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- PDB-1y64: Bni1p Formin Homology 2 Domain complexed with ATP-actin -

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Basic information

Entry
Database: PDB / ID: 1y64
TitleBni1p Formin Homology 2 Domain complexed with ATP-actin
Components
  • Actin, alpha skeletal muscle
  • BNI1 protein
KeywordsSTRUCTURAL PROTEIN / FH2 ACTIN CYTOSKELETON / COILED COIL / ACTIN / TETRAMETHYLRHODAMINE-5-MALEIMIDE / ATP-STATE
Function / homology
Function and homology information


polarisome / formin-nucleated actin cable assembly / budding cell apical bud growth / mitotic actomyosin contractile ring / mitotic actomyosin contractile ring assembly / vesicle targeting / prospore membrane / establishment or maintenance of actin cytoskeleton polarity / actin nucleation / incipient cellular bud site ...polarisome / formin-nucleated actin cable assembly / budding cell apical bud growth / mitotic actomyosin contractile ring / mitotic actomyosin contractile ring assembly / vesicle targeting / prospore membrane / establishment or maintenance of actin cytoskeleton polarity / actin nucleation / incipient cellular bud site / cellular bud tip / profilin binding / cellular bud neck / barbed-end actin filament capping / mating projection tip / cellular hyperosmotic response / cytoskeletal motor activator activity / cell division site / myosin heavy chain binding / tropomyosin binding / establishment of cell polarity / actin filament bundle / troponin I binding / filamentous actin / mesenchyme migration / establishment of mitotic spindle orientation / actin filament bundle assembly / skeletal muscle myofibril / striated muscle thin filament / skeletal muscle thin filament assembly / actin monomer binding / skeletal muscle fiber development / stress fiber / titin binding / actin filament polymerization / filopodium / actin filament / regulation of actin cytoskeleton organization / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / small GTPase binding / calcium-dependent protein binding / actin filament binding / lamellipodium / regulation of protein localization / cell body / hydrolase activity / protein domain specific binding / calcium ion binding / positive regulation of gene expression / magnesium ion binding / ATP binding / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Lyase 2-enoyl-coa Hydratase; Chain A, domain 2 - #50 / Lyase 2-enoyl-coa Hydratase; Chain A, domain 2 / : / Formin, FH2 domain / Diaphanous autoregulatory (DAD) domain / Diaphanous autoregulatory domain (DAD) profile. / Formin, FH3 domain / Formin, GTPase-binding domain / Diaphanous FH3 Domain / Diaphanous GTPase-binding Domain ...Lyase 2-enoyl-coa Hydratase; Chain A, domain 2 - #50 / Lyase 2-enoyl-coa Hydratase; Chain A, domain 2 / : / Formin, FH2 domain / Diaphanous autoregulatory (DAD) domain / Diaphanous autoregulatory domain (DAD) profile. / Formin, FH3 domain / Formin, GTPase-binding domain / Diaphanous FH3 Domain / Diaphanous GTPase-binding Domain / Diaphanous FH3 Domain / Diaphanous GTPase-binding Domain / Rho GTPase-binding/formin homology 3 (GBD/FH3) domain / Rho GTPase-binding/formin homology 3 (GBD/FH3) domain profile. / Formin, FH2 domain / Formin, FH2 domain superfamily / Formin Homology 2 Domain / Formin homology-2 (FH2) domain profile. / Formin Homology 2 Domain / ATPase, substrate binding domain, subdomain 4 / Actin; Chain A, domain 4 / ATPase, nucleotide binding domain / Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Actin / Actin family / Actin / Helix non-globular / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Special / ATPase, nucleotide binding domain / Armadillo-like helical / Nucleotidyltransferase; domain 5 / Armadillo-type fold / Alpha-Beta Complex / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Protein BNI1 / Actin, alpha skeletal muscle
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Oryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.05 Å
AuthorsOtomo, T. / Tomchick, D.R. / Otomo, C. / Panchal, S.C. / Machius, M. / Rosen, M.K.
Citation
Journal: Nature / Year: 2005
Title: Structural basis of actin filament nucleation and processive capping by a formin homology 2 domain
Authors: Otomo, T. / Tomchick, D.R. / Otomo, C. / Panchal, S.C. / Machius, M. / Rosen, M.K.
#1: Journal: Cell(Cambridge,Mass.) / Year: 2004
Title: Crystal Structures Of A Formin Homology-2 Domain Reveal A Tethered-Dimer Architecture
Authors: Xu, Y. / Moseley, J.B. / Sagot, I. / Poy, F. / Pellman, D. / Goode, B.L. / Eck, M.J.
#2: Journal: Mol.Cell / Year: 2004
Title: The Core FH2 Domain of Diaphanous-Related Formins Is an Elongated Actin Binding Protein that Inhibits Polymerization
Authors: Shimada, A. / Nyitrai, M. / Vetter, I.R. / Kuhlmann, D. / Bugyi, B. / Narumiya, S. / Geeves, M.A. / Wittinghofer, A.
History
DepositionDec 3, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 18, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 26, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.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.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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 / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: Actin, alpha skeletal muscle
B: BNI1 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,3454
Polymers92,7982
Non-polymers5472
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)231.997, 56.229, 100.945
Angle α, β, γ (deg.)90.00, 107.70, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Actin, alpha skeletal muscle / Alpha-actin 1


Mass: 41875.633 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Tissue: muscle / References: UniProt: P68135
#2: Protein BNI1 protein / Synthetic lethal 39


Mass: 50921.957 Da / Num. of mol.: 1 / Fragment: FH2 DOMAIN, RESIDUES 1327-1769
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: BNI1, PPF3, SHE5 / Production host: Escherichia coli (E. coli) / References: UniProt: P41832
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
Has protein modificationY

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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: 3.3 Å3/Da / Density % sol: 60 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: potassium bromide, hepes, DTT, Tris, ATP, calcium chloride, ethylene glycol, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.99987, 0.9797, 0.97981, 0.96411
DetectorType: SBC-2 / Detector: CCD / Date: Feb 20, 2004
RadiationMonochromator: Silicon crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.999871
20.97971
30.979811
40.964111
ReflectionResolution: 3.05→31.78 Å / Num. all: 26458 / Num. obs: 26458 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2 % / Biso Wilson estimate: 113 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 24.4
Reflection shellResolution: 3.05→3.08 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.391 / Mean I/σ(I) obs: 1.8 / Num. unique all: 1314 / % possible all: 90.8

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
MLPHAREphasing
CNSrefinement
HKL-2000data reduction
RefinementMethod to determine structure: MAD / Resolution: 3.05→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.313 1145 random
Rwork0.289 --
all0.313 23883 -
obs0.313 22738 -
Refine analyzeLuzzati sigma a free: 1.16 Å
Refinement stepCycle: LAST / Resolution: 3.05→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6130 0 32 0 6162
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.78

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