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- PDB-5zzb: LokiProfilin2/Rabbit Actin Complex -

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Basic information

Entry
Database: PDB / ID: 5zzb
TitleLokiProfilin2/Rabbit Actin Complex
Components
  • Actin, alpha skeletal muscle
  • Uncharacterized protein
KeywordsSTRUCTURAL PROTEIN / Actin / Archaea / Loki
Function / homology
Function and homology information


cytoskeletal motor activator activity / myosin heavy chain binding / tropomyosin binding / actin filament bundle / troponin I binding / filamentous actin / mesenchyme migration / actin filament bundle assembly / skeletal muscle myofibril / striated muscle thin filament ...cytoskeletal motor activator activity / myosin heavy chain binding / tropomyosin binding / actin filament bundle / troponin I binding / filamentous actin / mesenchyme migration / 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 / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / calcium-dependent protein binding / lamellipodium / actin binding / cell body / cytoskeleton / hydrolase activity / protein domain specific binding / calcium ion binding / positive regulation of gene expression / magnesium ion binding / ATP binding / identical protein binding / cytoplasm
Similarity search - Function
Actin; Chain A, domain 2 / Actin; Chain A, domain 2 / : / Profilin / Profilin superfamily / ATPase, substrate binding domain, subdomain 4 / Actin; Chain A, domain 4 / ATPase, nucleotide binding domain / Actins signature 1. / Actin, conserved site ...Actin; Chain A, domain 2 / Actin; Chain A, domain 2 / : / Profilin / Profilin superfamily / 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 / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / Roll / Alpha-Beta Complex / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / LATRUNCULIN B / Loki profilin-2 / Actin, alpha skeletal muscle
Similarity search - Component
Biological speciesLokiarchaeum sp. GC14_75 (archaea)
Oryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsRobinson, R.C. / Akil, C.
CitationJournal: Nature / Year: 2018
Title: Genomes of Asgard archaea encode profilins that regulate actin.
Authors: Akil, C. / Robinson, R.C.
History
DepositionMay 31, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 10, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 17, 2018Group: Data collection / Database references / Structure summary
Category: citation / citation_author / entity
Item: _citation.pdbx_database_id_PubMed / _citation.title / _entity.formula_weight
Revision 1.2Oct 31, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Dec 5, 2018Group: Data collection / Database references / Category: pdbx_related_exp_data_set
Revision 1.4Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / refine_hist / struct_conn
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _refine_hist.d_res_low / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Actin, alpha skeletal muscle
A: Uncharacterized protein
D: Actin, alpha skeletal muscle
C: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,21210
Polymers112,3264
Non-polymers1,8866
Water8,611478
1
B: Actin, alpha skeletal muscle
A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,1065
Polymers56,1632
Non-polymers9433
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Actin, alpha skeletal muscle
C: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,1065
Polymers56,1632
Non-polymers9433
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.850, 123.300, 88.240
Angle α, β, γ (deg.)90.00, 96.90, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 4 molecules BDAC

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


Mass: 41374.207 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: P68135
#2: Protein Uncharacterized protein / LokiProfilin2


Mass: 14788.970 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lokiarchaeum sp. GC14_75 (archaea) / Gene: Lokiarch_27400 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0F8XMN8

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Non-polymers , 4 types, 484 molecules

#3: Chemical ChemComp-LAB / LATRUNCULIN B


Mass: 395.513 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H29NO5S
#4: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 478 / 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: 2.61 Å3/Da / Density % sol: 52.84 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 100 mM PCTP 25% PEG1500

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Feb 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.3→61.7 Å / Num. obs: 50253 / % possible obs: 99.3 % / Redundancy: 3.5 % / CC1/2: 0.961 / Rmerge(I) obs: 0.117 / Rpim(I) all: 0.073 / Rrim(I) all: 0.139 / Net I/σ(I): 10.9
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.292 / Mean I/σ(I) obs: 3.4 / Num. unique obs: 2600 / CC1/2: 0.899 / Rpim(I) all: 0.185 / Rrim(I) all: 0.346 / % possible all: 97.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
PDB_EXTRACT3.24data extraction
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5YEE

5yee


Resolution: 2.3→61.65 Å / Cor.coef. Fo:Fc: 0.904 / Cor.coef. Fo:Fc free: 0.866 / SU B: 16.974 / SU ML: 0.212 / Cross valid method: THROUGHOUT / ESU R: 0.411 / ESU R Free: 0.27 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27448 2562 5.1 %RANDOM
Rwork0.22753 ---
obs0.22993 47691 98.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.106 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20 Å2-0.01 Å2
2--0 Å20 Å2
3----0.06 Å2
Refinement stepCycle: 1 / Resolution: 2.3→61.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7769 0 118 478 8365
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0198054
X-RAY DIFFRACTIONr_bond_other_d0.0020.027529
X-RAY DIFFRACTIONr_angle_refined_deg1.4841.98710935
X-RAY DIFFRACTIONr_angle_other_deg0.97317525
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.125997
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.82624.826344
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.301151405
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5721542
X-RAY DIFFRACTIONr_chiral_restr0.0810.21241
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0218825
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021519
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.0990.6073988
X-RAY DIFFRACTIONr_mcbond_other0.0990.6073987
X-RAY DIFFRACTIONr_mcangle_it0.1830.914976
X-RAY DIFFRACTIONr_mcangle_other0.1830.914977
X-RAY DIFFRACTIONr_scbond_it0.0640.6134066
X-RAY DIFFRACTIONr_scbond_other0.0640.6134066
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.120.9155956
X-RAY DIFFRACTIONr_long_range_B_refined4.9968.0168941
X-RAY DIFFRACTIONr_long_range_B_other4.9457.558839
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 193 -
Rwork0.228 3468 -
obs--97.01 %
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)
13.27690.9185-0.20881.5948-0.17941.12650.0504-0.170.35990.0985-0.0980.1703-0.2027-0.01190.04760.0432-0.0114-0.03160.24040.00920.2735-42.5728.02599.495
22.3398-0.4457-0.7813.90260.51026.02940.11420.1336-0.0056-0.1612-0.03680.2157-0.22030.0782-0.07740.11150.0422-0.08050.2526-0.0050.2798-56.1-17.70377.082
33.1204-0.0750.09021.09980.46821.1938-0.03440.1312-0.11270.07480.01610.0070.071-0.02570.01820.0076-0.01160.0060.22210.00080.1777-19.858-27.34118.346
41.8277-0.42650.48034.86391.12514.23360.0108-0.2399-0.13370.0995-0.13250.14730.2456-0.0750.12180.0405-0.00510.01840.2828-0.00080.383-34.293-2.817143.24
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B5 - 375
2X-RAY DIFFRACTION2A1 - 134
3X-RAY DIFFRACTION3D5 - 375
4X-RAY DIFFRACTION4C-1 - 134

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