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- PDB-2vac: Structure of N-terminal Actin Depolymerizing Factor homology (ADF... -

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Basic information

Entry
Database: PDB / ID: 2vac
TitleStructure of N-terminal Actin Depolymerizing Factor homology (ADF-H) domain of human twinfilin-2
ComponentsTWINFILIN-2
KeywordsTRANSFERASE / ACTIN BINDING / PHOSPHORYLATION / COFILIN-LIKE / CYTOSKELETON / ACTIN-BINDING / PROTEIN TYROSINE KINASE-9 / ACTIN DEPOLYMERIZING FACTOR TRANSFERASE
Function / homology
Function and homology information


regulation of microvillus length / negative regulation of actin filament polymerization / barbed-end actin filament capping / cell projection organization / actin filament depolymerization / stereocilium / regulation of lamellipodium assembly / Sensory processing of sound by outer hair cells of the cochlea / Sensory processing of sound by inner hair cells of the cochlea / myofibril ...regulation of microvillus length / negative regulation of actin filament polymerization / barbed-end actin filament capping / cell projection organization / actin filament depolymerization / stereocilium / regulation of lamellipodium assembly / Sensory processing of sound by outer hair cells of the cochlea / Sensory processing of sound by inner hair cells of the cochlea / myofibril / actin monomer binding / positive regulation of axon extension / positive regulation of lamellipodium assembly / cellular response to retinoic acid / phosphatidylinositol-4,5-bisphosphate binding / protein kinase C binding / filopodium / actin filament / regulation of actin cytoskeleton organization / positive regulation of neuron projection development / cellular response to growth factor stimulus / actin filament binding / lamellipodium / growth cone / cadherin binding / perinuclear region of cytoplasm / RNA binding / extracellular exosome / ATP binding / cytoplasm
Similarity search - Function
Twinfilin / Actin-depolymerising factor homology domain / Cofilin/tropomyosin-type actin-binding protein / ADF-H domain profile. / Actin depolymerisation factor/cofilin -like domains / Severin / Severin / ADF-H/Gelsolin-like domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsElkins, J.M. / Pike, A.C.W. / King, O. / Salah, E. / Savitsky, P. / von Delft, F. / Weigelt, J. / Edwards, A. / Arrowsmith, C.H. / Sundstrom, M. / Knapp, S.
CitationJournal: To be Published
Title: Crystal Structure of N-Terminal Actin Depolymerizing Factor Homology (Adf-H) Domain of Human Twinfilin-2
Authors: Elkins, J.M. / Pike, A.C.W. / King, O. / Salah, E. / Savitsky, P. / von Delft, F. / Weigelt, J. / Edwards, A. / Arrowsmith, C.H. / Sundstrom, M. / Knapp, S.
History
DepositionAug 30, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 16, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jan 24, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Dec 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_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_asym_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.ptnr3_symmetry / _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.ptnr1_symmetry / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TWINFILIN-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,4405
Polymers15,1811
Non-polymers2584
Water2,900161
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)35.817, 48.560, 70.127
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 TWINFILIN-2 / TWINFILIN-1-LIKE PROTEIN / A6-RELATED PROTEIN / HA6RP / PROTEIN TYROSINE KINASE 9-LIKE


Mass: 15181.217 Da / Num. of mol.: 1
Fragment: ACTIN DEPOLYMERIZING FACTOR HOMOLOGY (ADF-H) DOMAIN 1, RESIDUES 6-137
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC28-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3-PRARE2 / References: UniProt: Q6IBS0
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / 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: 2.01 Å3/Da / Density % sol: 38.8 % / Description: NONE
Crystal growpH: 8
Details: 0.01M ZINC CHLORIDE,10% ETHYLENE GLYCOL,20% PEG6000, 0.1M TRIS PH8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.5418
DetectorType: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: Aug 2, 2007 / Details: MULTI-LAYER VARIMAX HR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→20.1 Å / Num. obs: 13653 / % possible obs: 97.5 % / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Biso Wilson estimate: 18.66 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 24.4
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 2.5 / % possible all: 94.9

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Processing

Software
NameVersionClassification
REFMAC5.3.0040refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1M4J

1m4j


Resolution: 1.7→20 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.939 / SU B: 4.125 / SU ML: 0.076 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.117 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.214 678 5 %RANDOM
Rwork0.17 ---
obs0.172 12971 97.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.83 Å2
Baniso -1Baniso -2Baniso -3
1--0.31 Å20 Å20 Å2
2---0.72 Å20 Å2
3---1.03 Å2
Refinement stepCycle: LAST / Resolution: 1.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1065 0 7 161 1233
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0221107
X-RAY DIFFRACTIONr_bond_other_d0.0030.02762
X-RAY DIFFRACTIONr_angle_refined_deg1.291.9591494
X-RAY DIFFRACTIONr_angle_other_deg1.81131852
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2755133
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.35624.18255
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.42415192
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.983157
X-RAY DIFFRACTIONr_chiral_restr0.0850.2158
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021232
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02232
X-RAY DIFFRACTIONr_nbd_refined0.2080.2205
X-RAY DIFFRACTIONr_nbd_other0.1990.2792
X-RAY DIFFRACTIONr_nbtor_refined0.1730.2527
X-RAY DIFFRACTIONr_nbtor_other0.0960.2538
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1230.299
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.180.217
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3020.232
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1570.226
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.7753734
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.97851065
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.0018500
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it6.2311429
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: 1.7→1.74 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.406 43
Rwork0.309 904
Refinement TLS params.Method: refined / Origin x: 19.1915 Å / Origin y: 1.1239 Å / Origin z: 35.9492 Å
111213212223313233
T-0.1209 Å2-0.0093 Å20.0061 Å2--0.1376 Å2-0.0027 Å2---0.0983 Å2
L1.5177 °2-0.2412 °2-0.0393 °2-1.4278 °2-0.4019 °2--1.147 °2
S0.0301 Å °0.0121 Å °0.0517 Å °0.0021 Å °-0.016 Å °0.0048 Å °-0.005 Å °0.0311 Å °-0.014 Å °

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