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- PDB-9ff9: Crystal structure of N-terminal acetylated tropomyosin Cdc8 -

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Basic information

Entry
Database: PDB / ID: 9ff9
TitleCrystal structure of N-terminal acetylated tropomyosin Cdc8
ComponentsTropomyosin
KeywordsSTRUCTURAL PROTEIN / Tropomyosin / cdc8 / yeast / overlap complex
Function / homology
Function and homology information


plasma membrane fusion involved in cytogamy / formin-nucleated actin cable / actin lateral binding / mating projection actin fusion focus / RHOV GTPase cycle / actin cortical patch organization / mitotic actomyosin contractile ring / mitotic actomyosin contractile ring assembly / mitotic actomyosin contractile ring contraction / actomyosin contractile ring ...plasma membrane fusion involved in cytogamy / formin-nucleated actin cable / actin lateral binding / mating projection actin fusion focus / RHOV GTPase cycle / actin cortical patch organization / mitotic actomyosin contractile ring / mitotic actomyosin contractile ring assembly / mitotic actomyosin contractile ring contraction / actomyosin contractile ring / actin cortical patch / mating projection tip / cell division site / mitotic cytokinesis / actin filament organization / actin filament / actin filament binding / cytoplasm
Similarity search - Function
Tropomyosin / Tropomyosin
Similarity search - Domain/homology
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.195 Å
AuthorsZahn, M. / Heiringhoff, R.S. / Fedorov, R. / Manstein, D.J.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)AB 1234/1-1 Germany
CitationJournal: J.Biol.Chem. / Year: 2024
Title: Crystal structures of cables formed by the acetylated and unacetylated forms of the Schizosaccharomyces pombe tropomyosin ortholog Tpm Cdc8 .
Authors: Reinke, P.Y.A. / Heiringhoff, R.S. / Reindl, T. / Baker, K. / Taft, M.H. / Meents, A. / Mulvihill, D.P. / Davies, O.R. / Fedorov, R. / Zahn, M. / Manstein, D.J.
History
DepositionMay 22, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 6, 2024Provider: repository / Type: Initial release
Revision 2.0Feb 12, 2025Group: Atomic model / Author supporting evidence ...Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Polymer sequence / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / citation / entity_poly / pdbx_contact_author / pdbx_entity_instance_feature / pdbx_modification_feature / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_conf / struct_conn / struct_ref_seq / struct_ref_seq_dif
Item: _atom_site.auth_asym_id / _atom_site_anisotrop.pdbx_auth_asym_id ..._atom_site.auth_asym_id / _atom_site_anisotrop.pdbx_auth_asym_id / _citation.journal_volume / _citation.title / _entity_poly.pdbx_strand_id / _pdbx_modification_feature.auth_asym_id / _pdbx_modification_feature.modified_residue_auth_asym_id / _pdbx_nonpoly_scheme.pdb_strand_id / _pdbx_poly_seq_scheme.pdb_strand_id / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _struct_conf.beg_auth_asym_id / _struct_conf.end_auth_asym_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_ref_seq.pdbx_strand_id / _struct_ref_seq_dif.pdbx_pdb_strand_id
Revision 2.1Apr 2, 2025Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details ..._pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tropomyosin
B: Tropomyosin


Theoretical massNumber of molelcules
Total (without water)38,0422
Polymers38,0422
Non-polymers00
Water34219
1
A: Tropomyosin
B: Tropomyosin

A: Tropomyosin
B: Tropomyosin


Theoretical massNumber of molelcules
Total (without water)76,0844
Polymers76,0844
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_916x+4,y-4,z+11
Unit cell
Length a, b, c (Å)25.401, 38.318, 97.542
Angle α, β, γ (deg.)97.71, 94.71, 101.5
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Tropomyosin


Mass: 19021.082 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: acetylated N-terminus
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Gene: cdc8, SPAC27F1.02c / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q02088
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.41 Å3/Da / Density % sol: 48.88 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.1M Tris pH 8.0 43% MPD 350 mM ammonium acetat

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Apr 14, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.195→37.1 Å / Num. obs: 6580 / % possible obs: 78 % / Redundancy: 3.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.043 / Net I/σ(I): 8
Reflection shellResolution: 2.195→2.546 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.515 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 329 / CC1/2: 0.835 / Rpim(I) all: 0.367 / % possible all: 51.3

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487:refinement
autoPROCdata reduction
STARANISOdata scaling
Arcimboldophasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.195→37.1 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.3149 301 -
Rwork0.2604 --
obs0.263 6580 36.47 %
Refinement stepCycle: LAST / Resolution: 2.195→37.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2658 0 0 19 2677
Refinement TLS params.Origin x: 25.9419 Å / Origin y: -28.4822 Å / Origin z: 43.2985 Å
111213212223313233
T0.3754 Å20.0489 Å2-0.1983 Å2-0.2678 Å20.2096 Å2--0.6905 Å2
L0.3766 °2-0.6784 °20.9376 °2-0.7616 °2-1.0937 °2---0.5408 °2
S-0.1539 Å °0.1868 Å °0.3135 Å °0.1868 Å °-0.0858 Å °0.0501 Å °0.3135 Å °0.0501 Å °-0.4382 Å °
Refinement TLS groupSelection details: all

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