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- PDB-2xqn: Complex of the 2nd and 3rd LIM domains of TES with the EVH1 DOMAI... -

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Basic information

Entry
Database: PDB / ID: 2xqn
TitleComplex of the 2nd and 3rd LIM domains of TES with the EVH1 DOMAIN of MENA and the N-Terminal domain of actin-like protein Arp7A
Components
  • ACTIN-LIKE PROTEIN 7A
  • ENABLED HOMOLOG
  • TESTIN
KeywordsMETAL BINDING PROTEIN / METAL-BINDING PROTEIN / CYTOSKELETON / FOCAL ADHESION / ACROSOME
Function / homology
Function and homology information


postsynaptic cytoskeleton organization / actin polymerization-dependent cell motility / acrosome assembly / profilin binding / Signaling by ROBO receptors / actin polymerization or depolymerization / fertilization / motile cilium / WW domain binding / Generation of second messenger molecules ...postsynaptic cytoskeleton organization / actin polymerization-dependent cell motility / acrosome assembly / profilin binding / Signaling by ROBO receptors / actin polymerization or depolymerization / fertilization / motile cilium / WW domain binding / Generation of second messenger molecules / spermatid development / single fertilization / acrosomal vesicle / axon guidance / male germ cell nucleus / filopodium / GABA-ergic synapse / structural constituent of cytoskeleton / SH3 domain binding / cell junction / lamellipodium / actin binding / cytoskeleton / postsynapse / cadherin binding / negative regulation of cell population proliferation / focal adhesion / Golgi apparatus / protein-containing complex / RNA binding / zinc ion binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Actin-like protein 7A, N-terminal / Actin-like protein 7A N-terminus / PET domain / PET testin / Testin, LIM domain 1 / Testin, LIM domain 2 / Testin, LIM domain 3 / : / PET Domain / PET domain profile. ...Actin-like protein 7A, N-terminal / Actin-like protein 7A N-terminus / 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 / Actin / Actin family / Actin / Ribbon / ATPase, nucleotide binding domain / PH-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
Protein enabled homolog / Testin / Actin-like protein 7A
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.62 Å
AuthorsKnowles, P.P. / Briggs, D.C. / Murray-Rust, J. / McDonald, N.Q.
CitationJournal: J. Biol. Chem. / Year: 2011
Title: Molecular recognition of the Tes LIM2-3 domains by the actin-related protein Arp7A.
Authors: Boeda, B. / Knowles, P.P. / Briggs, D.C. / Murray-Rust, J. / Soriano, E. / Garvalov, B.K. / McDonald, N.Q. / Way, M.
History
DepositionSep 3, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 26, 2011Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2011Group: Database references / Other ...Database references / Other / Structure summary / Version format compliance
Revision 1.2Jun 28, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.3Feb 28, 2018Group: Database references / Structure summary / Category: audit_author / citation / citation_author
Item: _audit_author.name / _citation.journal_abbrev ..._audit_author.name / _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name
Revision 1.4May 8, 2019Group: Data collection / Experimental preparation
Category: database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp
Revision 1.5Dec 20, 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 / struct_site
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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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.ptnr1_symmetry / _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_asym_id / _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.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_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 / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ACTIN-LIKE PROTEIN 7A
M: ENABLED HOMOLOG
T: TESTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0578
Polymers34,7303
Non-polymers3275
Water88349
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4040 Å2
ΔGint-24.7 kcal/mol
Surface area17750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.829, 86.791, 115.266
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein ACTIN-LIKE PROTEIN 7A / ARP7A / ACTIN-LIKE-7-ALPHA


Mass: 7015.960 Da / Num. of mol.: 1 / Fragment: N-TERMINAL DOMAIN, RESIDUES 1-65
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: Q9Y615
#2: Protein ENABLED HOMOLOG / MENA


Mass: 13343.019 Da / Num. of mol.: 1 / Fragment: EVH1 DOMAIN, RESIDUES 1-115
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
#3: Protein TESTIN / TESS


Mass: 14370.611 Da / Num. of mol.: 1 / Fragment: LIM DOMAINS 2 AND 3, RESIDUES 296-421
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
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / 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: 2.96 Å3/Da / Density % sol: 58.54 % / Description: NONE
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: PROTEIN: 37.5 MG/ML OF PROTEIN COMPLEX IN 20MM TRIS-HCL PH 8.0, 100MM NACL RESERVOIR: 17.5 PEG 8K, 0.1MTRIS PH 8.5, 0.15M KSCN SITTING DROPS 2:1 PROTEIN:RESERVOIR, 22 DEG C CRYOPROTECTANT: N-PARATONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 17, 2007 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→25.74 Å / Num. obs: 12008 / % possible obs: 96.9 % / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Biso Wilson estimate: 56.2 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 14.2
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 4 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2.9 / % possible all: 79.7

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2IYB

2iyb


Resolution: 2.62→25.56 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.894 / SU B: 11.816 / SU ML: 0.239 / Cross valid method: THROUGHOUT / ESU R: 0.477 / ESU R Free: 0.306 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.26811 565 4.7 %RANDOM
Rwork0.21525 ---
obs0.21776 11400 99.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 43.715 Å2
Baniso -1Baniso -2Baniso -3
1--1.22 Å20 Å20 Å2
2--4.2 Å20 Å2
3----2.98 Å2
Refinement stepCycle: LAST / Resolution: 2.62→25.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2035 0 5 49 2089
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0212106
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8941.9142841
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.975262
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.62124.12497
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.02415339
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5251510
X-RAY DIFFRACTIONr_chiral_restr0.1390.2305
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211600
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8051.51310
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.55722104
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.243796
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.7154.5736
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: 2.618→2.686 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.407 35 -
Rwork0.338 786 -
obs--95.02 %

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