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- PDB-2iyb: Structure of complex between the 3rd LIM domain of TES and the EV... -

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Basic information

Entry
Database: PDB / ID: 2iyb
TitleStructure of complex between the 3rd LIM domain of TES and the EVH1 domain of Mena
Components
  • PROTEIN ENABLED HOMOLOG
  • TESTIN
KeywordsMETAL-BINDING / LIM DOMAIN / SH3-BINDING / TUMOUR SUPRESSOR LIM DOMAIN EVH1 DOMAIN CELL MOTILITY / PHOSPHORYLATION / CYTOSKELETON / ACTIN-BINDING
Function / homology
Function and homology information


actin polymerization-dependent cell motility / WW domain binding / profilin binding / Signaling by ROBO receptors / actin polymerization or depolymerization / Generation of second messenger molecules / filopodium / axon guidance / SH3 domain binding / lamellipodium ...actin polymerization-dependent cell motility / WW domain binding / profilin binding / Signaling by ROBO receptors / actin polymerization or depolymerization / Generation of second messenger molecules / filopodium / axon guidance / SH3 domain binding / lamellipodium / cell junction / actin binding / cytoskeleton / cadherin binding / negative regulation of cell population proliferation / focal adhesion / synapse / protein-containing complex / RNA binding / zinc ion binding / nucleus / plasma membrane / cytosol
Similarity search - Function
PET domain / PET testin / Testin, LIM domain 1 / Testin, LIM domain 2 / Testin, LIM domain 3 / : / PET Domain / PET domain profile. / VASP tetramerisation / VASP tetramerisation domain superfamily ...PET domain / PET testin / Testin, LIM domain 1 / Testin, LIM domain 2 / Testin, LIM domain 3 / : / PET Domain / PET domain profile. / VASP tetramerisation / VASP tetramerisation domain superfamily / VASP tetramerisation domain / Cysteine Rich Protein / WH1/EVH1 domain / WH1 domain / WH1 domain profile. / WASP homology region 1 / Cysteine Rich Protein / LIM zinc-binding domain signature. / LIM domain / Zinc-binding domain present in Lin-11, Isl-1, Mec-3. / Zinc finger, LIM-type / LIM domain profile. / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / Ribbon / PH-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
Protein enabled homolog / Testin
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsBriggs, D.C. / McDonald, N.Q.
CitationJournal: Mol. Cell / Year: 2007
Title: Tes, a specific Mena interacting partner, breaks the rules for EVH1 binding.
Authors: Boeda, B. / Briggs, D.C. / Higgins, T. / Garvalov, B.K. / Fadden, A.J. / McDonald, N.Q. / Way, M.
History
DepositionJul 14, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 16, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Feb 28, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _citation_author.name
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN ENABLED HOMOLOG
B: PROTEIN ENABLED HOMOLOG
C: PROTEIN ENABLED HOMOLOG
D: PROTEIN ENABLED HOMOLOG
E: TESTIN
F: TESTIN
G: TESTIN
H: TESTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,28517
Polymers80,6968
Non-polymers5899
Water6,918384
1
A: PROTEIN ENABLED HOMOLOG
E: TESTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,3705
Polymers20,1742
Non-polymers1963
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1710 Å2
ΔGint-6.4 kcal/mol
Surface area11250 Å2
MethodPQS
2
B: PROTEIN ENABLED HOMOLOG
F: TESTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,3054
Polymers20,1742
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1640 Å2
ΔGint-6 kcal/mol
Surface area11050 Å2
MethodPQS
3
C: PROTEIN ENABLED HOMOLOG
G: TESTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,3054
Polymers20,1742
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1780 Å2
ΔGint-5.6 kcal/mol
Surface area10510 Å2
MethodPQS
4
D: PROTEIN ENABLED HOMOLOG
H: TESTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,3054
Polymers20,1742
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1680 Å2
ΔGint-7 kcal/mol
Surface area10660 Å2
MethodPQS
Unit cell
Length a, b, c (Å)66.548, 292.927, 37.126
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.9949, -0.068, 0.0744), (-0.0686, -0.9976, 0.005), (0.0739, -0.0101, -0.9972)2.4238, 149.1503, 72.408
2given(0.0544, 0.0966, -0.9938), (-0.1929, 0.9776, 0.0844), (0.9797, 0.1871, 0.0718)27.16, 72.8928, 34.7171
3given(0.025, 0.2567, -0.9662), (-0.2243, 0.9433, 0.2448), (0.9742, 0.2106, 0.0811)18.8523, 79.1112, 3.1666
4given(0.9995, -0.0257, 0.0201), (-0.0249, -0.999, -0.0376), (0.021, 0.0371, -0.9991)1.9884, 150.0217, 71.0608
5given(0.0983, 0.0708, -0.9926), (-0.1401, 0.9885, 0.0567), (0.9853, 0.1335, 0.1071)27.828, 72.983, 35.7444
6given(0.0945, 0.2178, -0.9714), (-0.156, 0.9669, 0.2017), (0.9832, 0.1325, 0.1254)17.6756, 76.8093, 4.4886
DetailsFOR THE HETERO-ASSEMBLY DESCRIBED BY REMARK 350

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Components

#1: Protein
PROTEIN ENABLED HOMOLOG / MENA


Mass: 12842.518 Da / Num. of mol.: 4 / Fragment: EVH1 DOMAIN, RESIDUES 1-113
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PMW172 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): FB810 / References: UniProt: Q8N8S7
#2: Protein
TESTIN / TESS / TES


Mass: 7331.590 Da / Num. of mol.: 4 / Fragment: 3RD LIM DOMAIN, RESIDUES 357-421
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PMW172 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): FB810 / References: UniProt: Q9UGI8
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 384 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENA/VASP PROTEINS ARE ACTIN-ASSOCIATED PROTEINS INVOLVED IN A RANGE OF PROCESSES DEPENDENT ON ...ENA/VASP PROTEINS ARE ACTIN-ASSOCIATED PROTEINS INVOLVED IN A RANGE OF PROCESSES DEPENDENT ON CYTOSKELETON REMODELLING AND CELL POLARITY SUCH AS AXON GUIDANCE AND LAMELLIPODIAL AND FILOPODIAL DYNAMICS IN MIGRATING CELLS.

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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: 44.79 % / Description: NONE
Crystal growpH: 6.5 / Details: 100MM BISTRIS PH 6.5, 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 13, 2004 / Details: MIRROR
RadiationMonochromator: SI CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.35→60 Å / Num. obs: 39369 / % possible obs: 98.5 % / Observed criterion σ(I): 1 / Redundancy: 12.9 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 5.4
Reflection shellResolution: 2.35→2.48 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 2.7 / % possible all: 90.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EVH WITHOUT FP4 LIGAND

1evh


Resolution: 2.35→64.96 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.885 / SU B: 15.685 / SU ML: 0.197 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.454 / ESU R Free: 0.275 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DISORDER RESIDUES AND ATOMS WERE OMMITED.
RfactorNum. reflection% reflectionSelection details
Rfree0.259 1587 5.1 %RANDOM
Rwork0.199 ---
obs0.202 31115 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 27.98 Å2
Baniso -1Baniso -2Baniso -3
1--0.098 Å20 Å20 Å2
2---0.022 Å20 Å2
3---0.121 Å2
Refinement stepCycle: LAST / Resolution: 2.35→64.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5387 0 9 384 5780
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0215521
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3461.8957473
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.5955700
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.23323.9259
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.29615859
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5021529
X-RAY DIFFRACTIONr_chiral_restr0.1260.2813
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024249
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2180.22465
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3010.23738
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.2389
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1880.285
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1370.217
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5541.53596
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.96125591
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.17432211
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.8854.51881
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 10.38→64.96 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.254 16
Rwork0.266 447
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)
10.91490.5654-0.05532.185-0.35180.88230.02690.0058-0.01150.0666-0.0246-0.0222-0.02260.0204-0.0024-0.02820.0115-0.002-0.01440.0052-0.07749.99685.87544.449
21.1048-0.47370.21931.4316-0.19290.71710.00910.02820.0144-0.02720.00920.02960.00580.02-0.0183-0.0253-0.00920.0051-0.00140.0011-0.07579.77162.84128.154
31.1857-0.67720.24193.3486-0.39261.0473-0.04760.02560.0360.07760.0332-0.0932-0.00110.04250.0145-0.08780.01530.0041-0.0398-0.0048-0.00946.01413.32118.935
40.9999-0.32920.15461.8731-0.451.16440.00310.0361-0.0444-0.0576-0.02860.0157-0.00720.03810.0254-0.08350.00320.0181-0.05640.00910.033838.5713.03913.685
51.8963-0.5201-1.39312.6598-0.21061.90940.12580.158-0.0309-0.0278-0.1350.0036-0.1192-0.00680.0093-0.03120.0141-0.0088-0.02190.015-0.077720.799100.83433.888
62.1121.07210.84934.0590.93971.20340.0181-0.0802-0.06660.115-0.08910.01250.0019-0.02520.0709-0.0265-0.0035-0.01-0.03360.0111-0.07519.27247.00439.255
71.1698-0.71950.35853.7276-0.32890.92790.188-0.0143-0.0726-0.185-0.15360.09420.0343-0.04-0.0344-0.00590.017-0.0247-0.060.0077-0.0411-6.42327.0348.555
80.99970.06720.62522.97670.90233.10530.080.0161-0.08760.0051-0.09070.03210.0212-0.14060.0108-0.08050.0169-0.0043-0.0433-0.0097-0.004425.54228.1435.598
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 113
2X-RAY DIFFRACTION2B1 - 113
3X-RAY DIFFRACTION3C3 - 113
4X-RAY DIFFRACTION4D2 - 113
5X-RAY DIFFRACTION5E358 - 421
6X-RAY DIFFRACTION6F358 - 420
7X-RAY DIFFRACTION7G358 - 420
8X-RAY DIFFRACTION8H358 - 420

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