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- PDB-1ux4: Crystal structures of a Formin Homology-2 domain reveal a tethere... -

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Basic information

Entry
Database: PDB / ID: 1ux4
TitleCrystal structures of a Formin Homology-2 domain reveal a tethered-dimer architecture
ComponentsBNI1 PROTEIN
KeywordsSTRUCTURAL PROTEIN / FH2 ACTIN CYTOSKELETON / COILED COIL
Function / homology
Function and homology information


polarisome / formin-nucleated actin cable assembly / budding cell apical bud growth / 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 ...polarisome / formin-nucleated actin cable assembly / budding cell apical bud growth / 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 / mating projection tip / barbed-end actin filament capping / cell division site / establishment of cell polarity / establishment of mitotic spindle orientation / actin filament bundle assembly / actin filament / regulation of actin cytoskeleton organization / small GTPase binding / regulation of protein localization / actin binding / identical protein binding / plasma membrane
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 / Diaphanous FH3 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 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Helix non-globular / Special / Armadillo-like helical / Armadillo-type fold / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsXu, Y. / Moseley, J.B. / Sagot, I. / Poy, F. / Pellman, D. / Goode, B.L. / Eck, M.J.
Citation
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.
#1: Journal: Nat.Cell Biol. / Year: 2002
Title: Yeast Formins Regulate Cell Polarity by Controlling the Assembly of Actin Cables
Authors: Sagot, I. / Klee, S.K. / Pellman, D.
History
DepositionFeb 19, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 11, 2004Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Advisory / Data collection ...Advisory / Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.4May 8, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BNI1 PROTEIN
B: BNI1 PROTEIN


Theoretical massNumber of molelcules
Total (without water)94,4152
Polymers94,4152
Non-polymers00
Water0
1
A: BNI1 PROTEIN

A: BNI1 PROTEIN


Theoretical massNumber of molelcules
Total (without water)94,4152
Polymers94,4152
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
MethodPQS
2
B: BNI1 PROTEIN

B: BNI1 PROTEIN


Theoretical massNumber of molelcules
Total (without water)94,4152
Polymers94,4152
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
MethodPQS
Unit cell
Length a, b, c (Å)98.100, 172.200, 120.600
Angle α, β, γ (deg.)90.00, 112.30, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.9999, -0.0011, -0.016), (0.0012, -1, -0.0039), (-0.016, -0.0039, 0.9999)
Vector: 4.1126, 48.602, 0.0168)

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Components

#1: Protein BNI1 PROTEIN / FORMIN / SYNTHETIC LETHAL 39


Mass: 47207.695 Da / Num. of mol.: 2 / Fragment: FH2 DOMAIN, RESIDUES 1352-1765 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P41832
Compound detailsENGINEERED MUTATION IN CHAIN A AND B, ARG 1411 GLU ENGINEERED MUTATION IN CHAIN A AND B, LYS 1412 ...ENGINEERED MUTATION IN CHAIN A AND B, ARG 1411 GLU ENGINEERED MUTATION IN CHAIN A AND B, LYS 1412 PHE RESIDUES 1411-1416 (RKEDLQ) MUTATED INTO EF ORGANIZES MICROTUBULES BY MEDIATING SPINDLE POSITIONING AND MOVEMENT IN THE BUDDING PROCESS.

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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: 4.99 Å3/Da / Density % sol: 70 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.5
Details: HANGING DROP AGAINST 0.8M SODIUM POTASSIUM PHOSPHATE, 30% GLYCEROL, HEPES PH7.5, pH 7.50
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
18 mg/mlprotein1drop
22.5 mMPCMBS1drop
30.8 Msodium potassium phosphate1reservoir
4100 mMHEPES1reservoirpH7.5
530 %glycerol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 8-BM / Wavelength: 0.978
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 3.3→30 Å / Num. obs: 22747 / % possible obs: 82 % / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 12.5
Reflection
*PLUS
Highest resolution: 3.3 Å / % possible obs: 82 % / Num. measured all: 50090 / Rmerge(I) obs: 0.058
Reflection shell
*PLUS
% possible obs: 61 % / Rmerge(I) obs: 0.143 / Mean I/σ(I) obs: 4.5

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Processing

Software
NameVersionClassification
CNS1.1refinement
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.3→20 Å / Cross valid method: THROUGHOUT / σ(F): 2
Details: OCCUPANCY WAS ASSIGNED TO 0 FOR ATOMS WITH NO OBSERVED ELECTRON DENSITY
RfactorNum. reflection% reflectionSelection details
Rfree0.289 -7 %RANDOM
Rwork0.234 ---
obs0.234 22588 81 %-
Refinement stepCycle: LAST / Resolution: 3.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6644 0 0 0 6644
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refinement
*PLUS
Lowest resolution: 30 Å / Rfactor Rfree: 0.288
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_angle_deg / Dev ideal: 1.37

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