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- PDB-3ue5: ECP-cleaved Actin in complex with Spir domain D -

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Basic information

Entry
Database: PDB / ID: 3ue5
TitleECP-cleaved Actin in complex with Spir domain D
Components
  • Actin, alpha skeletal muscle
  • Protein spire
KeywordsCONTRACTILE PROTEIN/TRANSPORT PROTEIN / CONTRACTILE PROTEIN / CONTRACTILE PROTEIN-TRANSPORT PROTEIN complex
Function / homology
Function and homology information


chorion-containing eggshell formation / pole plasm RNA localization / establishment of meiotic spindle localization / oocyte karyosome formation / actin filament-based process / pole plasm oskar mRNA localization / pole plasm assembly / polar body extrusion after meiotic divisions / actin filament network formation / actin nucleation ...chorion-containing eggshell formation / pole plasm RNA localization / establishment of meiotic spindle localization / oocyte karyosome formation / actin filament-based process / pole plasm oskar mRNA localization / pole plasm assembly / polar body extrusion after meiotic divisions / actin filament network formation / actin nucleation / Golgi vesicle transport / cleavage furrow formation / cytoskeletal motor activator activity / oogenesis / positive regulation of mitochondrial fission / myosin heavy chain binding / tropomyosin binding / regulation of cytoskeleton organization / troponin I binding / filamentous actin / mesenchyme migration / actin filament bundle / actin filament bundle assembly / skeletal muscle myofibril / striated muscle thin filament / skeletal muscle thin filament assembly / actin monomer binding / intracellular transport / stress fiber / skeletal muscle fiber development / vesicle-mediated transport / titin binding / actin filament polymerization / cytoplasmic vesicle membrane / actin filament organization / filopodium / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / calcium-dependent protein binding / protein transport / lamellipodium / actin binding / cell body / actin cytoskeleton organization / cell cortex / microtubule binding / mitochondrial outer membrane / cytoskeleton / hydrolase activity / protein domain specific binding / calcium ion binding / positive regulation of gene expression / perinuclear region of cytoplasm / magnesium ion binding / ATP binding / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
Protein Spire / Kinase non-catalytic C-lobe domain / KIND domain / KIND domain profile. / kinase non-catalytic C-lobe domain / Wiskott Aldrich syndrome homology region 2 / WH2 domain / WH2 domain profile. / ATPase, substrate binding domain, subdomain 4 / Actin; Chain A, domain 4 ...Protein Spire / Kinase non-catalytic C-lobe domain / KIND domain / KIND domain profile. / kinase non-catalytic C-lobe domain / Wiskott Aldrich syndrome homology region 2 / WH2 domain / WH2 domain profile. / 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 / Zinc finger, FYVE/PHD-type / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / Zinc finger, RING/FYVE/PHD-type / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Actin, alpha skeletal muscle / Protein spire
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
Oryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.76 Å
AuthorsChen, C. / Phillips, M. / Sawaya, M.R. / Ralston, C.Y. / Quinlan, M.E.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Multiple Forms of Spire-Actin Complexes and their Functional Consequences.
Authors: Chen, C.K. / Sawaya, M.R. / Phillips, M.L. / Reisler, E. / Quinlan, M.E.
History
DepositionOct 28, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 7, 2012Group: Database references
Revision 1.2Apr 11, 2012Group: Database references
Revision 1.3Nov 27, 2024Group: 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.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.value / _struct_conn.pdbx_dist_value / _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_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

Downloads & links

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Assembly

Deposited unit
A: Actin, alpha skeletal muscle
B: Protein spire
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,8016
Polymers49,1832
Non-polymers6184
Water72140
1
A: Actin, alpha skeletal muscle
B: Protein spire
hetero molecules

A: Actin, alpha skeletal muscle
B: Protein spire
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,60312
Polymers98,3664
Non-polymers1,2368
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area6950 Å2
ΔGint-95 kcal/mol
Surface area32860 Å2
MethodPISA
2
A: Actin, alpha skeletal muscle
B: Protein spire
hetero molecules

A: Actin, alpha skeletal muscle
B: Protein spire
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,60312
Polymers98,3664
Non-polymers1,2368
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x,y,-z-11
Buried area6910 Å2
ΔGint-113 kcal/mol
Surface area33150 Å2
MethodPISA
3
A: Actin, alpha skeletal muscle
hetero molecules

A: Actin, alpha skeletal muscle
hetero molecules

B: Protein spire

B: Protein spire


Theoretical massNumber of molelcules
Total (without water)99,60312
Polymers98,3664
Non-polymers1,2368
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x,y,-z-11
crystal symmetry operation1_554x,y,z-11
crystal symmetry operation2_555-x,y,-z1
Buried area4430 Å2
ΔGint-87 kcal/mol
Surface area35630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.837, 53.551, 100.578
Angle α, β, γ (deg.)90.000, 92.650, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-376-

CL

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Components

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Protein , 2 types, 2 molecules AB

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


Mass: 41862.613 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: skeletal / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: P68135
#2: Protein Protein spire


Mass: 7320.585 Da / Num. of mol.: 1 / Fragment: UNP residues 428-485
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: CG10076, p150-Spir, spir / Production host: Escherichia coli (E. coli) / References: UniProt: Q9U1K1

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Non-polymers , 4 types, 44 molecules

#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
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.32 Å3/Da / Density % sol: 46.99 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: Tris pH 8.5, magnesium chloride, PEG-8000, vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 5, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.76→90 Å / Num. all: 10542 / Num. obs: 10542 / % possible obs: 89.6 % / Observed criterion σ(I): -3 / Redundancy: 2.7 % / Biso Wilson estimate: 46 Å2 / Rmerge(I) obs: 0.105 / Χ2: 0.963 / Net I/σ(I): 8.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.8-2.920.2376410.752155.4
2.9-3.022.40.2358570.74172.3
3.02-3.152.60.2019820.799184.5
3.15-3.322.70.1610850.662193.6
3.32-3.532.80.13411440.866197.9
3.53-3.82.90.10711450.849198.6
3.8-4.182.90.09311660.863198.6
4.18-4.792.90.09111490.94197.3
4.79-6.032.80.09111741.03199.2
6.03-902.70.07511991.831197.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation4 Å50.24 Å
Translation4 Å50.24 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER1.3.2phasing
BUSTER-TNTrefinement
PDB_EXTRACT3.1data extraction
BOSdata collection
BUSTER2.8.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.76→50.24 Å / Cor.coef. Fo:Fc: 0.8964 / Cor.coef. Fo:Fc free: 0.8718 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2402 499 4.82 %RANDOM
Rwork0.1974 ---
all0.1995 ---
obs0.1995 10358 --
Displacement parametersBiso max: 149.31 Å2 / Biso mean: 48.4404 Å2 / Biso min: 15.64 Å2
Baniso -1Baniso -2Baniso -3
1--14.7702 Å20 Å2-12.9464 Å2
2--7.1506 Å20 Å2
3---7.6196 Å2
Refine analyzeLuzzati coordinate error obs: 0.364 Å
Refinement stepCycle: LAST / Resolution: 2.76→50.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3040 0 34 40 3114
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1149SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes74HARMONIC2
X-RAY DIFFRACTIONt_gen_planes446HARMONIC5
X-RAY DIFFRACTIONt_it3136HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion422SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3749SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3136HARMONIC20.009
X-RAY DIFFRACTIONt_angle_deg4252HARMONIC21.08
X-RAY DIFFRACTIONt_omega_torsion2.42
X-RAY DIFFRACTIONt_other_torsion19.55
LS refinement shellResolution: 2.76→3.08 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.2656 106 5.06 %
Rwork0.2303 1987 -
all0.2322 2093 -
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.63930.20690.14811.79230.13361.61540.00320.0916-0.01050.06070.0531-0.05930.03710.1326-0.0563-0.08740.02870.0449-0.08570.0194-0.097913.196-13.3743-28.5027
21.59141.1873-2.36032.06992.91120.55420.01990.00530.10590.0685-0.10510.11050.061-0.09560.0852-0.0094-0.02370.1514-0.10060.0037-0.0321-6.2291-10.9061-12.6846
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A5 - 382
2X-RAY DIFFRACTION2{ B|* }B70 - 94

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