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- PDB-4b1y: Structure of the Phactr1 RPEL-3 bound to G-actin -

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Basic information

Entry
Database: PDB / ID: 4b1y
TitleStructure of the Phactr1 RPEL-3 bound to G-actin
Components
  • ACTIN, ALPHA SKELETAL MUSCLE
  • PHOSPHATASE AND ACTIN REGULATOR 1
KeywordsSTRUCTURAL PROTEIN / NUCLEOTIDE-BINDING / TRANSCRIPTION REGULATION / TRANSCRIPTION / MUSCLE PROTEIN / ATP-BINDING / CYTOSKELETON
Function / homology
Function and homology information


dendrite arborization / regulation of neuron migration / protein phosphatase 1 binding / regulation of phosphorylation / actomyosin structure organization / protein phosphatase inhibitor activity / cytoskeletal motor activator activity / stress fiber assembly / tropomyosin binding / mesenchyme migration ...dendrite arborization / regulation of neuron migration / protein phosphatase 1 binding / regulation of phosphorylation / actomyosin structure organization / protein phosphatase inhibitor activity / cytoskeletal motor activator activity / stress fiber assembly / tropomyosin binding / mesenchyme migration / troponin I binding / myosin heavy chain binding / filamentous actin / actin filament bundle / skeletal muscle thin filament assembly / striated muscle thin filament / actin filament bundle assembly / skeletal muscle myofibril / actin monomer binding / skeletal muscle fiber development / stress fiber / titin binding / actin filament polymerization / filopodium / cell motility / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / cerebral cortex development / calcium-dependent protein binding / lamellipodium / actin binding / cell body / actin cytoskeleton organization / hydrolase activity / protein domain specific binding / synapse / calcium ion binding / positive regulation of gene expression / magnesium ion binding / ATP binding / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
RPEL repeat / RPEL repeat / RPEL repeat profile. / Repeat in Drosophila CG10860, human KIAA0680 and C. elegans F26H9.2 / ATPase, substrate binding domain, subdomain 4 / Actin; Chain A, domain 4 / ATPase, nucleotide binding domain / Actins signature 1. / Actin, conserved site / Actins signature 2. ...RPEL repeat / RPEL repeat / RPEL repeat profile. / Repeat in Drosophila CG10860, human KIAA0680 and C. elegans F26H9.2 / 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 / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / LATRUNCULIN B / DI(HYDROXYETHYL)ETHER / Phosphatase and actin regulator 1 / Actin, alpha skeletal muscle / Phosphatase and actin regulator 1
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
ORYCTOLAGUS CUNICULUS (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.29 Å
AuthorsMouilleron, S. / Wiezlak, M. / O'Reilly, N. / Treisman, R. / McDonald, N.Q.
CitationJournal: Structure / Year: 2012
Title: Structures of the Phactr1 RPEL domain and RPEL motif complexes with G-actin reveal the molecular basis for actin binding cooperativity.
Authors: Mouilleron, S. / Wiezlak, M. / O'Reilly, N. / Treisman, R. / McDonald, N.Q.
History
DepositionJul 12, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 31, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 22, 2014Group: Database references
Revision 1.2Oct 29, 2014Group: Derived calculations
Revision 1.3Feb 28, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.page_last ..._citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name
Revision 1.4May 2, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_beamline
Revision 1.5Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _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
B: ACTIN, ALPHA SKELETAL MUSCLE
M: PHOSPHATASE AND ACTIN REGULATOR 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,88811
Polymers46,0302
Non-polymers1,8589
Water10,016556
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2630 Å2
ΔGint-13 kcal/mol
Surface area20390 Å2
MethodPQS
Unit cell
Length a, b, c (Å)52.580, 63.560, 62.570
Angle α, β, γ (deg.)90.00, 108.83, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Protein/peptide , 2 types, 2 molecules BM

#1: Protein ACTIN, ALPHA SKELETAL MUSCLE / ALPHA SKELETAL MUSCLE ACTIN / ALPHA-ACTIN-1


Mass: 41965.754 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit) / Tissue: MUSCLE / References: UniProt: P68135
#2: Protein/peptide PHOSPHATASE AND ACTIN REGULATOR 1 / PHOSPHATASE AND ACTIN REGULATOR 1\ / ISOFORM CRA_C


Mass: 4063.843 Da / Num. of mol.: 1 / Fragment: RESIDUES 562-593
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): ROSETTA PLYSS / References: UniProt: G5E8P7, UniProt: Q2M3X8*PLUS

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Non-polymers , 8 types, 565 molecules

#3: Chemical ChemComp-LAB / LATRUNCULIN B


Mass: 395.513 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H29NO5S / Comment: toxin*YM
#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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#9: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 556 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.74 Å3/Da / Density % sol: 28.76 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Type: ESRF / Wavelength: 0.9763
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.29→30 Å / Num. obs: 98023 / % possible obs: 99.7 % / Observed criterion σ(I): 1.8 / Redundancy: 3.1 % / Biso Wilson estimate: 10.35 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 5.5
Reflection shellResolution: 1.29→1.36 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 1.8 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2V52

2v52


Resolution: 1.29→29.419 Å / SU ML: 0.11 / σ(F): 1.42 / Phase error: 16.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1744 4841 5.1 %
Rwork0.1503 --
obs0.1515 95813 97.75 %
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 2 Å2 / ksol: 2 e/Å3
Refinement stepCycle: LAST / Resolution: 1.29→29.419 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3097 0 121 556 3774
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073613
X-RAY DIFFRACTIONf_angle_d1.2964942
X-RAY DIFFRACTIONf_dihedral_angle_d19.2861506
X-RAY DIFFRACTIONf_chiral_restr0.086552
X-RAY DIFFRACTIONf_plane_restr0.006629
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.29-1.33610.26614670.2338735X-RAY DIFFRACTION94
1.3361-1.38960.21384540.19988906X-RAY DIFFRACTION96
1.3896-1.45280.2134630.18439017X-RAY DIFFRACTION97
1.4528-1.52940.18994860.16549069X-RAY DIFFRACTION98
1.5294-1.62530.16955020.14629105X-RAY DIFFRACTION98
1.6253-1.75070.184730.14469229X-RAY DIFFRACTION99
1.7507-1.92690.17065250.14429172X-RAY DIFFRACTION99
1.9269-2.20560.16994810.13629289X-RAY DIFFRACTION100
2.2056-2.77850.17155310.14359294X-RAY DIFFRACTION100
2.7785-29.42620.15454590.14119156X-RAY DIFFRACTION96
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)
12.3275-0.850.68332.3764-0.98442.33210.07180.02190.12030.07120.02620.2452-0.1487-0.1346-0.09110.08770.00390.00730.06870.0090.0846-1.752313.921611.406
21.29650.8584-0.55683.0882-0.93390.5986-0.0422-0.1816-0.35480.29120.07560.54020.3285-0.5281-0.05240.2304-0.09170.01790.21380.03920.2131-4.3606-2.861422.8337
30.88690.13920.24320.89020.24690.63670.04960.0201-0.1350.04750.01330.03030.142-0.0567-0.04480.109-0.0089-0.01410.06910.00470.05631.58772.48438.5653
40.46280.1997-0.35140.7014-0.63451.00860.0068-0.0287-0.0573-0.0036-0.0115-0.02890.10930.02530.00630.092-0.0002-0.01210.07020.00420.046317.0813.925723.9613
50.81060.11880.05611.1237-0.18250.9660.0251-0.1439-0.00470.1816-0.1182-0.0436-0.07960.07880.07890.1462-0.024-0.02530.11530.01370.064122.69887.41436.6993
61.2568-0.2368-0.55890.7302-0.4471.85520.03670.03630.0263-0.0116-0.0542-0.10220.01460.16140.01540.0737-0.0076-0.00840.07960.00140.047626.912513.292313.0285
71.37910.16460.56620.4951-0.0040.6612-0.0273-0.07780.10760.0033-0.0179-0.0224-0.03980.02280.04540.0872-0.00070.01140.0606-0.00070.048220.914617.539717.122
80.56070.46240.34611.26830.61980.775-0.08680.19050.011-0.22820.1441-0.07010.01730.1253-0.0370.1772-0.0272-0.01360.13410.00220.07163.35148.4351-6.0004
92.6464-1.8005-0.88211.98510.49171.24380.06710.3210.0184-0.1948-0.166-0.0069-0.0116-0.04270.05680.20680.0103-0.00630.17120.01470.143117.663619.8209-1.1812
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN B AND (RESSEQ 0:28)
2X-RAY DIFFRACTION2CHAIN B AND (RESSEQ 29:61)
3X-RAY DIFFRACTION3CHAIN B AND (RESSEQ 62:145)
4X-RAY DIFFRACTION4CHAIN B AND (RESSEQ 146:216)
5X-RAY DIFFRACTION5CHAIN B AND (RESSEQ 217:273)
6X-RAY DIFFRACTION6CHAIN B AND (RESSEQ 274:308)
7X-RAY DIFFRACTION7CHAIN B AND (RESSEQ 309:348)
8X-RAY DIFFRACTION8CHAIN B AND (RESSEQ 349:375)
9X-RAY DIFFRACTION9CHAIN M AND (RESSEQ 493:522)

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