1392593X-RAY DIFFRACTION99.82
1.89-2.030.16661360.14082574X-RAY DIFFRACTION99.89
2.03-2.240.16091430.12512586X-RAY DIFFRACTION99.96
2.24-2.560.16041350.12982570X-RAY DIFFRACTION99.93
2.56-3.220.17621360.14392599X-RAY DIFFRACTION99.96
3.22-330.13761420.15232571X-RAY DIFFRACTION99.96
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)
10.9729962230510.3894076741050.184840499170.637101388914-0.7964472196471.60929966615-0.04083271073030.70014941082-0.223649146902-1.498686825230.266590579046-0.826513208274-0.2228975569280.477402768321-0.089833123970.5882549073650.07330625914490.255994513970.611267159317-0.0561543507180.44067852338222.57677236116.60372405540.0982331231889
24.887961617090.340058017901-1.032648972653.107894503934.979920721828.527937872050.0822304710750.09153502823250.231323641436-0.5510325506410.163639577562-0.479293910196-0.3426703302480.392940096614-0.2233498973010.178960507638-0.02122503037150.03359694240860.1569141121520.002355217428770.13174088021216.341551193719.76363692578.75590245446
35.936998411872.27745866215-1.341981456883.737616446411.338086991191.672457655640.0710052159858-0.3128702875050.3356918523960.235287177062-0.1015640180730.162367783193-0.148204039787-0.05868961214890.02817098332050.153703574603-0.0105019111467-0.004891651389010.151148709274-0.02878621157880.16038253195415.212350800323.907107913519.5296834104
42.540903519371.965787392082.218462515871.667241113471.906446654442.84277861053-0.0275886448596-0.08022555861350.199948184674-0.0738045479159-0.06185607697540.16472657841-0.207437844243-0.1771540906490.07412838486770.1435831995170.0312355112577-0.02224605499270.1370075936160.0004593627068680.1709699389934.1288350405322.261398151711.4943111647
55.02845507987-0.4809312126981.14470871013.02454352001-0.06225790091654.070721553520.0702885459657-0.100774781580.01997436757770.104185012184-0.06149250697560.104356973238-0.0207689456752-0.296581195734-0.002637568907640.140328941048-0.003354348494660.002244088170060.146210484903-0.0238908036920.144616086831-0.020156019103814.401914424715.6469277743
63.057266300181.141546723410.3311929561982.766974920171.291011969974.016862633880.0802041016979-0.264562103097-0.156471917150.253844119955-0.0151555631615-0.09722940046410.1760581903790.0464743169876-0.06492535082480.1403457948240.0114627993674-0.01316861722930.1275991483490.0136837380580.1137391470559.8582466697612.940516359615.0187702775
70.1938112079451.27363466169-0.8193499280859.86445694098-7.470773226396.37184248791-0.3338110093890.415581075550.205553549323-1.018281154840.8210546613490.9495875400470.202612032966-0.336273887015-0.2963264724840.237043331519-0.0712430514392-0.07045666021470.2785477777420.01190269993420.245002908429-1.213394759176.312004159455.50878460721
87.46962604084-0.229856881405-3.075357574942.13337330927-1.321510169574.565415515160.09080362379360.254953875341-0.0568082388266-0.115813382138-0.0853502613810.1799264179560.142556983078-0.231304975341-0.0155614279390.1260329823080.00803125280146-0.0143075093410.121771376637-0.02410944345460.1653293359237.673377588731.4019525637510.5690882441
97.23322237278-5.121265177250.8492270892594.47803705346-2.799798216865.770019647020.2974070139720.2755302409230.513854174584-0.637059307742-0.307736577969-0.395601007279-0.2373773649110.196857245075-0.05654114314680.150515123805-0.01109943596890.005036301855080.1719875832830.006527335603150.1243192426329.5374226117916.93389392923.06109501008
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 9 )A5 - 9
2X-RAY DIFFRACTION2chain 'A' and (resid 10 through 18 )A10 - 18
3X-RAY DIFFRACTION3chain 'A' and (resid 19 through 27 )A19 - 27
4X-RAY DIFFRACTION4chain 'A' and (resid 28 through 41 )A28 - 41
5X-RAY DIFFRACTION5chain 'A' and (resid 42 through 52 )A42 - 52
6X-RAY DIFFRACTION6chain 'A' and (resid 53 through 76 )A53 - 76
7X-RAY DIFFRACTION7chain 'A' and (resid 77 through 82 )A77 - 82
8X-RAY DIFFRACTION8chain 'A' and (resid 83 through 97 )A83 - 97
9X-RAY DIFFRACTION9chain 'A' and (resid 98 through 105 )A98 - 105

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